Running as unit: rb-build-amd64_19-68930.service; invocation ID: bb28b0c11716429bb0c0e780a2c6eeb7 ==================================================================================== Sun Sep 14 23:24:03 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_19) on jenkins, called using "ionos1-amd64 ionos15-amd64" as arguments. Sun Sep 14 23:24:03 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-nr94JM1Q" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Sep 14 23:24:03 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Sun Sep 14 23:24:03 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-hf60hN' Sun Sep 14 23:24:05 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Sun Sep 14 23:24:05 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-YQXZXb' ok, let's check if python-cogent is building anywhere yet… ok, python-cogent is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of python-cogent in unstable on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Sun Sep 14 23:24:13 UTC 2025 I: starting to build python-cogent/unstable/amd64 on jenkins on '2025-09-14 23:24' Sun Sep 14 23:24:13 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_19/68930/console.log 1757892253 amd64 unstable python-cogent Sun Sep 14 23:24:14 UTC 2025 I: Downloading source for unstable/python-cogent=2024.5.7a1+dfsg-3 --2025-09-14 23:24:14-- http://deb.debian.org/debian/pool/main/p/python-cogent/python-cogent_2024.5.7a1%2bdfsg-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2634 (2.6K) [text/prs.lines.tag] Saving to: ‘python-cogent_2024.5.7a1+dfsg-3.dsc’ 0K .. 100% 298M=0s 2025-09-14 23:24:14 (298 MB/s) - ‘python-cogent_2024.5.7a1+dfsg-3.dsc’ saved [2634/2634] --2025-09-14 23:24:14-- http://deb.debian.org/debian/pool/main/p/python-cogent/python-cogent_2024.5.7a1%2bdfsg-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2634 (2.6K) [text/prs.lines.tag] Saving to: ‘python-cogent_2024.5.7a1+dfsg-3.dsc’ 0K .. 100% 298M=0s 2025-09-14 23:24:14 (298 MB/s) - ‘python-cogent_2024.5.7a1+dfsg-3.dsc’ saved [2634/2634] Sun Sep 14 23:24:14 UTC 2025 I: python-cogent_2024.5.7a1+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-cogent Binary: python3-cogent3, python-cogent-doc Architecture: any all Version: 2024.5.7a1+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Homepage: https://github.com/cogent3/cogent3 Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/python-cogent Vcs-Git: https://salsa.debian.org/med-team/python-cogent.git Testsuite: autopkgtest, autopkgtest-pkg-python Testsuite-Triggers: python3-pytest Build-Depends: architecture-is-64-bit, architecture-is-little-endian, cython3, debhelper-compat (= 13), dh-sequence-python3, flit, libjs-requirejs, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-chardet, python3-isort, python3-jupyter-sphinx-theme, python3-jupyterlab-server, python3-matplotlib, python3-nbsphinx, python3-numba, python3-numpy, python3-numpydoc, python3-pandas, python3-plotly , python3-pydata-sphinx-theme, python3-pytest , python3-pytest-cov , python3-pytest-xdist , python3-scipy, python3-scitrack, python3-sphinx, python3-sphinx-bootstrap-theme, python3-sphinx-design, python3-sphinx-gallery, python3-sphinxcontrib.bibtex, python3-stevedore, python3-tinydb, python3-tqdm, python3-typing-extensions Package-List: python-cogent-doc deb doc optional arch=all python3-cogent3 deb python optional arch=any Checksums-Sha1: 4c596fb13b9c8a2e24179e6758c2de76f751a4bd 14846556 python-cogent_2024.5.7a1+dfsg.orig.tar.xz 0d0a703332c2378c2ff0b2a26b0848ca1ef286e3 12180 python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz Checksums-Sha256: e4fe6bc1d1ce9df1f91ca84123df8427c37327847564244c0abc97ccc3357f2c 14846556 python-cogent_2024.5.7a1+dfsg.orig.tar.xz 4d5837beed17582651dabe60b4b6ce0f2781a68e4c2ab57fad48a5befb2a9c2c 12180 python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz Files: 21ad4f0d79bc3a240bf1c58a5fd74099 14846556 python-cogent_2024.5.7a1+dfsg.orig.tar.xz a5479a4fbe9c77308149bbe0ec587ad9 12180 python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEE1Uw7+v+wQt44LaXXQc5/C58bizIFAmaIJNgACgkQQc5/C58b izJNMAf/aNfniQYvYU4D1doMXSxHuVgf9Vxtf9ar16FiRyWQJJNZsR2qpy0Pq/rZ gFPeEIHg+M6MnJYxtEXcw6QzT+GCM4guyQViKAk3WZxfgtAC1JLolk9JgZBgfH+v pDYTH7RUNKvhDj897e3Qg/kZry9fA01eAfvcJ2iwmKOo/cLiqMLzg1VrpfgaYxoT VeqvmtcUGYnA3RAjTEkxIRiQJ0QOfv3QTuOXKHXyDiw3f6IYt0kKePdSHkzVCAcv nN3vBQFYWVI8YzjGaVMArn9KEjGU0NFJexEiKi6HYx8v96XLevkQ+nR/TDlh1SLO LyChw5VT4ri1wRn++aof5DwNfKt2KA== =kZpK -----END PGP SIGNATURE----- Sun Sep 14 23:24:14 UTC 2025 I: Checking whether the package is not for us Sun Sep 14 23:24:14 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Sun Sep 14 23:24:14 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Sun Sep 14 23:24:14 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Sun Sep 14 23:24:14 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-colYDq' ==================================================================================== Sun Sep 14 23:24:14 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 python-cogent unstable /srv/reproducible-results/rbuild-debian/r-b-build.xWOmV7M4 2024.5.7a1+dfsg-3" as arguments. Sun Sep 14 23:24:14 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-a7c7Onj8" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Sep 14 23:24:14 UTC 2025 I: Downloading source for unstable/python-cogent=2024.5.7a1+dfsg-3 Reading package lists... NOTICE: 'python-cogent' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-cogent.git Please use: git clone https://salsa.debian.org/med-team/python-cogent.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 14.9 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main python-cogent 2024.5.7a1+dfsg-3 (dsc) [2634 B] Get:2 http://deb.debian.org/debian unstable/main python-cogent 2024.5.7a1+dfsg-3 (tar) [14.8 MB] Get:3 http://deb.debian.org/debian unstable/main python-cogent 2024.5.7a1+dfsg-3 (diff) [12.2 kB] Fetched 14.9 MB in 0s (86.7 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'python-cogent' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-cogent.git Please use: git clone https://salsa.debian.org/med-team/python-cogent.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 14.9 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main python-cogent 2024.5.7a1+dfsg-3 (dsc) [2634 B] Get:2 http://deb.debian.org/debian unstable/main python-cogent 2024.5.7a1+dfsg-3 (tar) [14.8 MB] Get:3 http://deb.debian.org/debian unstable/main python-cogent 2024.5.7a1+dfsg-3 (diff) [12.2 kB] Fetched 14.9 MB in 0s (86.7 MB/s) Download complete and in download only mode ============================================================================= Building python-cogent in unstable on amd64 on ionos1-amd64 now. Date: Sun Sep 14 23:24:16 UTC 2025 Date UTC: Sun Sep 14 23:24:16 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Sep 14 11:24:16 -12 2025 I: pbuilder-time-stamp: 1757892256 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-cogent_2024.5.7a1+dfsg-3.dsc] I: copying [./python-cogent_2024.5.7a1+dfsg.orig.tar.xz] I: copying [./python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-cogent_2024.5.7a1+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting python-cogent in python-cogent-2024.5.7a1+dfsg dpkg-source: info: unpacking python-cogent_2024.5.7a1+dfsg.orig.tar.xz dpkg-source: info: unpacking python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sphinx.patch dpkg-source: info: applying fix_interpreter.patch dpkg-source: info: applying remove-jupyter-sphinx.patch dpkg-source: info: applying ignore_tests_accessing_network.patch dpkg-source: info: applying skip-parallel-tests-on-single-cpu-systems.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/553802/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='904a55863bf44d45a2c870c23e3a581b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='553802' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.xWOmV7M4/pbuilderrc_EKw7 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xWOmV7M4/b1 --logfile b1/build.log python-cogent_2024.5.7a1+dfsg-3.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/553802/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: architecture-is-64-bit, architecture-is-little-endian, cython3, debhelper-compat (= 13), dh-sequence-python3, flit, libjs-requirejs, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-chardet, python3-isort, python3-jupyter-sphinx-theme, python3-jupyterlab-server, python3-matplotlib, python3-nbsphinx, python3-numba, python3-numpy, python3-numpydoc, python3-pandas, python3-plotly, python3-pydata-sphinx-theme, python3-pytest, python3-pytest-cov, python3-pytest-xdist, python3-scipy, python3-scitrack, python3-sphinx, python3-sphinx-bootstrap-theme, python3-sphinx-design, python3-sphinx-gallery, python3-sphinxcontrib.bibtex, python3-stevedore, python3-tinydb, python3-tqdm, python3-typing-extensions dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on flit; however: Package flit is not installed. pbuilder-satisfydepends-dummy depends on libjs-requirejs; however: Package libjs-requirejs is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-chardet; however: Package python3-chardet is not installed. pbuilder-satisfydepends-dummy depends on python3-isort; however: Package python3-isort is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyter-sphinx-theme; however: Package python3-jupyter-sphinx-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyterlab-server; however: Package python3-jupyterlab-server is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-nbsphinx; however: Package python3-nbsphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-numba; however: Package python3-numba is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-numpydoc; however: Package python3-numpydoc is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-plotly; however: Package python3-plotly is not installed. pbuilder-satisfydepends-dummy depends on python3-pydata-sphinx-theme; however: Package python3-pydata-sphinx-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-cov; however: Package python3-pytest-cov is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-scitrack; however: Package python3-scitrack is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-bootstrap-theme; however: Package python3-sphinx-bootstrap-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-design; however: Package python3-sphinx-design is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-gallery; however: Package python3-sphinx-gallery is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.bibtex; however: Package python3-sphinxcontrib.bibtex is not installed. pbuilder-satisfydepends-dummy depends on python3-stevedore; however: Package python3-stevedore is not installed. pbuilder-satisfydepends-dummy depends on python3-tinydb; however: Package python3-tinydb is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-typing-extensions; however: Package python3-typing-extensions is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} flit{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-glyphicons-halflings{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} jupyter-sphinx-theme-common{a} libabsl20240722{a} libaom3{a} libarchive-zip-perl{a} libargon2-1{a} libavif16{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdav1d7{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhwloc15{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-bootstrap{a} libjs-bootstrap5{a} libjs-bootswatch{a} libjs-jquery{a} libjs-jquery-hotkeys{a} libjs-jquery-isonscreen{a} libjs-jquery-metadata{a} libjs-jquery-tablesorter{a} libjs-jquery-throttle-debounce{a} libjs-requirejs{a} libjs-sphinxdoc{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm19{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libnorm1t64{a} libnuma1{a} libopenjp2-7{a} libp11-kit0{a} libpfm4{a} libpgm-5.3-0t64{a} libpipeline1{a} libpng16-16t64{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsodium23{a} libssh2-1t64{a} libsvtav1enc2{a} libtasn1-6{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2-16{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libyuv0{a} libz3-4{a} libzmq5{a} libzopfli1{a} llvm-19{a} llvm-19-linker-tools{a} llvm-19-runtime{a} m4{a} man-db{a} media-types{a} netbase{a} node-fortawesome-fontawesome-free{a} node-popper2{a} openssl{a} pandoc{a} pandoc-data{a} po-debconf{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python-matplotlib-data{a} python-tinycss2-common{a} python3{a} python3-accessible-pygments{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-anyio{a} python3-argon2{a} python3-argon2-cffi-bindings{a} python3-arrow{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-bleach{a} python3-brotli{a} python3-bs4{a} python3-build{a} python3-certifi{a} python3-cffi{a} python3-cffi-backend{a} python3-chardet{a} python3-charset-normalizer{a} python3-click{a} python3-contourpy{a} python3-coverage{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-execnet{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fqdn{a} python3-fs{a} python3-html5lib{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-installer{a} python3-isoduration{a} python3-isort{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-json-pointer{a} python3-json5{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-jupyter-client{a} python3-jupyter-core{a} python3-jupyter-events{a} python3-jupyter-server{a} python3-jupyter-server-terminals{a} python3-jupyter-sphinx-theme{a} python3-jupyterlab-pygments{a} python3-jupyterlab-server{a} python3-kiwisolver{a} python3-latexcodec{a} python3-linkify-it{a} python3-llvmlite{a} python3-lxml{a} python3-lz4{a} python3-markdown-it{a} python3-markupsafe{a} python3-matplotlib{a} python3-mdit-py-plugins{a} python3-mdurl{a} python3-minimal{a} python3-mistune{a} python3-more-itertools{a} python3-mpmath{a} python3-myst-parser{a} python3-nbclient{a} python3-nbconvert{a} python3-nbformat{a} python3-nbsphinx{a} python3-numba{a} python3-numpy{a} python3-numpy-dev{a} python3-numpydoc{a} python3-overrides{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pandocfilters{a} python3-pbr{a} python3-pil{a} python3-pil.imagetk{a} python3-pip{a} python3-pkg-resources{a} python3-platformdirs{a} python3-plotly{a} python3-pluggy{a} python3-ply{a} python3-prometheus-client{a} python3-psutil{a} python3-ptyprocess{a} python3-pybtex{a} python3-pybtex-docutils{a} python3-pycparser{a} python3-pydata-sphinx-theme{a} python3-pygments{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pytest{a} python3-pytest-cov{a} python3-pytest-xdist{a} python3-pythonjsonlogger{a} python3-pytz{a} python3-referencing{a} python3-requests{a} python3-rfc3339-validator{a} python3-rfc3986-validator{a} python3-rich{a} python3-roman{a} python3-roman-numerals{a} python3-rpds-py{a} python3-scipy{a} python3-scitrack{a} python3-send2trash{a} python3-setuptools{a} python3-sniffio{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-bootstrap-theme{a} python3-sphinx-design{a} python3-sphinx-gallery{a} python3-sphinxcontrib.bibtex{a} python3-stevedore{a} python3-sympy{a} python3-tenacity{a} python3-terminado{a} python3-tinycss2{a} python3-tinydb{a} python3-tk{a} python3-tomli-w{a} python3-tornado{a} python3-tqdm{a} python3-traitlets{a} python3-typeguard{a} python3-typeshed{a} python3-typing-extensions{a} python3-tz{a} python3-uc-micro{a} python3-ufolib2{a} python3-uritemplate{a} python3-urllib3{a} python3-webcolors{a} python3-webencodings{a} python3-websocket{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3-zmq{a} python3-zopfli{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} x11-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: binfmt-support curl isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libhwloc-plugins libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules llvm-19-dev lynx numba-doc optipng publicsuffix python3-bottleneck python3-cssselect python3-gi python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-rfc3987 python3-tables shared-mime-info systemd wget xdg-user-dirs 0 packages upgraded, 334 newly installed, 0 to remove and 0 not upgraded. Need to get 246 MB of archives. After unpacking 1194 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.2-1 [1493 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.6 [2336 B] Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get: 59 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 66 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-roman all 5.1-1 [11.0 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 python3-pip all 25.2+dfsg-1 [1386 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 84 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.3-1 [131 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.5.0-1 [116 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.5+dfsg-1 [72.4 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-tomli-w all 1.2.0-1 [9100 B] Get: 90 http://deb.debian.org/debian unstable/main amd64 flit all 3.12.0-3 [96.5 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [163 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.4-1 [190 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 node-popper2 all 2.11.2-8 [100.0 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libjs-bootstrap5 all 5.3.8+dfsg-1 [460 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libjs-bootswatch all 3.3.7+dfsg2-1.3 [133 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libjs-bootstrap all 3.4.1+dfsg-6 [173 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-bootstrap-theme all 0.8.1+ds-1 [160 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 jupyter-sphinx-theme-common all 0.0.6+ds1-14 [12.8 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libargon2-1 amd64 0~20190702+dfsg-5 [21.2 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1916.20250814-1 [172 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.3.0-1 [135 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 114 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.1-2 [161 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.55-2 [88.1 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.12.2-1 [164 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-hotkeys all 0.2.0-1 [12.6 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 143 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-metadata all 12-4 [6532 B] Get: 144 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [184 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libjs-requirejs all 2.3.7+ds+~2.1.37-1 [196 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.7-6 [25.9 MB] Get: 153 http://deb.debian.org/debian unstable/main amd64 liblua5.4-0 amd64 5.4.8-1 [146 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1+b2 [221 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libpfm4 amd64 4.13.0+git106-g3e4031b-1 [372 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1+b1 [162 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.7-1 [1068 B] Get: 164 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-7 [248 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libsodium23 amd64 1.0.18-1+b2 [165 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libtbbbind-2-5 amd64 2022.1.0-2 [14.5 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libtbbmalloc2 amd64 2022.1.0-2 [54.8 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libtbb12 amd64 2022.1.0-2 [101 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.43-0.2 [155 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libzmq5 amd64 4.3.5-1+b3 [283 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 llvm-19-runtime amd64 1:19.1.7-6 [550 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 llvm-19-linker-tools amd64 1:19.1.7-6 [1261 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 llvm-19 amd64 1:19.1.7-6 [16.3 MB] Get: 182 http://deb.debian.org/debian unstable/main amd64 node-fortawesome-fontawesome-free all 6.7.2+ds1-1 [1521 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 pandoc amd64 3.1.11.1+ds-3 [26.4 MB] Get: 185 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.2-4 [36.2 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 6.20250414 [11.8 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.10.1+dfsg1-5 [2737 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python-tinycss2-common all 1.4.0-2 [44.7 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-accessible-pygments all 0.0.5-2 [1306 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.7-1 [1048 B] Get: 196 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.7-1 [1068 B] Get: 199 http://deb.debian.org/debian unstable/main amd64 python3-sniffio all 1.3.1-1 [7120 B] Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-anyio all 4.8.0-3 [63.6 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 python3-cffi-backend amd64 2.0.0~b1-1 [94.4 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 python3-ply all 3.11-9 [62.9 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-pycparser all 2.22-2 [78.0 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-cffi all 2.0.0~b1-1 [90.3 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-argon2-cffi-bindings amd64 25.1.0-2 [15.2 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-argon2 amd64 25.1.0-2 [18.2 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-typeshed all 0.0~git20241223.ea91db2-4 [1531 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-arrow all 1.3.0-1.1 [64.7 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.17.0-1 [117 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-webencodings all 0.5.1-5 [11.1 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-html5lib all 1.2-2 [92.1 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 python3-bleach all 6.2.0-1 [51.2 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 python3-soupsieve all 2.7-2 [39.0 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-bs4 all 4.13.5-1 [114 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 python3-click all 8.2.0+0.really.8.1.8-1 [95.4 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-2 [215 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-coverage amd64 7.8.2+dfsg1-1 [182 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-2 [9616 B] Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-execnet all 2.1.1-1 [40.2 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-fastjsonschema all 2.21.1-1 [22.4 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-8 [95.2 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 6.0.1-1 [1434 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.4+dfsg-1 [25.4 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 unicode-data all 16.0.0-1 [9197 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.57.0-2 [1457 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-fqdn all 1.5.1-2 [7592 B] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 245 http://deb.debian.org/debian unstable/main amd64 python3-isoduration all 20.11.0+git20211126.ae0bd61-2 [12.3 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 python3-isort all 6.0.1-1 [72.3 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 253 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 python3-json-pointer all 2.4-3 [14.6 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 python3-json5 all 0.10.0-1 [25.9 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 python3-rpds-py amd64 0.21.0-2+b1 [257 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 python3-referencing all 0.36.2-1 [23.7 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 260 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema all 4.19.2-6 [71.4 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-core all 5.7.2-5 [35.3 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 python3-psutil amd64 7.0.0-2 [220 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 python3-tornado amd64 6.4.2-3 [349 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 python3-zmq amd64 27.1.0-1 [189 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-client all 8.6.3-3 [92.4 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 python3-pythonjsonlogger all 3.3.0-1 [16.0 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 python3-rfc3339-validator all 0.1.4-2 [4060 B] Get: 269 http://deb.debian.org/debian unstable/main amd64 python3-rfc3986-validator all 0.1.1-2 [4884 B] Get: 270 http://deb.debian.org/debian unstable/main amd64 python3-mdurl all 0.1.2-1 [9444 B] Get: 271 http://deb.debian.org/debian unstable/main amd64 python3-uc-micro all 1.0.3-1 [5744 B] Get: 272 http://deb.debian.org/debian unstable/main amd64 python3-linkify-it all 2.0.3-1 [18.7 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 python3-markdown-it all 3.0.0-3 [59.5 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 python3-rich all 13.9.4-1 [203 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 python3-uritemplate all 4.1.1-3 [10.6 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 python3-webcolors all 1.13-1 [15.3 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-2 [137 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-events all 0.12.0-2 [19.2 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 python3-ptyprocess all 0.7.0-6 [14.5 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 python3-terminado all 0.18.1-1 [17.3 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-server-terminals all 0.5.3-3 [14.0 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 python3-tinycss2 all 1.4.0-2 [25.0 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Get: 284 http://deb.debian.org/debian unstable/main amd64 python3-mistune all 3.1.4-1 [35.7 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 python3-nbclient all 0.8.0-3 [62.3 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 python3-pandocfilters all 1.5.1-1 [23.7 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 python3-nbconvert all 7.16.6-1 [160 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 python3-overrides all 7.7.0-2 [14.2 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 python3-prometheus-client all 0.21.1+ds1-1 [44.9 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 python3-send2trash all 1.8.3-1 [15.8 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 python3-websocket all 1.8.0-2 [45.5 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-server all 2.15.0-1 [215 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 python3-mdit-py-plugins all 0.5.0-1 [33.4 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.2.3-6 [619 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 python3-roman-numerals all 3.1.0-2 [8740 B] Get: 297 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 3.0.1-1 [63.5 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.2.3-6 [477 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 python3-myst-parser all 4.0.1-1 [78.8 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 python3-nbsphinx all 0.9.5+ds-1 [39.9 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-sphinx-theme all 0.0.6+ds1-14 [2992 B] Get: 302 http://deb.debian.org/debian unstable/main amd64 python3-jupyterlab-server all 2.25.2-1 [50.9 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 python3-latexcodec all 3.0.0-1 [17.5 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 python3-llvmlite amd64 0.44.0-1 [231 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.7-1 [108 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.5-1 [9604 B] Get: 309 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 11.3.0-1 [81.1 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-5 [23.8 MB] Get: 312 http://deb.debian.org/debian unstable/main amd64 python3-numba amd64 0.61.2+dfsg-1 [1773 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 python3-numpydoc all 1.9.0-1 [52.3 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 python3-pytz all 2025.2-3 [152 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4595 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-9 [3097 kB] Get: 317 http://deb.debian.org/debian unstable/main amd64 python3-pbr all 6.1.1-2 [57.1 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2025.2-3 [4280 B] Get: 319 http://deb.debian.org/debian unstable/main amd64 python3-tenacity all 8.4.2+really8.4.1-2 [46.0 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 python3-plotly all 5.20.0+dfsg-1 [2726 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 python3-pybtex all 0.25.1-1 [75.2 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 python3-pybtex-docutils all 1.0.3-1 [8224 B] Get: 324 http://deb.debian.org/debian unstable/main amd64 python3-pydata-sphinx-theme all 0.16.1+dfsg-3 [917 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.4.2-1 [266 kB] Get: 326 http://deb.debian.org/debian unstable/main amd64 python3-pytest-cov all 5.0.0-1 [26.8 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 python3-pytest-xdist all 3.8.0-1 [45.7 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 python3-scitrack all 2024.10.8-1 [9420 B] Get: 329 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-design all 0.6.1-1 [883 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-gallery all 0.17.1-1 [401 kB] Get: 331 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.bibtex all 2.6.5-2 [33.2 kB] Get: 332 http://deb.debian.org/debian unstable/main amd64 python3-stevedore all 5.4.1-2 [20.9 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 python3-tinydb all 4.8.2-1 [29.1 kB] Get: 334 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.67.1-5 [90.8 kB] Fetched 246 MB in 9s (26.8 MB/s) 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up x11-common (1:7.7+25) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libgcrypt20:amd64 (1.11.2-2) ... Setting up libqhull-r8.0:amd64 (2020.2-7) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up node-fortawesome-fontawesome-free (6.7.2+ds1-1) ... Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Setting up libjs-requirejs (2.3.7+ds+~2.1.37-1) ... Setting up libabsl20240722:amd64 (20240722.0-4) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up python-babel-localedata (2.17.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Sep 14 23:28:17 UTC 2025. Universal Time is now: Sun Sep 14 23:28:17 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (16.0.0-1) ... Setting up libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1+b1) ... Setting up autotools-dev (20240727.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpfm4:amd64 (4.13.0+git106-g3e4031b-1) ... Setting up libexpat1-dev:amd64 (2.7.1-2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libzopfli1 (1.0.3-3) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libsvtav1enc2:amd64 (2.3.0+dfsg-1) ... Setting up libjs-bootswatch (3.3.7+dfsg2-1.3) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (4.4.0-3) ... 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Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libjs-bootstrap (3.4.1+dfsg-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up libllvm19 (1:19.1.7-6) ... Setting up libavif16:amd64 (1.3.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2+b1) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up libtool (2.5.4-5) ... Setting up fontconfig-config (2.15.0-2.4) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up libtbbbind-2-5:amd64 (2022.1.0-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libglib2.0-0t64:amd64 (2.84.4-3) ... No schema files found: doing nothing. Setting up pandoc (3.1.11.1+ds-3) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libjs-jquery-metadata (12-4) ... Setting up sphinx-common (8.2.3-6) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Setting up groff-base (1.23.0-9) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (11.4.5-1) ... Setting up llvm-19-linker-tools (1:19.1.7-6) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2.4) ... 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Setting up python3-all-dev (3.13.7-1) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up python3-pytest-xdist (3.8.0-1) ... Setting up python3-rich (13.9.4-1) ... Setting up python3-pbr (6.1.1-2) ... Setting up pybuild-plugin-pyproject (6.20250414) ... Setting up python3-cffi (2.0.0~b1-1) ... Setting up python3-mdit-py-plugins (0.5.0-1) ... Setting up python3-llvmlite (0.44.0-1) ... Setting up python3-argon2-cffi-bindings (25.1.0-2) ... Setting up python3-argon2 (25.1.0-2) ... Setting up python3-stevedore (5.4.1-2) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up python3-numba (0.61.2+dfsg-1) ... update-alternatives: using /usr/share/python3-numba/numba to provide /usr/bin/numba (numba) in auto mode Setting up python3-jsonschema (4.19.2-6) ... Setting up python3-jupyter-events (0.12.0-2) ... Setting up python3-nbformat (5.9.1-1) ... Setting up python3-nbclient (0.8.0-3) ... Setting up python3-plotly (5.20.0+dfsg-1) ... Setting up python3-nbconvert (7.16.6-1) ... Setting up python3-jupyter-server (2.15.0-1) ... Setting up python3-jupyterlab-server (2.25.2-1) ... Setting up python3-fonttools (4.57.0-2) ... Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... Setting up python3-matplotlib (3.10.1+dfsg1-5) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up flit (3.12.0-3) ... Setting up python3-pybtex-docutils (1.0.3-1) ... Setting up python3-sphinx (8.2.3-6) ... Setting up python3-myst-parser (4.0.1-1) ... Setting up python3-sphinx-gallery (0.17.1-1) ... Setting up python3-sphinxcontrib.bibtex (2.6.5-2) ... Setting up python3-sphinx-design (0.6.1-1) ... Setting up python3-nbsphinx (0.9.5+ds-1) ... Setting up python3-numpydoc (1.9.0-1) ... Setting up python3-pydata-sphinx-theme (0.16.1+dfsg-3) ... Setting up python3-jupyter-sphinx-theme (0.0.6+ds1-14) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-cogent_2024.5.7a1+dfsg-3_source.changes dpkg-buildpackage: info: source package python-cogent dpkg-buildpackage: info: source version 2024.5.7a1+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' #These files are rebuilt on-the-fly for f in `find -name '*.c'` ; do \ head -n 1 "$f" | grep -q '^/\* Generated by Cython' && rm "$f" ; \ done rm -rf build build-stamp rm -rf doc/_build dh_clean make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.13 with "build" module I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3 * Building wheel... Successfully built cogent3-2024.5.7a1-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' set -x; cd doc; PYTHONPATH=/build/reproducible-path/python-cogent-2024.5.7a1+dfsg http_proxy='127.0.0.1:9' /usr/bin/make html + cd doc + PYTHONPATH=/build/reproducible-path/python-cogent-2024.5.7a1+dfsg http_proxy=127.0.0.1:9 /usr/bin/make html make[2]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v8.2.3 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist WARNING: The config value `today' has type `date'; expected `str'. checking bibtex cache... out of date parsing bibtex file /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cogent3.bib... parsed 21 entries Writing evaluated template result to /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/_build/html/_static/nbsphinx-code-cells.css building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 176 source files that are out of date updating environment: [new config] 176 added, 0 changed, 0 removed reading sources... [ 1%] COGENT3_LICENSE reading sources... [ 1%] api/__init__/cogent3.__init__.available_apps reading sources... [ 2%] api/__init__/cogent3.__init__.available_codes reading sources... [ 2%] api/__init__/cogent3.__init__.available_models reading sources... [ 3%] api/__init__/cogent3.__init__.available_moltypes reading sources... [ 3%] api/__init__/cogent3.__init__.get_code reading sources... [ 4%] api/__init__/cogent3.__init__.get_model reading sources... [ 5%] api/__init__/cogent3.__init__.get_moltype reading sources... [ 5%] api/__init__/cogent3.__init__.load_aligned_seqs reading sources... [ 6%] api/__init__/cogent3.__init__.load_annotations reading sources... [ 6%] api/__init__/cogent3.__init__.load_delimited reading sources... [ 7%] api/__init__/cogent3.__init__.load_seq reading sources... [ 7%] api/__init__/cogent3.__init__.load_table reading sources... [ 8%] api/__init__/cogent3.__init__.load_tree reading sources... 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[ 23%] api/app/sqlite_data_store/classes/cogent3.app.sqlite_data_store.DataStoreSqlite reading sources... [ 23%] api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode reading sources... [ 24%] api/genetic_code/genetic_code reading sources... [ 24%] api/index reading sources... [ 25%] api/moltype/classes/cogent3.core.moltype.MolType reading sources... [ 26%] api/moltype/moltype reading sources... [ 26%] api/sequence/classes/cogent3.core.sequence.DnaSequence reading sources... [ 27%] api/sequence/classes/cogent3.core.sequence.ProteinSequence reading sources... [ 27%] api/sequence/classes/cogent3.core.sequence.RnaSequence reading sources... [ 28%] api/sequence/sequence reading sources... [ 28%] api/table/classes/cogent3.parse.table.FilteringParser reading sources... [ 29%] api/table/classes/cogent3.util.table.Columns reading sources... [ 30%] api/table/classes/cogent3.util.table.Table reading sources... [ 30%] api/table/table reading sources... [ 31%] api/tree/classes/cogent3.core.tree.PhyloNode reading sources... [ 31%] api/tree/tree reading sources... [ 32%] api/util/deserialise/classes/cogent3.util.deserialise.register_deserialiser reading sources... [ 32%] api/util/deserialise/deserialise_object reading sources... [ 33%] app/app_cookbook/align-codon reading sources... [ 34%] app/app_cookbook/align-nucleotide reading sources... [ 34%] app/app_cookbook/align-protein reading sources... [ 35%] app/app_cookbook/index-align reading sources... [ 35%] app/app_cookbook/index-loaders reading sources... [ 36%] app/app_cookbook/index-sample reading sources... [ 36%] app/app_cookbook/index-writers reading sources... [ 37%] app/app_cookbook/load-aligned reading sources... [ 38%] app/app_cookbook/load-json reading sources... [ 38%] app/app_cookbook/load-tabular reading sources... [ 39%] app/app_cookbook/load-unaligned reading sources... [ 39%] app/app_cookbook/sample-concat reading sources... 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[100%] templates/class WARNING: autodoc: failed to import function '__init__.available_apps' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.available_codes' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.available_models' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.available_moltypes' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.get_code' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.get_model' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.get_moltype' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_aligned_seqs' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_annotations' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_delimited' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_seq' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_table' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_tree' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_unaligned_seqs' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.make_aligned_seqs' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.make_seq' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.make_table' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.make_tree' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.make_unaligned_seqs' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.open_' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.open_data_store' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alignment/alignment.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst SequenceCollection Alignment ArrayAlignment [docutils] WARNING: autodoc: failed to import class 'core.alignment.Alignment' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.alignment.ArrayAlignment' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.alignment.SequenceCollection' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alphabet/alphabet.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Alphabet [docutils] WARNING: autodoc: failed to import class 'core.alphabet.Alphabet' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation/annotation.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Feature [docutils] WARNING: autodoc: failed to import class 'core.annotation.Feature' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation_db/annotation_db.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst BasicAnnotationDb GffAnnotationDb GenbankAnnotationDb [docutils] WARNING: autodoc: failed to import class 'core.annotation_db.BasicAnnotationDb' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.annotation_db.GenbankAnnotationDb' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.annotation_db.GffAnnotationDb' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function 'app.composable.define_app' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'app.data_store.DataMember' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'app.data_store.DataStoreDirectory' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'app.data_store.ReadOnlyDataStoreZipped' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function 'app.io.register_datastore_reader' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'app.sqlite_data_store.DataStoreSqlite' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.genetic_code.GeneticCode' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/genetic_code/genetic_code.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst GeneticCode [docutils] WARNING: autodoc: failed to import class 'core.moltype.MolType' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/moltype/moltype.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst MolType [docutils] WARNING: autodoc: failed to import class 'core.sequence.DnaSequence' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.sequence.ProteinSequence' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.sequence.RnaSequence' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/sequence/sequence.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst DnaSequence RnaSequence ProteinSequence [docutils] WARNING: autodoc: failed to import class 'parse.table.FilteringParser' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'util.table.Columns' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'util.table.Table' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/table.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Table Columns [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/table.rst:15: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst FilteringParser [docutils] WARNING: autodoc: failed to import class 'core.tree.PhyloNode' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/tree/tree.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst PhyloNode [docutils] WARNING: autodoc: failed to import class 'util.deserialise.register_deserialiser' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function 'util.deserialise.deserialise_object' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") seqs = loader("data/SCA1-cds.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app codon_aligner = get_app("progressive_align", "codon") aligned = codon_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: nt_aligner = get_app("progressive_align", "codon", distance="paralinear") aligned = nt_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" codon_aligner = get_app("progressive_align", "codon", guide_tree=tree) aligned = codon_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: codon_aligner = get_app("progressive_align", "codon", guide_tree=tree, indel_rate=0.001, indel_length=0.01 ) aligned = codon_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: codon_aligner = get_app("progressive_align", "CNFHKY", guide_tree=tree, param_vals=dict(omega=0.1, kappa=3) ) aligned = codon_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligned.info [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") seqs = loader("data/SCA1-cds.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app nt_aligner = get_app("progressive_align", "nucleotide") aligned = nt_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: nt_aligner = get_app("progressive_align", "nucleotide", distance="TN93") aligned = nt_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = get_app("progressive_align", "nucleotide", guide_tree=tree) aligned = nt_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = get_app("progressive_align", "F81", guide_tree=tree) aligned = nt_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligned.info [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") to_aa = get_app("translate_seqs") process = loader + to_aa seqs = process("data/SCA1-cds.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app aa_aligner = get_app("progressive_align", "protein") aligned = aa_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aa_aligner = get_app("progressive_align", "protein", distance="paralinear") aligned = aa_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligned.info [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/index-sample.rst:6: WARNING: toctree contains reference to nonexisting document 'app/app_cookbook/sample-trim-stop' [toc.not_readable] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/index-writers.rst:5: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/brca1-bats.fasta") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_aligned_app = get_app("load_aligned", moltype="protein", format="phylip") aln = load_aligned_app("data/abglobin_aa.phylip") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:59: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") process = loader + cpos3 + writer [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process.apply_to(fasta_seq_dstore) print(result[0].read()[:50]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-json.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-json.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import get_app, open_data_store from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name # create lf object to write load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/primate_brca1.fasta") gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree") lf = gn_model_app(aln).lf out_dstore = open_data_store(path_to_dir, mode="w", suffix="json") # write with the same identifier as the write_json example write_json_app = get_app("write_json", data_store=out_dstore) data_member = write_json_app(lf, identifier="gn_params.json") path_to_dstore = data_member.data_store.source [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-json.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_json_app = get_app("load_json") lf = load_json_app(f"{path_to_dstore}/gn_params.json") lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_tsv_app = get_app("load_tabular", sep="\t") tsv_data = load_tsv_app("data/stats.tsv") tsv_data [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import NamedTemporaryFile tmpdir = NamedTemporaryFile(dir=".") path_to_csv_file = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app tsv_data.write(path_to_csv_file, sep=",") load_csv_app = get_app("load_tabular", sep=",") csv_data = load_csv_app(path_to_csv_file) csv_data [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="protein") seqs = load_unaligned_app("data/inseqs_protein.fasta") seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: out_dstore = open_data_store(path_to_dir, suffix="tsv", mode="w") load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="dna") jdist = get_app("jaccard_dist") writer = get_app("write_tabular", out_dstore, format="tsv") process = load_unaligned_app + jdist + writer [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process.apply_to(fasta_seq_dstore) print(result[1].read()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:6: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app concat_alns_app = get_app("concat", moltype="dna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln1 = make_aligned_seqs({"s1": "AAA", "s2": "CAA", "s3": "AAA"}, moltype="dna") aln2 = make_aligned_seqs({"s1": "GCG", "s2": "GGG", "s3": "GGT"}, moltype="dna") aln1 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = concat_alns_app([aln1, aln2]) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs, get_app concat_missing = get_app("concat", moltype="dna", intersect=False) aln3 = make_aligned_seqs({"s4": "GCG", "s5": "GGG"}, moltype="dna") result = concat_missing([aln1, aln3]) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app concat_delim = get_app("concat", join_seq="N", moltype="dna") result = concat_delim([aln1, aln2]) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:6: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="protein", format="phylip") aln = loader("data/abglobin_aa.phylip") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app first_20 = get_app("fixed_length", length=20) first_20(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app skip_10_take_20 = get_app("fixed_length", length=20, start=10) skip_10_take_20(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app random_20 = get_app("fixed_length", length=20, random=True) random_20(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", moltype="dna", format="fasta") aln = loader("data/SCA1-cds.fasta") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app over_240s = get_app("min_length", 240) aln_fltrd = over_240s(aln) aln_fltrd [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store dstore = open_data_store("data", suffix="fasta", limit=2) reader = get_app("load_aligned", format="fasta", moltype="dna") min_length = get_app("min_length", 300) out_dstore = open_data_store(path_to_dir, mode="w", suffix="fasta") writer = get_app("write_seqs", out_dstore) process = reader + min_length + writer result = process.apply_to(dstore) result.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-bad.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( { "s1": "---ACC---TT-", "s2": "---ACC---TT-", "s3": "---ACC---TT-", "s4": "--AACCG-GTT-", "s5": "--AACCGGGTTT", "s6": "AGAACCGGGTT-", "s7": "------------", }, moltype="dna", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-bad.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_frac_05 = get_app("omit_bad_seqs", gap_fraction=0.5) omit_frac_05(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-bad.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_quant_08 = get_app("omit_bad_seqs", quantile=0.8) omit_quant_08(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs({"s1": "ACGA-GACG", "s2": "GATGATGYT"}, moltype="dna") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_degens = get_app("omit_degenerates", moltype="dna") result = omit_degens(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_degens_keep_gaps = get_app("omit_degenerates", moltype="dna", gap_is_degen=False) result = omit_degens_keep_gaps(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_degenerates_app = get_app("omit_degenerates", moltype="dna", motif_length=2) result = omit_degenerates_app(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs data = { "a": "ACGT", "b": "ACG-", # identical to 'a' except has a gap "c": "ACGG", # duplicate "d": "ACGG", # duplicate "e": "AGTC", # unique } aln = make_aligned_seqs(data, moltype="dna") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_shorter_duplicate = get_app("omit_duplicated", moltype="dna", choose="longest") omit_shorter_duplicate(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_all_duplicates = get_app("omit_duplicated", moltype="dna", choose=None) omit_all_duplicates(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( { "s1": "ATCG", "s2": "ATYG", # matches s1 with ambiguity "s3": "GGTA", }, moltype="dna", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app app_dna = get_app("omit_duplicated", mask_degen=True, choose="longest", moltype="dna") app_dna(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:9: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs({"s1": "ACGA-GA-CG", "s2": "GATGATG-AT"}, moltype="dna") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_gap_pos_app = get_app("omit_gap_pos", moltype="dna") result = omit_gap_pos_app(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: omit_gap_pos_app = get_app("omit_gap_pos", allowed_frac=0.49, moltype="dna") result = omit_gap_pos_app(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: omit_gap_pos_app = get_app( "omit_gap_pos", allowed_frac=0, motif_length=3, moltype="dna" ) result = omit_gap_pos_app(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="dna") aln = loader("data/primate_brca1.fasta") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app first_3 = get_app("take_n_seqs", number=3) first_3(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app random_n = get_app("take_n_seqs", random=True, number=3, seed=1) random_n(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="dna") aln1 = loader("data/primate_brca1.fasta") aln2 = loader("data/brca1.fasta") aln1.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:64: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: fixed_choice = get_app("take_n_seqs", number=2, random=True, fixed_choice=True) result1 = fixed_choice(aln1).names result2 = fixed_choice(aln2).names result1 == result2 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs({"s1": "ACGACGACG", "s2": "GATGATGAT"}, moltype="dna") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app take_pos3 = get_app("take_codon_positions", 3, moltype="dna") result = take_pos3(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app take_pos12 = get_app("take_codon_positions", 1, 2, moltype="dna") result = take_pos12(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, make_aligned_seqs aln_ff = make_aligned_seqs({"s1": "GCAAGCGTTTAT", "s2": "GCTTTTGTCAAT"}) take_fourfold = get_app("take_codon_positions", fourfold_degenerate=True, moltype="dna") result = take_fourfold(aln_ff) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") process = loader + cpos3 + writer [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: out_dstore = process.apply_to(fasta_seq_dstore) out_dstore.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="dna") aln = loader("data/primate_brca1.fasta") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app greater_ape_selector = get_app("take_named_seqs", "Human", "Chimpanzee", "Gorilla") ape_aln = greater_ape_selector(aln) ape_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") select_seqs = get_app("take_named_seqs", "Human", "Rhesus", "Galago") process = loader + select_seqs hrg_aln = process("data/primate_brca1.fasta") hrg_aln.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app no_galagos = get_app("take_named_seqs", "Galago", negate=True) no_galago_aln = no_galagos(hrg_aln) no_galago_aln.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-trim-stops.rst:6: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ACGTAA---", "seq2": "ACGACA---", "seq3": "ACGCAATGA"}, moltype="dna", ) no_stops = get_app("trim_stop_codons", gc=1) no_stops(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store dstore = open_data_store("data", suffix="fasta", limit=2) reader = get_app("load_aligned", format="fasta", moltype="dna") min_length = get_app("min_length", 300) out_dstore = open_data_store(f"{path_to_dir}.sqlitedb", mode="w") writer = get_app("write_db", out_dstore) process = reader + min_length + writer result = process.apply_to(dstore) result.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: out_dstore is result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app # Load the alignment load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/primate_brca1.fasta") # Fit the GN model gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree") model_result = gn_model_app(aln) model_result.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store # Initialise the write_json app with a data store out_dstore = open_data_store(path_to_dir, mode="w", suffix="json") write_json_app = get_app("write_json", data_store=out_dstore) write_json_app(model_result.lf, identifier="gn_params.json") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/primate_brca1.fasta") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store seq_dstore = open_data_store(path_to_dir, suffix="phylip", mode="w") write_seqs_app = get_app("write_seqs", data_store=seq_dstore, format="phylip") result = write_seqs_app(aln) result.read()[:50] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_unaligned", format="fasta", moltype="dna") keep_translatable = get_app("select_translatable") translate = get_app("translate_seqs") writer = get_app("write_seqs", out_dstore, format="fasta") process = loader + keep_translatable + translate + writer [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process.apply_to(fasta_seq_dstore) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result.summary_not_completed [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app # load alignment load_aligned_app = get_app("load_aligned", moltype="dna") aln = load_aligned_app("data/primate_brca1.fasta") # fit GN model gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree") model_result = gn_model_app(aln) # tabulate the model result tabulator = get_app("tabulate_stats") model_result_tab = tabulator(model_result) motif_params = model_result_tab["motif params"] print(type(motif_params)) motif_params [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, mode="w", suffix="csv") write_tabular_app = get_app("write_tabular", data_store=out_dstore, format="csv") write_tabular_app(motif_params, identifier="gn_model_results.csv") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, mode="w", suffix="tsv") write_tabular_app = get_app("write_tabular", data_store=out_dstore, format="tsv") write_tabular_app(motif_params, identifier="gn_model_results.tsv") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store loader = get_app("load_unaligned", moltype="dna") jdist = get_app("jaccard_dist") out_dstore = open_data_store(path_to_dir, mode="w", suffix="tsv") writer = get_app("write_tabular", data_store=out_dstore, format="tsv") process = loader + jdist + writer in_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) result = process.apply_to(in_dstore) result.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-get.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app just_nucs = get_app("omit_degenerates", moltype="dna") just_nucs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-help.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import app_help app_help("omit_degenerates") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:95: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = loader("data/primate_brca1.fasta") just3rd = cpos3(data) m = writer(just3rd) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:138: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: process = loader + cpos3 + writer m = process("data/primate_brca1.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:148: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data", suffix="fasta", mode="r") result = process.apply_to(dstore) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:163: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_logs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:185: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result = process.apply_to(dstore, show_progress=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:205: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import shutil shutil.rmtree(path_to_dir, ignore_errors=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/available-apps.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_apps available_apps() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/available-apps.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: available_apps(name_filter="load") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import open_data_store dstore = open_data_store("data/raw.zip", suffix="fa", mode="r") print(dstore) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m = dstore[0] m [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:102: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for m in dstore[:5]: print(m) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m.read()[:20] # truncating [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data/demo-locked.sqlitedb") dstore.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.unlock(force=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.summary_logs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.logs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(dstore.logs[0].read()[:225]) # truncated for clarity [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import open_data_store in_dstore = open_data_store("data/raw.zip", suffix="fa") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore = open_data_store("translated.sqlitedb", mode="w") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:189: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app load = get_app("load_unaligned", moltype="dna") translate = get_app("translate_seqs") write = get_app("write_db", data_store=out_dstore) app = load + translate + write app [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore = app.apply_to(in_dstore) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:216: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.validate() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:222: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:232: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: len(out_dstore.not_completed) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:238: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.not_completed[:2] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:242: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib fn = pathlib.Path("translated.sqlitedb") fn.unlink() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:11: WARNING: download file not readable: /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/data/raw.zip [download.not_readable] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app reader = get_app("load_aligned", format="fasta") select_seqs = get_app("take_named_seqs", "Mouse", "Human") aln = reader("data/primate_brca1.fasta") result = select_seqs(aln) assert result == False result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.source [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.origin [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.message [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = reader("primate_brca1.fasta") result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: app = reader + select_seqs result = app("data/primate_brca1.fasta") result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = app("primate_brca1.fasta") result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta") aln = loader("data/primate_brca1.fasta") gn = get_app("model", "GN", tree="data/primate_brca1.tree") result = gn(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reconstuctor = get_app("ancestral_states") states_result = reconstuctor(result) states_result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: states_result["edge.0"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.tree.get_figure(contemporaneous=True).show(width=500, height=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = get_app("model", "BH", tree="data/primate_brca1.tree") result = model(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = result.tree fig = tree.get_figure() fig.scale_bar = "top right" fig.show(width=500, height=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = get_app("tabulate_stats") stats = tabulator(result) stats [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stats["edge motif motif2 params"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = get_app("model", "GN", tree="data/primate_brca1.tree") result = model(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = get_app("tabulate_stats") tabulated = tabulator(result) tabulated [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["edge params"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["global params"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["motif params"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") tree = "data/primate_brca1.tree" null = get_app("model", "GTR", tree=tree, optimise_motif_probs=True) alt = get_app("model", "GN", tree=tree, optimise_motif_probs=True) hyp = get_app("hypothesis", null, alt) result = hyp(aln) type(result) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.LR, result.df, result.pvalue [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") select_seqs = get_app("take_named_seqs", "Human", "Rhesus", "Galago") process = loader + select_seqs aln = process("data/primate_brca1.fasta") aln.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN") gn [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) type(fitted) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lnL, fitted.nfp [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.source [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.tree, fitted.alignment [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.total_length(length_as="paralinear") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN", split_codons=True) fitted = gn(aln) fitted [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted[3] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3 import get_app tree = load_tree("data/primate_brca1.tree") fig = tree.get_figure(contemporaneous=True) fig.style_edges( "Human", tip2="Orangutan", outgroup="Galago", line=dict(color="red") ) fig.show(width=500, height=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: time_het = get_app("model", "GN", tree=tree, time_het=[dict(tip_names=["Human", "Orangutan"], outgroup_name="Galago")], ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: loader = get_app("load_aligned", format="fasta") aln = loader("data/primate_brca1.fasta") result = time_het(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") aln.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3 import get_app tree = load_tree("data/primate_brca1.tree") gn = get_app("model", "GN", tree=tree) gn [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN", tree="data/primate_brca1.tree") gn [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) fitted [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") omega_eq_1 = get_app("natsel_neutral", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = omega_eq_1(aln) type(result) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") sites_differ = get_app("natsel_sitehet", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = sites_differ(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = result.alt.lf.get_bin_probs() bprobs[:, :20] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_timehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") hc_differ = get_app("natsel_timehet", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False, tip1="Human", tip2="Chimpanzee", ) result = hc_differ(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_timehet.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_zhang.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_zhang.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from IPython.core.display import HTML from numpy import array from cogent3 import make_table header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges'] data = {'Site Class': array(['0', '1', '2a', '2b'], dtype=' 1', '0 < omega0 < 1'], dtype=' AlignedSeqsType: return val[:index] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: first4 = up_to(index=4) first4 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=dict(a="GCAAGCGTTTAT", b="GCTTTTGTCAAT"), array_align=False, moltype="dna" ) result = first4(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from typing import Union from cogent3.app.composable import define_app from cogent3.app.typing import SeqsCollectionType, SerialisableType T = Union[SeqsCollectionType, SerialisableType] @define_app def rename_seqs(seqs: SeqsCollectionType) -> T: """upper case names""" return seqs.rename_seqs(lambda x: x.upper()) renamer = rename_seqs() result = renamer(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.composable import define_app from cogent3.app.typing import AlignedSeqsType, PairwiseDistanceType @define_app def get_dists(aln: AlignedSeqsType, calc="hamming") -> PairwiseDistanceType: return aln.distance_matrix(calc=calc, show_progress=False) percent_dist = get_dists(calc="pdist") result = percent_dist(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT") my_seq.moltype.label [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq = make_seq("AGTACACTGGT", moltype="bytes") my_seq.moltype.label [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") rnaseq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", "my_gene", moltype="dna") my_seq type(my_seq) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq.name = "my_gene" my_seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq.complement() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq.rc() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("GCTTGGGAAAGTCAAATGGAA", name="s1", moltype="dna") pep = my_seq.get_translation() type(pep) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:144: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ACGTACGTACGTACGT", moltype="dna") rnaseq = my_seq.to_rna() rnaseq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:155: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") dnaseq = rnaseq.to_dna() dnaseq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:166: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq a = make_seq("AGTACACTGGT", moltype="dna") a.can_pair(a.complement()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: a.can_pair(a.rc()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") extra_seq = make_seq("CTGAC", moltype="dna") long_seq = my_seq + extra_seq long_seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:192: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq[1:6] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq("ATGATGATGATG", moltype="dna") pos3 = seq[2::3] assert str(pos3) == "GGGG" [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq("ATGATGATGATG", moltype="dna") indices = [(i, i + 2) for i in range(len(seq))[::3]] pos12 = seq.add_feature(biotype="pos12", name="pos12", spans=indices) pos12 = pos12.get_slice() assert str(pos12) == "ATATATAT" [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:227: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rnaseq.shuffle() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:234: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq s = make_seq("--AUUAUGCUAU-UAu--", moltype="rna") s.degap() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna") type(seqs) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = make_unaligned_seqs(dna, moltype="dna") type(seqs) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna", array_align=True) print(type(seqs)) seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/test.paml") seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_seqs = make_aligned_seqs( [("seq0", "ATG-AGT-AGG"), ("seq4", "ATGCC------")], moltype="dna" ) new_aln = aln.add_seqs(new_seqs) new_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:98: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, before_name="seq2") new_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:103: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, after_name="seq2") new_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:113: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) ref_aln = make_aligned_seqs( [("seq3", "ATAGGATG"), ("seq0", "ATG-AGCG"), ("seq4", "ATGCTGGG")], moltype="dna", ) new_aln = aln.add_from_ref_aln(ref_aln) new_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:135: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) new_aln = aln.get_degapped_relative_to("seq1") new_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:154: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", array_align=False, ) seq = aln.get_seq("seq1") seq.name type(seq) seq.is_gapped() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = aln.get_gapped_seq("seq1") seq.is_gapped() seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:187: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_unaligned_seqs fn = "data/long_testseqs.fasta" seqs = load_unaligned_seqs(fn, moltype="dna") my_seq = seqs.seqs[0] my_seq[:24] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(my_seq) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:200: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs(fn, moltype="dna") aln.seqs[0][:24] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:209: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/test.paml", moltype="dna") aln.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:216: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new = aln.take_seqs(["Human", "HowlerMon"]) new.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs from cogent3.core.alignment import Alignment seq = load_unaligned_seqs("data/test.paml", moltype="dna") seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:237: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = Alignment(seq) aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("a", "ACG---"), ("b", "CCTGGG")] aln = make_aligned_seqs(data=data) dna = aln.to_dna() dna [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.to_moltype("dna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:264: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("a", "ACG---"), ("b", "CCUGGG")] aln = make_aligned_seqs(data=data) rna = aln.to_rna() rna [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:275: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("x", "TYV"), ("y", "TE-")] aln = make_aligned_seqs(data=data) prot = aln.to_protein() prot [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:292: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") degapped = aln.degap() print(type(degapped)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:307: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} aln = make_aligned_seqs(data=dna, moltype="dna") aln.write("sample.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:317: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.write("sample", format="fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:323: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.io import remove_files remove_files(["sample", "sample.fasta"], error_on_missing=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:332: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/long_testseqs.fasta") aln = Alignment(seq) fasta_align = aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:344: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/test.paml") aln = Alignment(seq) got = aln.to_phylip() print(got) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:357: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/test.paml") aln = Alignment(seq) string_list = aln.to_dict().values() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:374: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs fn = "data/long_testseqs.fasta" aln = load_aligned_seqs(fn, moltype="dna") aln[:24] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:384: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3 import load_unaligned_seqs fn = "data/long_testseqs.fasta" seqs = load_unaligned_seqs(fn) seqs[:24] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:396: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/test.paml") column_four = aln[3] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:406: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") region = aln[50:70] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:416: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() type(col) list(col) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:430: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=False ) list(range(len(aln))[2::3]) indices = [(i, i + 1) for i in range(len(aln))[2::3]] indices [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:441: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pos3 = aln.add_feature(biotype="pos3", name="pos3", spans=indices) pos3 = pos3.get_slice() pos3 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:452: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=True ) pos3 = aln[2::3] pos3 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:472: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ACGTAA---", "seq2": "ACGACA---", "seq3": "ACGCAATGA"}, moltype="dna", ) new = aln.trim_stop_codons() new [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:485: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln = make_aligned_seqs( data={ "seq1": "ACGTAA---", "seq2": "ACGAC----", # terminal codon incomplete "seq3": "ACGCAATGA", }, moltype="dna", ) new = aln.trim_stop_codons(strict=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:504: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:519: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nucs = aln.no_degenerates() nucs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:526: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trinucs = aln.no_degenerates(motif_length=3) trinucs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:534: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") pos = aln.variable_positions() just_variable_aln = aln.take_positions(pos) just_variable_aln[:10] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:546: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") pos = aln.variable_positions() just_constant_aln = aln.take_positions(pos, negate=True) just_constant_aln[:10] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:560: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") variable_codons = aln.filtered( lambda x: len(set(map(tuple, x))) > 1, motif_length=3 ) just_variable_aln[:9] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:572: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = aln.to_type(array_align=False) variable_codons = aln.filtered(lambda x: len(set("".join(x))) > 1, motif_length=3) just_variable_aln[:9] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:586: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") aln.take_seqs(["Human", "Mouse"]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:595: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs(["Human", "Mouse"], negate=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:604: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) def no_N_chars(s): return "N" not in s aln.take_seqs_if(no_N_chars) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:624: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs_if(no_N_chars, negate=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:636: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) counts = aln.counts() counts [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:651: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.counts(motif_length=3) counts [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:656: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.counts(include_ambiguity=True) counts [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:670: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs() motif_probs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:680: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, load_aligned_seqs trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs(alphabet=trinuc_alphabet) for m in sorted(motif_probs, key=lambda x: motif_probs[x], reverse=True): print("%s %.3f" % (m, motif_probs[m])) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:694: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs(data=[("a", "AACAAC"), ("b", "AAGAAG")], moltype="dna") motif_probs = aln.get_motif_probs() assert motif_probs["T"] == 0.0 motif_probs = aln.get_motif_probs(pseudocount=1e-6) assert 0 < motif_probs["T"] <= 1e-6 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:706: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("a", "AACGTAAG"), ("b", "AACGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) motif_probs = aln.get_motif_probs(alphabet=dinuc_alphabet) assert motif_probs["AA"] == 0.25 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:716: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("my_seq", "AAAGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") my_seq = aln.get_seq("my_seq") my_seq.count("AA") "AAA".count("AA") "AAAA".count("AA") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:727: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq(moltype="dna", seq="AAAGTAAG") seq di_nucs = [seq[i : i + 2] for i in range(len(seq) - 1)] sum([nn == "AA" for nn in di_nucs]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:742: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() c1, c2 = list(col) c1, c2 list(filter(lambda x: x == "-", c1)) list(filter(lambda x: x == "-", c2)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") for column in aln[113:150].iter_positions(): ungapped = list(filter(lambda x: x == "-", column)) gap_fraction = len(ungapped) * 1.0 / len(column) print(gap_fraction) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:771: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGG-TG--"), ("seq2", "ATG-AGGTGATG"), ("seq3", "ATGAAG--GATG"), ], moltype="dna", ) seq_to_aln_map = aln.get_gapped_seq("seq1").gap_maps()[0] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:787: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq_to_aln_map[3] seq_to_aln_map[8] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:796: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_to_seq_map = aln.get_gapped_seq("seq1").gap_maps()[1] aln_to_seq_map[3] aln_to_seq_map[8] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:804: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError seq_pos = aln_to_seq_map[7] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:818: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) aln.omit_gap_runs(2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:832: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) aln.omit_gap_pos(0.40) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:846: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) filtered_aln = aln.omit_gap_seqs(0.50) filtered_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:861: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: filtered_aln.omit_gap_pos() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, PROTEIN print(DNA.alphabet) print(PROTEIN.alphabet) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: PROTEIN.alphabet.moltype == PROTEIN [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) print(dinuc_alphabet) trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) print(trinuc_alphabet) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = "TAGT" indices = DNA.alphabet.to_indices(seq) indices [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_indices([0, 2, 3, 0]) seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3.core.annotation_db import BasicAnnotationDb anno_db = BasicAnnotationDb() anno_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gff_db = load_annotations(path="data/mycoplasma-genitalium.gff") gff_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gb_db = load_annotations(path="data/mycoplasma-genitalium.gb") gb_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: summary = gff_db.describe summary [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:82: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: anno_db.add_feature( seqid="NC_000908", biotype="gene", name="interesting_gene", spans=[(1, 4)], strand="+", ) anno_db.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.add_feature( seqid="seq1", biotype="gene", name="interesting_gene", spans=[(1, 4)], strand="+", ) gff_db.describe[-2:, :] # showing just last two rows [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: mg_16s = list( gb_db.get_features_matching( name="MG_RS00775", biotype="gene", seqid="NC_000908" ) ) mg_16s [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogenes = list(gff_db.get_features_matching(biotype="pseudogene")) pseudogenes[:2] # showing just the first two [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: operon_cds = list( gff_db.get_features_matching(start=220600, end=229067, biotype="CDS") ) operon_cds [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:188: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: replication_records = list( gff_db.get_records_matching(attributes="replication", biotype="CDS") ) replication_records[0] # showing just the first match [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gb_db.num_matches(biotype="gene") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:215: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: total_genes = gb_db.count_distinct(biotype="gene", name=True) single_copy = total_genes[total_genes.columns["count"] == 1, :] len(single_copy) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:226: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: total_genes = gff_db.num_matches(biotype="gene") print("total genes: ", total_genes) genes = gff_db.count_distinct(biotype="gene", name=True) single_copy = genes[genes.columns["count"] == 1, :] print("single copy genes: ", len(single_copy)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:246: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: children = list(gff_db.get_feature_children(name="gene-MG_RS00035")) children [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: parents = list(gff_db.get_feature_parent(name="cds-WP_009885556.1")) parents [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:273: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.compatible(anno_db) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.compatible(gb_db) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: union_db = gb_db.union(anno_db) union_db.describe[-2:, :] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:307: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.update(anno_db) gff_db.describe[-2:, :] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:318: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3.core.annotation_db import GenbankAnnotationDb new_gb_db = GenbankAnnotationDb(source="m-genitalium-database.gbdb", db=anno_db) new_gb_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:331: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gff_db = load_annotations(path="data/mycoplasma-genitalium.gff") just_cds = gff_db.subset(biotype="CDS") just_cds.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:354: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq seq1 = make_seq( "AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAGGGAACCCT", name="NC_000908", moltype="dna", ) seq1.annotation_db = anno_db seq1.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:376: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq gb_seq = load_seq("data/mycoplasma-genitalium.gb") gb_seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:389: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_seq = load_seq( "data/mycoplasma-genitalium.fa", annotation_path="data/mycoplasma-genitalium.gff", ) gff_seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:402: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq = load_seq( "data/mycoplasma-genitalium.fa", annotation_path="data/mycoplasma-genitalium.gff", label_to_name=lambda x: x.split()[0], ) seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:412: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib # clean up files path = pathlib.Path("m-genitalium-database.gbdb") path.unlink() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import tree_align [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") aln, tree = tree_align("HKY85", seqs, show_progress=False) aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = make_tree( "(((NineBande:0.013,Mouse:0.185):0.023,DogFaced:0.046):0.027,Human:0.034,HowlerMon:0.019)" ) params = {"kappa": 4.0} aln, tree = tree_align( "HKY85", seqs, tree=tree, param_vals=params, show_progress=False ) aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import tree_align seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") tree = make_tree( "((NineBande:0.058,Mouse:0.595):0.079,DogFaced:0.142,(HowlerMon:0.062,Human:0.103):0.079)" ) params = {"kappa": 4.0, "omega": 1.3} aln, tree = tree_align( "MG94HKY", seqs, tree=tree, param_vals=params, show_progress=False ) aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs from cogent3.align.progressive import tree_align from cogent3.evolve.models import get_model seqs = [ ( "hum", "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", ), ( "mus", "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", ), ("rat", "CTGAACAAGCAGCCACTTTCAAACAAGAAA"), ] unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") unaligned_DNA [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_DNA.get_translation() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aligned_aa_seqs = [ ("hum", "KQIQESSENGSLAARQERQAQVNLT"), ("mus", "KQIQESGESGSLAARQERQAQVNLT"), ("rat", "LNKQ------PLS---------NKK"), ] aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA, aa_to_codon=True) aligned_DNA [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = aln.quick_tree(calc="TN93", show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = aln.quick_tree(calc="TN93", bootstrap=100, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = dists.quick_tree(show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.phylo import nj aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = nj.nj(dists, show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo import nj dists = {("a", "b"): 2.7, ("c", "b"): 2.33, ("c", "a"): 0.73} tree = nj.nj(dists, show_progress=False) print(tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo.least_squares import WLS from cogent3.util.deserialise import deserialise_object dists = deserialise_object("data/dists_for_phylo.json") ls = WLS(dists) stat, tree = ls.trex(a=5, k=5, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve.models import F81 from cogent3.phylo.maximum_likelihood import ML aln = load_aligned_seqs("data/primate_brca1.fasta") ml = ML(F81(), aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_distances available_distances() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_distance_calculator, load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta") dist_calc = get_distance_calculator("tn93", alignment=aln) dist_calc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.run(show_progress=False) dists = dist_calc.get_pairwise_distances() dists [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.stderr [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_model, load_aligned_seqs from cogent3.evolve import distance aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") d = distance.EstimateDistances(aln, submodel=get_model("F81")) d.run(show_progress=False) dists = d.get_pairwise_distances() dists [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:82: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists.max_pair() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: dists[dists.max_pair()] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists.min_pair() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: dists[dists.min_pair()] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model hky = get_model("HKY85") print(hky) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("GTR", with_rate=True, distribution="gamma") print(sub_mod) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("CNFGTR", with_rate=True, distribution="gamma") print(sub_mod) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("JTT92", with_rate=True, distribution="gamma") print(sub_mod) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:80: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) aln = make_aligned_seqs( [("a", "ACGT"), ("b", "AC-T"), ("c", "ACGT"), ("d", "AC-T")] ) lf.set_alignment(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:112: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") print(tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule( "omega", tip_names=["Human", "Orangutan"], outgroup_name="Galago", clade=True, init=0.5, ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", is_constant=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1, lower=1e-9, upper=20.0) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:190: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_param_rule("length", upper=1.0) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:207: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, digits=2) lf.set_param_rule("bprobs", is_constant=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:222: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, sites_independent=False, digits=2) lf.set_param_rule("bprobs", is_constant=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:239: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:253: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, max_restarts=5, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=False, global_tolerance=1.0, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:265: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False, max_restarts=5, tolerance=1e-8) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:276: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) try: lf.optimise( show_progress=False, limit_action="raise", max_evaluations=10, return_calculator=True, ) except ArithmeticError as err: print(err) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:303: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model sm = get_model("GTR") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree) aln = load_aligned_seqs("data/primate_brca1.fasta") lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:321: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lnL = lf.lnL lnL [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:326: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nfp = lf.nfp nfp [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:338: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:344: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic(second_order=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:353: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_bic() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:367: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: a_g = lf.get_param_value("A/G") a_g [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human = lf.get_param_value("length", "Human") human [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:380: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mprobs = lf.get_motif_probs() mprobs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tables = lf.get_statistics(with_motif_probs=True, with_titles=True) tables[0] # just displaying the first [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:398: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) null_lnL = lf.lnL null_nfp = lf.nfp lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:423: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) lf.set_name("Alt Hypothesis") lf.optimise(local=True, show_progress=False) alt_lnL = lf.lnL alt_nfp = lf.nfp lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:434: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from scipy.stats.distributions import chi2 LR = 2 * (alt_lnL - null_lnL) # the likelihood ratio statistic df = alt_nfp - null_nfp # the test degrees of freedom p = chi2.sf(LR, df) print(f"LR={LR:.4f} ; df={df}; p={df:.4f}") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:450: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) sim_aln = lf.simulate_alignment() sim_aln[:60] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:478: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("HKY85") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) kappa_lo, kappa_mle, kappa_hi = lf.get_param_interval("kappa") print(f"lo={kappa_lo:.2f} ; mle={kappa_mle:.2f} ; hi={kappa_hi:.2f}") human_lo, human_mle, human_hi = lf.get_param_interval("length", "Human") print(f"lo={human_lo:.2f} ; mle={human_mle:.2f} ; hi={human_hi:.2f}") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:501: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model aln = make_aligned_seqs(data=dict(a="ACGG", b="ATAG", c="ATGG")) tree = make_tree(tip_names=aln.names) sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) json = lf.to_json() json[:60] # just truncating the displayed string [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:516: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.deserialise import deserialise_object newlf = deserialise_object(json) newlf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:542: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestors = lf.likely_ancestral_seqs() ancestors[:60] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:549: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestral_probs = lf.reconstruct_ancestral_seqs() ancestral_probs["root"][:5] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq # create an example sequence seq = make_seq( "GCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAA", name="seq1", moltype="dna", ) # Add a feature seq.add_feature(biotype="gene", name="a_gene", spans=[(12, 48)], seqid="seq1") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # Add a feature as a series seq.add_feature( biotype="cpgsite", name="a_cpgsite", spans=[(12, 18), (21, 29), (35, 48)], seqid="seq1", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # make demo alignment aln1 = make_aligned_seqs( data=[["seq1", "-AAACCCCCA"], ["seq2", "TTTT--TTTT"]], array_align=False ) # add feature to seq1 aln1.add_feature( seqid="seq1", biotype="exon", name="A", spans=[(3, 8)], on_alignment=False ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:84: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # make demo alignment aln1 = make_aligned_seqs( data=[["seq1", "-AAACCCCCA"], ["seq2", "TTTT--TTTT"]], array_align=False ) aln1.add_feature( biotype="exon", name="aligned_exon", spans=[(0, 8)], on_alignment=True, ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:108: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq from cogent3.core.annotation_db import BasicAnnotationDb # init empty db and add feature db = BasicAnnotationDb() db.add_feature(seqid="seq1", biotype="exon", name="C", spans=[(45, 48)]) # make demo seq s1 = make_seq( "AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAGGGAACCCT", name="seq1", moltype="dna" ) # assign db to sequence s1.annotation_db = db s1.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq %timeit load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:150: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: :hide-code: seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( filename="data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", moltype="dna", ) seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:189: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:209: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import load_seq loaded_seq = load_seq( "data/C-elegans-chromosome-I.fa", label_to_name=lambda x: x.split()[0], moltype="dna", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:220: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # loaded_seq = < loaded / created the seq> loaded_seq.annotate_from_gff("data/C-elegans-chromosome-I.gff") loaded_seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import make_seq sub_seq = make_seq( "GCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAAGACTAAGCCTAAGA", name="I", moltype="dna", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # sub_seq = sub_seq.annotate_from_gff("data/C-elegans-chromosome-I.gff", offset=600) sub_seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:254: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs brca1_aln = load_aligned_seqs( "data/primate_brca1.fasta", array_align=False, moltype="dna" ) brca1_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:266: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: brca1_aln.annotate_from_gff("data/brca1_hsa_shortened.gff", seq_ids=["Human"]) brca1_aln.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:274: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: brca1_aln.get_seq("Human").annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:296: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") # note we wrap `get_features` in `list` as generator is returned gene = list(seq.get_features(name="WBGene00021661", biotype="gene")) gene [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:312: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS")) cds[:3] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:323: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: cds = list(seq.get_features(biotype="CDS", name="WBGene00021661")) cds [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") region_features = list(seq.get_features(start=10148, stop=26732)) region_features[:3] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:345: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: mRNA = list(seq.get_features(start=10148, stop=29322, biotype="mRNA"))[0] mRNA [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:358: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs # first load alignment and annotate the human seq aln = load_aligned_seqs( "data/primate_brca1.fasta", array_align=False, moltype="dna" ) aln.annotate_from_gff("data/brca1_hsa_shortened.gff", seq_ids=["Human"]) # query alignment providing seqid of interest human_exons = list(aln.get_features(biotype="exon", seqid="Human")) human_exons [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:383: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # add a feature to the alignment we created above on difference sequence aln.add_feature(biotype="gene", name="gene:101", spans=[(40, 387)], seqid="Rhesus") any_feature = list(aln.get_features(on_alignment=False)) any_feature [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:405: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # first we add the feature to the alignment aln.add_feature( biotype="pseudogene", name="pseudogene1", spans=[(420, 666)], on_alignment=True ) # query for features on the alignment aln_features = list(aln.get_features(on_alignment=True)) aln_features [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:426: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln3 = make_aligned_seqs( data=[["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], array_align=False, moltype="dna", ) exon = aln3.add_feature( seqid="x", biotype="exon", name="ex1", spans=[(0, 4)], on_alignment=False ) exon.get_slice() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:441: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln_exons = list(aln3.get_features(seqid="x", biotype="exon"))[0] aln_exons [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:451: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: exon.get_slice(allow_gaps=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:466: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) pseudogene = list(seq.get_features(start=10148, stop=26732, biotype="pseudogene"))[0] seq[pseudogene] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:484: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogene.get_slice() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:494: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") subseq = seq[25000:35000] fig = subseq.get_drawable(biotype=("gene", "mRNA", "CDS", "misc_RNA")) fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogene.get_coordinates() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:515: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS"))[0] exon_coords = cds.get_coordinates() exon_coords [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intron_coords = [] for i in range(len(exon_coords) - 1): intron_coords.append((exon_coords[i][1], exon_coords[i + 1][0])) intron_coords [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:540: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intron = seq.add_feature( biotype="intron", name="intron:Y74C9A.3.1", seqid="I", spans=intron_coords ) intron [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:553: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS")) union_cds = cds[0].union(cds[1:]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:572: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") genes = list(seq.get_features(biotype="gene")) genes = genes[0].union(genes[1:]) genes [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:584: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intergenic = genes.shadow() intergenic [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:592: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intergenic.get_slice() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:605: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") no_cds = seq.with_masked_annotations("CDS") no_cds[2575800:2575900] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:621: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]], moltype="dna", array_align=False, ) exon = aln.add_feature( seqid="x", biotype="exon", name="exon-be-gone", spans=[(0, 4)], on_alignment=False, ) aln.with_masked_annotations("exon", mask_char="?") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:642: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: rc = aln.rc() rc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:650: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: rc.with_masked_annotations("exon", mask_char="?") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:664: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) gene = list(seq.get_features(name="gene:WBGene00022276", biotype="gene"))[0] children = list(gene.get_children()) children [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:686: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: child = list(seq.get_features(name="transcript:Y74C9A.2a.3", biotype="mRNA"))[0] parent = list(child.get_parent()) parent [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:698: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False, moltype="dna", ) x, y = aln2.get_seq("x"), aln2.get_seq("y") x.annotation_db is y.annotation_db is aln2.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:711: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq = make_seq("CCCCCCCCCCCCCCCCCCCC", name="x", moltype="dna") match_exon = seq.add_feature(biotype="exon", name="A", spans=[(3, 8)]) aln2.copy_annotations(seq.annotation_db) aln2.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:721: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: copied = list(aln2.get_features(seqid="x", biotype="exon")) copied [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:732: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: unified = aln_exons.as_one_span() aln3[unified] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:743: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: plus = make_seq("CCCCCAAAAAAAAAATTTTTTTTTTAAAGG", moltype="dna") plus_rpt = plus.add_feature(biotype="blah", name="a", spans=[(5, 15), (25, 28)]) plus[plus_rpt] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:750: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: minus = plus.rc() minus [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: minus_rpt = list(minus.get_features(biotype="blah"))[0] minus[minus_rpt] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = { "s1": "GCTCATGCCAGCTCTTTACAGCATGAGAACA--AGT", "s2": "ACTCATGCCAACTCATTACAGCATGAGAACAGCAGT", "s3": "ACTCATGCCAGCTCATTACAGCATGAGAACAGCAGT", "s4": "ACTCATGCCAGCTCATTACAGCATGAGAACAGCAGT", "s5": "ACTCATGCCAGCTCAGTACAGCATGAGAACAGCAGT", } nt_seqs = make_aligned_seqs(data=data, moltype="dna") nt_seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_seqs.get_translation(gc=1, incomplete_ok=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") translations = standard_code.sixframes(seq) print(translations) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:62: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") stops_frame1 = standard_code.get_stop_indices(seq, start=0) stops_frame1 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stop_index = stops_frame1[0] seq[stop_index : stop_index + 3] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) standard_code["TTT"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: standard_code["A"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:95: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["TTT"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["A"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:115: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: targets = ["A", "C"] codons = [standard_code[aa] for aa in targets] codons [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: flat_list = sum(codons, []) flat_list [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(1) alphabet = gc.get_alphabet() print(alphabet) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:142: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna") codons = my_seq.get_in_motif_size(3) codons [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:155: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep = my_seq.get_translation() pep [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:163: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.core.alphabet import AlphabetError [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq seq = make_seq("ATGTGATGGTAA", name="s1", moltype="dna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:179: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AlphabetError pep = seq.get_translation() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep = seq.get_translation(include_stop=True) pep [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/mycoplasma-genitalium.fa", moltype="dna") seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = load_seq("data/brca1-bats.fasta", moltype="dna") seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna") type(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.info.source [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/long_testseqs.fasta", moltype="dna") type(seqs) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs( "https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/long_testseqs.fasta", moltype="dna", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna", format="fasta") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:101: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs protein_seqs = {"seq1": "DEKQL-RG", "seq2": "DDK--SRG"} proteins_loaded = make_aligned_seqs(protein_seqs) proteins_loaded.moltype proteins_loaded [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: proteins_loaded = make_aligned_seqs(protein_seqs, moltype="protein") proteins_loaded [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:123: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"} seqs_loaded = make_aligned_seqs(seqs) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:133: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"} seqs_loaded = make_aligned_seqs(seqs) seqs_loaded [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs DNA_seqs = { "sample1 Mus musculus": "AACCTGC--C", "sample2 Gallus gallus": "AAC-TGCAAC", } loaded_seqs = make_aligned_seqs( DNA_seqs, moltype="dna", label_to_name=lambda x: x.split()[0] ) loaded_seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs seqs = {"seq1": "AATCA", "seq2": "AATCGGA"} seqs = make_unaligned_seqs(data=seqs, moltype="dna") seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:184: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import MinimalFastaParser f = open("data/long_testseqs.fasta") seqs = [(name, seq) for name, seq in MinimalFastaParser(f)] seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:197: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import LabelParser def latin_to_common(latin): return {"Homo sapiens": "human", "Pan troglodtyes": "chimp"}[latin] label_parser = LabelParser( "%(species)s", [[1, "species", latin_to_common]], split_with=":" ) for label in ">abcd:Homo sapiens:misc", ">abcd:Pan troglodtyes:misc": label = label_parser(label) print(label, type(label)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:213: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import LabelParser, MinimalFastaParser fasta_data = [ ">gi|10047090|ref|NP_055147.1| small muscle protein, X-linked [Homo sapiens]", "MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGAKKLPGPAVNL", "SEIQNIKSELKYVPKAEQ", ">gi|10047092|ref|NP_037391.1| neuronal protein [Homo sapiens]", "MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLY", "PPGQEPIPKISESKMAFKQMEQISQFLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTKD", ] label_to_name = LabelParser( "%(ref)s", [[1, "gi", str], [3, "ref", str], [4, "description", str]], split_with="|", ) for name, seq in MinimalFastaParser(fasta_data, label_to_name=label_to_name): print(name) print(name.info.gi) print(name.info.description) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:54: WARNING: TODO entry found: add cross ref for description of Info class /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_moltypes available_moltypes() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_moltype dna = get_moltype("dna") dna [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.ambiguities [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.degenerates [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.complement("AGG") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = dna.make_seq("AGGCTT", name="seq1") seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rna = get_moltype("rna") rna.is_valid("ACGUACGUACGUACGU") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core import moltype as mt DNAgapped = mt.MolType( seq_constructor=mt.DnaSequence, motifset=mt.IUPAC_DNA_chars, ambiguities=mt.IUPAC_DNA_ambiguities, complements=mt.IUPAC_DNA_ambiguities_complements, pairs=mt.DnaStandardPairs, gaps=".", ) seq = DNAgapped.make_seq("ACG.") seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.sequence import DnaSequence DnaSequence.moltype = DNA [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq p = make_seq("THISISAPRQTEIN", "myProtein", moltype="protein") type(p) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: p [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq nuc = make_seq("TTTGCAAAC", moltype="dna") pep = nuc.get_translation() pep [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.write("data/temp.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") names = tr.get_node_names() names[:4] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: names[4:] names_nodes = tr.get_nodes_dict() names_nodes["Human"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_node_matching_name("Mouse") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tr.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: hu.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:70: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] type(hu) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(tr) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() for n in nodes.items(): print(n) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tr.iter_tips(): print(n) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for n in tr.iter_nontips(): print(n.get_newick()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") edges = tr.get_connecting_edges("edge.1", "Human") for edge in edges: print(edge.name) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] hu.distance(mu) hu.is_tip() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] lca = hu.last_common_ancestor(mu) lca [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:154: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(lca) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") for a in hu.ancestors(): print(a.name) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") node = tr.get_node_matching_name("edge.1") children = list(node.iter_tips()) + list(node.iter_nontips()) for child in children: print(child.name) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") dists = tr.get_distances() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human_dists = [names for names in dists if "Human" in names] for dist in human_dists: print(dist, dists[dist]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:204: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.max_tip_tip_distance() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tips = hu.tips_within_distance(0.2) for t in tips: print(t) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.rooted_at("edge.0").ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.root_at_midpoint().ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:254: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:261: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.rooted_with_tip("Mouse").ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:271: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.get_newick() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:278: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_newick(with_distances=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:285: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") xml = tr.get_xml() for line in xml.splitlines(): print(line) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:299: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:309: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.preorder(): print(t.get_newick()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:320: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.postorder(): print(t.get_newick()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for tip in tr.iter_nontips(): tip_names = tip.get_tip_names() print(tip_names) sub_tree = tr.get_sub_tree(tip_names) print(sub_tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:348: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.io import remove_files remove_files(["data/temp.tree", "data/temp.pdf"], error_on_missing=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:364: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree simple_tree_string = "(B:0.2,(D:0.4)E:0.5)F;" simple_tree = make_tree(simple_tree_string) print(simple_tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.prune() print(simple_tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:377: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:384: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = load_tree("data/test.tree") print(tr1.get_newick()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:391: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr2 = tr1.unrooted_deepcopy() print(tr2.get_newick()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:401: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tree_string = "(B:0.2,H:0.2,(C:0.3,D:0.4,E:0.1)F:0.5)G;" tr = make_tree(tree_string) print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:409: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.bifurcating().ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:422: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:429: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.balanced().ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:438: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr1 = make_tree("(B:0.2,(C:0.2,D:0.2)F:0.2)G;") tr2 = make_tree("((C:0.1,D:0.1)F:0.1,B:0.1)G;") tr1.same_topology(tr2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:467: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # Distance metrics for rooted trees from cogent3 import make_tree tr1 = make_tree(treestring="(a,(b,(c,(d,e))));") tr2 = make_tree(treestring="(e,(d,(c,(b,a))));") mc_distance = tr1.tree_distance(tr2, method="matching_cluster") # or method="mc" or method="matching" rooted_rf_distance = tr1.tree_distance(tr2, method="rooted_robinson_foulds") # or method="rrf" or method="rf" print("Matching Cluster Distance:", mc_distance) print("Rooted Robinson Foulds Distance:", rooted_rf_distance) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:481: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # Distance metrics for unrooted trees from cogent3 import make_tree tr1 = make_tree(treestring="(a,b,(c,(d,e)));") tr2 = make_tree(treestring="((a,c),(b,d),e);") lrm_distance = tr1.tree_distance(tr2, method="lin_rajan_moret") # or method="lrm" or method="matching" unrooted_rf_distance = tr1.tree_distance(tr2, method="unrooted_robinson_foulds") # or method="urf" or method="rf" print("Lin-Rajan-Moret Distance:", lrm_distance) print("Unrooted Robinson Foulds Distance:", unrooted_rf_distance) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:501: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.set_tip_distances() for t in tr.preorder(): print(t.name, t.TipDistance) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:517: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:524: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.scale_branch_lengths() print(tr) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:534: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:3,(C:2,D:4)F:5)G;") d, tips = tr.tip_to_tip_distances() for i, t in enumerate(tips): print(t.name, d[i]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:554: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr1 = make_tree("(B:2,(C:3,D:4)F:5)G;") tr2 = make_tree("(C:2,(B:3,D:4)F:5)G;") tr1.compare_by_tip_distances(tr2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table [docutils] cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv") [docutils] cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table [docutils] cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] [docutils] cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] [docutils] cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table [docutils] cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table [docutils] cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table [docutils] cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table [docutils] cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table [docutils] cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) [docutils] cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] [docutils] cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table [docutils] cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table [docutils] cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table [docutils] cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] [docutils] cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] [docutils] cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table [docutils] cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table [docutils] cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table [docutils] cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table [docutils] cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table [docutils] cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data, title="Sample title", legend="a legend") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table.title = "My title" table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") for row in table: print(row) break [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for row in table: print(row["Locus"]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3, 5], b=["a", "c", "d"]) table = make_table(data=data) table.shape[0] == 3 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.shape[1] == 2 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.columns [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Region"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:113: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for name in table.columns: print(name) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table[:2, "Region":] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:135: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table[:2, :1] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.format_column("Ratio", "%.1e") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", digits=1, space=2) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.space = " " table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table h = ["name", "A/C", "A/G", "A/T", "C/A"] rows = [["tardigrade", 0.0425, 0.1424, 0.0226, 0.0391]] wrap_table = make_table(header=h, data=rows, max_width=30) wrap_table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:184: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wrap_table = make_table(header=h, data=rows, max_width=30, index_name="name") wrap_table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:192: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data=dict(a=list(range(10)), b=list(range(10)))) table.head() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:199: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.head(2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail(1) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(random=3) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(head=2, tail=3) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:241: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.header) table = table.with_new_header("Ratio", "Stat") print(table.header) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:251: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:269: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table = table.with_new_column( "LargeCon", lambda r_v: r_v[0] == "Con" and r_v[1] > 10.0, columns=["Region", "Ratio"], ) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.array [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:292: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") locus = table.to_list("Locus") locus [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:300: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Locus"].tolist() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:311: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") rows = table.to_list(["Region", "Locus"]) rows [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:324: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.to_dict() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.columns.to_dict() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:342: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") df = table.to_pandas() df [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:350: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: df = table.to_pandas(categories="Region") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:359: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}, index_name="") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:364: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: contingency = table.to_categorical(["Ts", "Tv"]) contingency [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:369: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: g_test = contingency.G_independence() g_test [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:376: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}) contingency = table.to_categorical(["Ts", "Tv"], index_name="") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1 = load_table("data/stats.tsv") table2 = load_table("data/stats.tsv") table = table1.appended(None, table2) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:397: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1.title = "Data1" table2.title = "Data2" table = table1.appended("Data#", table2, title="") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:409: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.summed("Ratio") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:416: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Ratio"].sum() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:425: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table all_numeric = make_table( header=["A", "B", "C"], data=[range(3), range(3, 6), range(6, 9), range(9, 12)] ) all_numeric [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:436: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:442: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed(col_sum=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:451: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed = make_table( header=["A", "B", "C"], data=[["*", 1, 2], [3, "*", 5], [6, 7, "*"]] ) mixed [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:460: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(strict=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:466: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(col_sum=False, strict=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:475: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") sub_table = table.filtered(lambda x: x < 10.0, columns="Ratio") sub_table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:483: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0") sub_table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:490: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0 and Region == 'NonCon'") sub_table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:500: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: big_numeric = all_numeric.filtered_by_column(lambda x: sum(x) > 20) big_numeric [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.sorted(columns="Ratio") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:516: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns="Ratio", reverse="Ratio") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:523: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns=["Region", "Ratio"], reverse="Ratio") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:530: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.to_list("Region") raw [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:539: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.to_list(["Locus", "Region"]) raw [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:548: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.distinct_values("Region") == set(["NonCon", "Con"]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:556: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.count("Region == 'NonCon' and Ratio > 1") == 1 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:566: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( data=dict(A=["a", "b", "b", "b", "a"], B=["c", "c", "c", "c", "d"]) ) unique = table.count_unique("A") type(unique) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:576: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:582: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique = table.count_unique(["A", "B"]) unique [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:587: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: r = unique.to_table() r [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:597: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rows = [ ["NP_004893", True], ["NP_005079", True], ["NP_005500", False], ["NP_055852", False], ] region_type = make_table(header=["Locus", "LargeCon"], data=rows) stats_table = load_table("data/stats.tsv") new = stats_table.joined(region_type, columns_self="Locus") new [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:617: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["#OTU ID", "14SK041", "14SK802"] rows = [ [-2920, "332", 294], [-1606, "302", 229], [-393, 141, 125], [-2109, 138, 120], ] table = make_table(header=header, rows=rows) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:633: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tp = table.transposed(new_column_name="sample", select_as_header="#OTU ID") tp [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:643: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="md") print(table) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:655: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="tex") print(table) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:667: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_markdown(justify="ccr")) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:675: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_latex(justify="ccr", label="tab:table1")) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:685: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst(csv_table=True)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:695: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:707: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_string(format="latex")) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:717: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: rows = [ ["1", 100, 101, 1.123], ["1", 101, 102, 1.123], ["1", 102, 103, 1.123], ["1", 103, 104, 1.123], ["1", 104, 105, 1.123], ["1", 105, 106, 1.123], ["1", 106, 107, 1.123], ["1", 107, 108, 1.123], ["1", 108, 109, 1], ["1", 109, 110, 1], ["1", 110, 111, 1], ["1", 111, 112, 1], ["1", 112, 113, 1], ["1", 113, 114, 1], ["1", 114, 115, 1], ["1", 115, 116, 1], ["1", 116, 117, 1], ["1", 117, 118, 1], ["1", 118, 119, 2], ["1", 119, 120, 2], ["1", 120, 121, 2], ["1", 150, 151, 2], ["1", 151, 152, 2], ["1", 152, 153, 2], ["1", 153, 154, 2], ["1", 154, 155, 2], ["1", 155, 156, 2], ["1", 156, 157, 2], ["1", 157, 158, 2], ["1", 158, 159, 2], ["1", 159, 160, 2], ["1", 160, 161, 2], ] bgraph = make_table(header=["chrom", "start", "end", "value"], rows=rows) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bgraph.head() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:762: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print( bgraph.to_string( format="bedgraph", name="test track", description="test of bedgraph", color=(255, 0, 0), digits=0, ) ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:777: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") straight_html = table.to_html() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:789: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.format.table import known_formats known_formats [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:798: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.write("stats_tab.tex", justify="ccr", label="tab:table1") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:807: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.write("stats_tab.txt", sep="\t") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:814: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib for name in ("stats_tab.txt", "stats_tab.tex"): p = pathlib.Path(name) if p.exists(): p.unlink() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.a [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data["a"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.d [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.b |= {"d": 25} data.b [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.union({"d": [25]}) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b {"c": 24, "d": [25]} [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data["k"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AttributeError data.k [docutils] cookbook/union_dict.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.a [docutils] cookbook/union_dict.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data["a"] [docutils] cookbook/union_dict.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.d [docutils] cookbook/union_dict.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.b |= {"d": 25} data.b [docutils] cookbook/union_dict.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.union({"d": [25]}) [docutils] cookbook/union_dict.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b {"c": 24, "d": [25]} [docutils] cookbook/union_dict.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data["k"] [docutils] cookbook/union_dict.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AttributeError data.k [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy def DiffOmega(omega): def omega_from_S(S): omega_est = S / (1 - numpy.e ** (-1 * S)) return abs(omega - omega_est) ** 2 return omega_from_S omega = 0.1 f = DiffOmega(omega) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.optimisers import maximise, minimise S = minimise( f, # the function xinit=1.0, # the initial value bounds=(-100, 100), # [lower,upper] bounds for the parameter local=True, # just local optimisation, not Simulated Annealing show_progress=False, ) assert 0.0 <= f(S) < 1e-6 print("S=%.4f" % S) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3.util.misc import iterable my_var = 10 for i in my_var: print("will not work") for i in iterable(my_var): print(i) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import curry def foo(x, y): """Some function""" return x + y bar = curry(foo, 5) print(bar.__doc__) bar(10) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_iterable can_iter = [1, 2, 3, 4] cannot_iter = 1.234 is_iterable(can_iter) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_iterable(cannot_iter) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_char class foo: pass is_char("a") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char("ab") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:122: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char(foo()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:131: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import recursive_flatten l = [[[[1, 2], "abcde"], [5, 6]], [7, 8], [9, 10]] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: recursive_flatten(l) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import not_list_tuple not_list_tuple(1) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple([1]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple("ab") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import add_lowercase d = {"A": 5, "B": 6, "C": 7, "foo": 8, 42: "life"} add_lowercase(d) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:177: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from numpy import array from cogent3.util.misc import DistanceFromMatrix m = array([[1, 2, 3], [4, 5, 6], [7, 8, 9]]) f = DistanceFromMatrix(m) f(0, 0) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:187: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(1, 2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ClassChecker class not_okay(object): pass no = not_okay() class okay(object): pass o = okay() class my_dict(dict): pass md = my_dict() cc = ClassChecker(str, okay, dict) o in cc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:217: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: no in cc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 5 in cc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:225: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: {"a": 5} in cc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: "asasas" in cc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:233: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: md in cc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:242: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import Delegator class ListAndString(list, Delegator): def __init__(self, items, string): Delegator.__init__(self, string) for i in items: self.append(i) ls = ListAndString([1, 2, 3], "ab_cd") len(ls) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:255: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls[0] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.upper() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:263: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.split("_") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:272: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import FunctionWrapper f = FunctionWrapper(str) f [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(123) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:290: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.misc import ConstraintError [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:295: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ConstrainedDict d = ConstrainedDict({"a": 1, "b": 2, "c": 3}, constraint="abc") d [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:302: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ConstraintError d["d"] = 5 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:4: WARNING: duplicate label union_dict, other instance in /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/what_codes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/what_codes.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_codes available_codes() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/what_codes.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(4) gc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/brca1.fasta", moltype="dna") aln = aln.no_degenerates(motif_length=3) aln = aln.get_translation() aln = aln[:100] # for compute speed in testing the documentation coevo = aln.coevolution(show_progress=False, drawable="heatmap") coevo.drawable.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-coevolution.png" coevo.drawable.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: coevo = aln.coevolution(show_progress=False, drawable="violin") coevo.drawable.show(width=300) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: coevo = aln.coevolution(show_progress=False, drawable="box") coevo.drawable.show(width=300) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:11: WARNING: TODO entry found: add citation for NMI /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/SCA1-cds.fasta", moltype="dna") draw = seqs.dotplot() draw.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-1.png" draw.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", window=8, threshold=8) draw.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True) draw.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True, title="SCA1", width=400) draw.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:11: WARNING: TODO entry found: Change dotplot ref to a citation /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_json") seqs = loader("data/tp53.json") dp = seqs.dotplot(name1="Macaque", name2="Marmoset", width=600) dp.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-2.png" dp.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: help(dp.remove_track) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dp.remove_track(left_track=True) dp.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs, get_app seqs = load_aligned_seqs("data/brca1.fasta", moltype="dna").degap() seqs = seqs.take_seqs( ["LeafNose", "FalseVamp", "RoundEare", "Sloth", "Anteater", "HairyArma"] ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligner = get_app("progressive_align", "nucleotide", indel_rate=1e-2, indel_length=1e-9) aln = aligner(seqs) dp = aln[2200:2500].dotplot("HairyArma", "RoundEare") dp.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-3.png" dp.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln[2300:2500] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligner = get_app("progressive_align", "nucleotide") aln = aligner(seqs) aln[2200:2500].dotplot("HairyArma", "RoundEare").show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln[2300:2500] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/brca1.fasta", moltype="dna") counts = aln.count_gaps_per_seq(unique=True) counts[10: 20] # limiting the width of the displayed output [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="bar") counts.drawable.show(width=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-gaps-per-seq.png" counts.drawable.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="violin") counts.drawable.show(width=300, height=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="box") counts.drawable.show(width=300, height=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_aligned_seqs, make_seq s1 = make_seq("TGATGTAAGGTAGTT", name="s1", moltype="dna") s2 = make_seq("--CTGGAAGGGT---", name="s2", moltype="dna") seqs = make_aligned_seqs(data=[s1, s2], array_align=False, moltype="dna") draw = seqs.information_plot(window=2, include_gap=True) draw.show(width=500, height=400) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/brca1.fasta", moltype="protein") fig = aln.information_plot(stat="median") fig.show(width=500, height=400) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-info-plot.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.parse import jaspar _, pwm = jaspar.read("data/tbp.jaspar") freqarr = pwm.to_freq_array() freqarr[:5] # illustrating the contents of the MotifFreqsArray [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: logo = freqarr.logo() logo.show(height=250, width=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-seqlogo.png" logo.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") l = aln[:311].seqlogo(height=300, width=500, wrap=60, vspace=0.05) l.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa = aln.get_translation(incomplete_ok=True)[:120] logo = aa.seqlogo(width=500, height=300, wrap=50, vspace=0.1) logo.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = seq[25000:35000] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig = seq.get_drawable() fig.show(height=400, width=700) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig = seq.get_drawable(biotype=("gene", "CDS", "mRNA")) fig.show(height=300, width=650) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_seq-features.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure(style="angular", width=600, height=600) fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-angular.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure("circular", width=600, height=600) fig.scale_bar = "top right" fig.label_pad = 0.1 fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.style_edges( "AfricanEl", tip2="Manatee", legendgroup="Afrotheria", line=dict(color="magenta", width=2), ) fig.show(width=650, height=600) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.label_pad = 0.3 fig.show(width=650, height=600) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-circular.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:9: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure("radial", width=600, height=600) fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:19: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-radial.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.label_pad = 0.23 fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure(width=600, height=600) fig.scale_bar = "top right" fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-square.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.style_edges( "AfricanEl", tip2="Manatee", legendgroup="Afrotheria", line=dict(color="magenta"), ) fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() tree = reader("data/tree-with-support.json") fig = tree.get_figure(show_support=True, threshold=0.8) fig.scale_bar = None fig.show(width=500, height=400) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.support_xshift = 15 fig.support_yshift = 0 fig.show(width=500, height=400) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-support.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = { "hum": "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", "mus": "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", "rat": "CTGAACAAGCAGCCACTTTCAAACAAGAAA", } unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") unaligned_DNA [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_aa = unaligned_DNA.get_translation() unaligned_aa [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_aa_seqs = { "hum": "KQIQESSENGSLAARQERQAQVNLT", "mus": "KQIQESGESGSLAARQERQAQVNLT", "rat": "LNKQ------PLS---------NKK", } aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA) aligned_DNA [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.cluster.UPGMA import upgma from cogent3.evolve import distance [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/test.paml") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster = upgma(d.get_pairwise_distances()) print(mycluster.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster.write("test_upgma.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_upgma.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.phylo import nj [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=get_model("HKY85")) d.run(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree = nj.nj(d.get_pairwise_distances(), show_progress=False) print(mytree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree.write("test_nj.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_nj.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) d.get_pairwise_distances() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d.write("dists_for_phylo.phylip", format="phylip") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os for file_name in "dists_for_phylo.phylip", "dists_for_phylo.pickle": os.remove(file_name) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:48: WARNING: TODO entry found: write out in json format /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tf = get_model("GY94") nf = get_model("MG94GTR") cnf = get_model("CNFGTR") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = load_tree("data/primate_brca1.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:64: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_param_rule("omega", is_constant=True, value=1.0) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: optimiser_args = dict( local=True, max_restarts=5, tolerance=1e-8, show_progress=False ) lf.set_alignment(aln) lf.optimise(**optimiser_args) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: neutral_lnL = lf.get_log_likelihood() neutral_nfp = lf.get_num_free_params() lf.set_param_rule("omega", is_constant=False) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from scipy.stats.distributions import chi2 LR = 2 * (non_neutral_lnL - neutral_lnL) df = non_neutral_nfp - neutral_nfp print(chi2.sf(LR, df)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:114: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Chimpanzee", "Human"], outgroup_name="Galago", clade=True ) lf.optimise(**optimiser_args) lf chimp_human_clade_lnL = lf.get_log_likelihood() chimp_human_clade_nfp = lf.get_num_free_params() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:124: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (chimp_human_clade_lnL - non_neutral_lnL) df = chimp_human_clade_nfp - non_neutral_nfp print(chi2.sf(LR, df)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:149: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: annot_tree = lf.get_annotated_tree() omega_mle = lf.get_param_value("omega") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf = cnf.make_likelihood_function( annot_tree, bins=["neutral", "adaptive"], digits=2, space=3 ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("omega", bin="neutral", upper=1, init=omega_mle) rate_lf.set_param_rule( "omega", bin="adaptive", lower=1 + epsilon, upper=100, init=1 + 2 * epsilon ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:179: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("bprobs", init=[1 - epsilon, epsilon]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:185: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_alignment(aln) rate_lf.optimise(**optimiser_args) rate_lnL = rate_lf.get_log_likelihood() rate_nfp = rate_lf.get_num_free_params() LR = 2 * (rate_lnL - non_neutral_lnL) df = rate_nfp - non_neutral_nfp rate_lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(chi2.sf(LR, df)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pp = rate_lf.get_bin_probs() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from IPython.core.display import HTML from numpy import array from cogent3 import make_table header = ["Site Class", "Proportion", "Background Edges", "Foreground Edges"] data = { "Site Class": array(["0", "1", "2a", "2b"], dtype=" 1", "0 < omega0 < 1"], dtype=" 1.8: tips_to_delete.append(n) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/manipulating_tree_nodes.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tips_to_delete: n.parent.remove(n) complex_tree.prune() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/manipulating_tree_nodes.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(complex_tree.ascii_art(show_internal=False)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from scipy.stats.distributions import chi2 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree("data/test.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("MG94GTR") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(al) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(global_tolerance=1.0, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: at = lf.get_annotated_tree() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = chi2.sf(LR, df) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(f"Likelihood ratio statistic = {LR}") print(f"degrees-of-freedom = {df}") print(f"probability = {P}") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve import bootstrap from cogent3.evolve.models import HKY85 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_alt_function(): t = load_tree("data/test.tree") sm = HKY85() return sm.make_likelihood_function(t) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_null_function(): lf = create_alt_function() # set the local clock for humans & howler monkey lf.set_local_clock("Human", "HowlerMon") return lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP = bootstrap.EstimateProbability( create_null_function(), create_alt_function(), aln ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.set_num_replicates(5) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.run(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: p = estimateP.get_estimated_prob() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("%.2f, %.2f" % estimateP.get_observed_lnL()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import numpy numpy.random.seed(11) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy t = numpy.arange(0, 10, 0.1) n = numpy.random.randn(len(t)) nse = numpy.convolve(n, numpy.exp(-t / 0.05)) * 0.1 nse = nse[: len(t)] sig = numpy.sin(2 * numpy.pi * t) + nse [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import dft pwr, period = dft(sig) print(period) print(pwr) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pwr = abs(pwr) max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr pwr, period = auto_corr(sig) print(period) print(pwr) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s = ( "ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG" "GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT" "AATTTTTAACCGCGGAATTGCGTC" ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"]) symbols = seq_to_symbols(s) len(symbols) == len(s) symbols [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import ipdft powers, periods = ipdft(symbols) powers [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:123: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr, hybrid powers, periods = auto_corr(symbols) powers [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = hybrid(symbols) powers [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:139: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:151: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel pwr = goertzel(sig, 10) print(pwr) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = auto_corr(symbols) llim = 2 period5 = 5 - llim periods[period5] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers[period5] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel period = 4 power = goertzel(symbols, period) ipdft_powers, periods = ipdft(symbols) ipdft_power = abs(ipdft_powers[period - llim]) round(power, 6) == round(ipdft_power, 6) power [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:191: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: power = hybrid(symbols, period=period) power [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:204: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Goertzel goertzel_calc = Goertzel(len(sig), period=10) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap obs_stat, p = blockwise_bootstrap( sig, calc=goertzel_calc, block_size=10, num_reps=1000 ) print(obs_stat) print(p) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Hybrid hybrid_calculator = Hybrid(len(s), period=4) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"], length=len(s)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:248: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap stat, p = blockwise_bootstrap( s, calc=hybrid_calculator, block_size=10, num_reps=1000, seq_to_symbols=seq_to_symbols, ) print(stat) p < 0.1 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pickle from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.evolve.fast_distance import DistanceMatrix from cogent3.evolve.models import HKY85 al = load_aligned_seqs("data/long_testseqs.fasta") d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle from cogent3.phylo import least_squares [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: with open("dists_for_phylo.pickle", "rb") as f: dists = pickle.load(f) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls = least_squares.WLS(dists) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls_distance_matrix = least_squares.WLS(DistanceMatrix(dists)) ls_pairwise_matrix = least_squares.WLS(dists.to_dict()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: score, tree = ls.trex(a=5, k=1, show_progress=False) assert score < 1e-4 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trees = ls.trex(a=5, k=5, return_all=True, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:85: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(len(trees)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls_stats = [tree[0] for tree in trees] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:103: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: t1 = trees[0][1].balanced() t2 = trees[1][1].balanced() print(t1.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(t2.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree query_tree = make_tree( "((Human:.2,DogFaced:.2):.3,(NineBande:.1, Mouse:.5):.2,HowlerMon:.1)" ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.evaluate_tree(query_tree) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:136: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls, t = ls.evaluate_topology(query_tree) assert "%.4f" % wls == "0.0084" [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:148: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("dists_for_phylo.pickle") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.substitution_model import TimeReversibleNucleotide [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide(equal_motif_probs=True) tree = load_tree("data/test.tree") lf = model.make_likelihood_function(tree) lf.set_param_rule("length", value=0.6, is_constant=True) aln1 = lf.simulate_alignment(sequence_length=10000) lf.set_param_rule("length", value=0.2, is_constant=True) aln2 = lf.simulate_alignment(sequence_length=10000) aln3 = aln1 + aln2 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="free" ) lf = model.make_likelihood_function(tree, bins=2, digits=2, space=3) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = [t for t in lf.get_statistics() if "bin" in t.title][0] bprobs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="gamma" ) lf = model.make_likelihood_function(tree, bins=4) lf.set_param_rule("bprobs", is_constant=True) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from scipy.stats.distributions import chi2 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree(filename="data/test.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("HKY85") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=3) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_local_clock("Human", "HowlerMon") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("clock") lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:84: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("non clock") lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = chi2.sf(LR, df) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("Likelihood ratio statistic = ", LR) print("degrees-of-freedom = ", df) print("probability = ", P) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import MG94HKY aln = load_aligned_seqs("data/long_testseqs.fasta") tree = load_tree("data/test.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = MG94HKY() lf = sm.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["DogFaced", "Mouse"], outgroup_name="Human", init=2.0, clade=True, ) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", init=1.0) lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=False, ) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=True, ) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, value=1.0, is_constant=True, ) lf.optimise(local=True, show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_constant=False, ) lf.optimise(local=True, show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:194: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_independent=True, ) lf.optimise(local=True, show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) lf.optimise(local=True, show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simple.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simple.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_tree from cogent3.evolve.models import get_model model = get_model("HKY85") aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") tree = make_tree(tip_names=aln.names) lf = model.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import sys from cogent3 import make_tree from cogent3.evolve.models import get_model [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: t = make_tree("(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("F81") lf = sm.make_likelihood_function(t) lf.set_constant_lengths() lf.set_motif_probs(dict(A=0.1, C=0.2, G=0.3, T=0.4)) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simulated = lf.simulate_alignment(sequence_length=1000) simulated [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_table, make_tree from cogent3.evolve.models import HKY85 from scipy.stats.distributions import chi2 from cogent3.recalculation.scope import ALL, EACH aln = load_aligned_seqs("data/long_testseqs.fasta") half = len(aln) // 2 aln1 = aln[:half] aln2 = aln[half:] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: loci_names = ["1st-half", "2nd-half"] loci = [aln1, aln2] tree = make_tree(tip_names=aln.names) mod = HKY85() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = mod.make_likelihood_function(tree, loci=loci_names, digits=2, space=3) lf.set_param_rule("length", is_independent=False) lf.set_param_rule("kappa", loci=ALL) lf.set_alignment(loci) lf.optimise(show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_lnL = lf.lnL all_nfp = lf.nfp lf.set_param_rule("kappa", loci=EACH) lf.optimise(show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: each_lnL = lf.lnL each_nfp = lf.nfp LR = 2 * (each_lnL - all_lnL) df = each_nfp - all_nfp [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:62: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: make_table( header=["LR", "df", "p"], rows=[[LR, df, chi2.sf(LR, df)]], digits=2, space=3, ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/templates/class.rst:3: ERROR: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} [docutils] WARNING: invalid signature for autoclass ('{{ name }}') [autodoc] WARNING: don't know which module to import for autodocumenting '{{ name }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) [autodoc] looking for now-outdated files... none found pickling environment... done checking consistency... 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[ 35%] app/app_cookbook/index-loaders writing output... [ 36%] app/app_cookbook/index-sample writing output... [ 36%] app/app_cookbook/index-writers writing output... [ 37%] app/app_cookbook/load-aligned writing output... [ 38%] app/app_cookbook/load-json writing output... [ 38%] app/app_cookbook/load-tabular writing output... [ 39%] app/app_cookbook/load-unaligned writing output... [ 39%] app/app_cookbook/sample-concat writing output... [ 40%] app/app_cookbook/sample-fixed-len writing output... [ 40%] app/app_cookbook/sample-min-len writing output... [ 41%] app/app_cookbook/sample-omit-bad writing output... [ 41%] app/app_cookbook/sample-omit-degen writing output... [ 42%] app/app_cookbook/sample-omit-duplicated writing output... [ 43%] app/app_cookbook/sample-omit-gap writing output... [ 43%] app/app_cookbook/sample-take-n-seqs writing output... [ 44%] app/app_cookbook/sample-take-pos writing output... [ 44%] app/app_cookbook/sample-take-seqs writing output... 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[ 65%] community writing output... [ 65%] cookbook/DNA_and_RNA_sequences writing output... [ 66%] cookbook/alignments writing output... [ 66%] cookbook/alphabet writing output... [ 67%] cookbook/annotation_db writing output... [ 68%] cookbook/building_alignments writing output... [ 68%] cookbook/building_phylogenies writing output... [ 69%] cookbook/calc_genetic_distance writing output... [ 69%] cookbook/evo_modelling writing output... [ 70%] cookbook/features writing output... [ 70%] cookbook/genetic_code writing output... [ 71%] cookbook/index writing output... [ 72%] cookbook/loading_sequences writing output... [ 72%] cookbook/loading_tabular writing output... [ 73%] cookbook/manipulating_biological_data writing output... [ 73%] cookbook/moltypes writing output... [ 74%] cookbook/protein_sequences writing output... [ 74%] cookbook/simple_trees writing output... [ 75%] cookbook/tables writing output... [ 76%] cookbook/union_dict writing output... 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[ 98%] index writing output... [ 98%] install writing output... [ 99%] licenses writing output... [ 99%] pycogent writing output... [100%] templates/class generating indices... genindex done copying linked files... copying notebooks ... writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 1169 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. make[2]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc' # remove superfluous files and dirs find doc/_build -name "*.doctree*" -delete rm -f doc/_build/html/_sources/COGENT_LICENSE.txt rm -f doc/_build/html/_static/jquery.js rm -f doc/_build/html/_static/underscore.js rm -rf doc/_build/html/_images/math/ make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: cp -r /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/tests/data /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build I: pybuild base:311: cd /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build; python3.13 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip' ============================= test session starts ============================== platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 rootdir: /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build configfile: pyproject.toml plugins: xdist-3.8.0, typeguard-4.4.4, cov-5.0.0, anyio-4.8.0 collected 11030 items / 4 deselected / 11026 selected tests/test_align/test_align.py ...............................X... 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[100%] =================================== FAILURES =================================== ____________________ TableTests.test_cast_str_to_numerical _____________________ self = def test_cast_str_to_numerical(self): """correctly converts a series of strings to numeric values""" d = arange(4, step=0.1) r = cast_str_to_numeric(d) assert_equal(d, r) with numpy.testing.suppress_warnings() as sup: # we know that converting to real loses imaginary > sup.filter(numpy.ComplexWarning) ^^^^^^^^^^^^^^^^^^^^ /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/tests/test_util/test_table.py:1769: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ attr = 'ComplexWarning' def __getattr__(attr): # Warn for expired attributes import warnings if attr == "linalg": import numpy.linalg as linalg return linalg elif attr == "fft": import numpy.fft as fft return fft elif attr == "dtypes": import numpy.dtypes as dtypes return dtypes elif attr == "random": import numpy.random as random return random elif attr == "polynomial": import numpy.polynomial as polynomial return polynomial elif attr == "ma": import numpy.ma as ma return ma elif attr == "ctypeslib": import numpy.ctypeslib as ctypeslib return ctypeslib elif attr == "exceptions": import numpy.exceptions as exceptions return exceptions elif attr == "testing": import numpy.testing as testing return testing elif attr == "matlib": import numpy.matlib as matlib return matlib elif attr == "f2py": import numpy.f2py as f2py return f2py elif attr == "typing": import numpy.typing as typing return typing elif attr == "rec": import numpy.rec as rec return rec elif attr == "char": import numpy.char as char return char elif attr == "array_api": raise AttributeError("`numpy.array_api` is not available from " "numpy 2.0 onwards", name=None) elif attr == "core": import numpy.core as core return core elif attr == "strings": import numpy.strings as strings return strings elif attr == "distutils": if 'distutils' in __numpy_submodules__: import numpy.distutils as distutils return distutils else: raise AttributeError("`numpy.distutils` is not available from " "Python 3.12 onwards", name=None) if attr in __future_scalars__: # And future warnings for those that will change, but also give # the AttributeError warnings.warn( f"In the future `np.{attr}` will be defined as the " "corresponding NumPy scalar.", FutureWarning, stacklevel=2) if attr in __former_attrs__: raise AttributeError(__former_attrs__[attr], name=None) if attr in __expired_attributes__: raise AttributeError( f"`np.{attr}` was removed in the NumPy 2.0 release. " f"{__expired_attributes__[attr]}", name=None ) if attr == "chararray": warnings.warn( "`np.chararray` is deprecated and will be removed from " "the main namespace in the future. Use an array with a string " "or bytes dtype instead.", DeprecationWarning, stacklevel=2) import numpy.char as char return char.chararray > raise AttributeError("module {!r} has no attribute " "{!r}".format(__name__, attr)) E AttributeError: module 'numpy' has no attribute 'ComplexWarning' /usr/lib/python3/dist-packages/numpy/__init__.py:414: AttributeError =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1533 /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1533: PytestConfigWarning: No files were found in testpaths; consider removing or adjusting your testpaths configuration. Searching recursively from the current directory instead. self.args, self.args_source = self._decide_args( tests/test_align/test_align.py: 1360 warnings tests/test_app/test_align.py: 550 warnings tests/test_app/test_dist.py: 90 warnings /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/maths/markov.py:35: DeprecationWarning: numpy.core is deprecated and has been renamed to numpy._core. The numpy._core namespace contains private NumPy internals and its use is discouraged, as NumPy internals can change without warning in any release. In practice, most real-world usage of numpy.core is to access functionality in the public NumPy API. If that is the case, use the public NumPy API. If not, you are using NumPy internals. If you would still like to access an internal attribute, use numpy._core.multiarray. matrix = numpy.core.multiarray.dot(matrix, matrix) tests/test_app/test_evo.py: 27 warnings tests/test_app/test_result.py: 3 warnings /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/evolve/likelihood_function.py:1064: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments. To learn more, see the migration guide https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword child_mprobs = numpy.dot(mprobs, psub) tests/test_app/test_evo.py: 27 warnings /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/maths/matrix_exponential_integration.py:102: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments. To learn more, see the migration guide https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword result = -dot(dot(p0, iexpm(t)), diag(Q)) tests/test_evolve/test_distance.py: 16900 warnings /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/maths/markov.py:35: DeprecationWarning: numpy.core is deprecated and has been renamed to numpy._core. The numpy._core namespace contains private NumPy internals and its use is discouraged, as NumPy internals can change without warning in any release. In practice, most real-world usage of numpy.core is to access functionality in the public NumPy API. If that is the case, use the public NumPy API. If not, you are using NumPy internals. If you would still like to access an internal attribute, use numpy._core.multiarray. tests/test_evolve/test_likelihood_function.py: 32 warnings tests/test_evolve/test_newq.py: 5 warnings tests/test_evolve/test_ns_substitution_model.py: 6 warnings /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/evolve/likelihood_function.py:1064: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments. To learn more, see the migration guide https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword tests/test_evolve/test_likelihood_function.py: 12 warnings /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/maths/matrix_exponential_integration.py:102: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments. To learn more, see the migration guide https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword tests/test_maths/test_stats/test_test.py::StatTests::test_t_two_sample_switch /usr/lib/python3/dist-packages/numpy/_core/_methods.py:223: RuntimeWarning: Degrees of freedom <= 0 for slice tests/test_util/test_deserialise.py::test_convert_annotation_to_annotation_db tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deser_annotated_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/util/warning.py:226: DeprecationWarning: class Map is discontinued and will be removed in version 2024.6 reason='Replaced by IndelMap and FeatureMap' tests/test_util/test_dictarray.py::DictArrayTest::test_numpy_ops /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/tests/test_util/test_dictarray.py:145: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments. To learn more, see the migration guide https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword tests/test_util/test_dictarray.py::DictArrayTest::test_numpy_ops /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/tests/test_util/test_dictarray.py:146: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments. To learn more, see the migration guide https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_util/test_table.py::TableTests::test_cast_str_to_numerical = 1 failed, 11013 passed, 9 skipped, 4 deselected, 1 xfailed, 2 xpassed, 19022 warnings in 762.01s (0:12:42) = E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=1: cd /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build; python3.13 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip' dh_auto_test: error: pybuild --test -i python{version} -p 3.13 returned exit code 13 make: *** [debian/rules:20: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/553802 and its subdirectories Starting cleanup. All cleanup done. Sun Sep 14 23:49:35 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-a7c7Onj8, removing. /srv/reproducible-results/rbuild-debian/r-b-build.xWOmV7M4: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 14 23:49 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 14 23:24 b2 -rw-rw-r-- 1 jenkins jenkins 2634 Jul 5 2024 python-cogent_2024.5.7a1+dfsg-3.dsc -rw------- 1 jenkins jenkins 3828 Sep 14 23:24 rbuildlog.jCOIvDb /srv/reproducible-results/rbuild-debian/r-b-build.xWOmV7M4/b1: total 540 -rw-r--r-- 1 jenkins jenkins 552170 Sep 14 23:49 build.log /srv/reproducible-results/rbuild-debian/r-b-build.xWOmV7M4/b2: total 0 Sun Sep 14 23:49:35 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Sep 14 11:24:16 -12 2025 I: pbuilder-time-stamp: 1757892256 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-cogent_2024.5.7a1+dfsg-3.dsc] I: copying [./python-cogent_2024.5.7a1+dfsg.orig.tar.xz] I: copying [./python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-cogent_2024.5.7a1+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting python-cogent in python-cogent-2024.5.7a1+dfsg dpkg-source: info: unpacking python-cogent_2024.5.7a1+dfsg.orig.tar.xz dpkg-source: info: unpacking python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sphinx.patch dpkg-source: info: applying fix_interpreter.patch dpkg-source: info: applying remove-jupyter-sphinx.patch dpkg-source: info: applying ignore_tests_accessing_network.patch dpkg-source: info: applying skip-parallel-tests-on-single-cpu-systems.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/553802/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='904a55863bf44d45a2c870c23e3a581b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='553802' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.xWOmV7M4/pbuilderrc_EKw7 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xWOmV7M4/b1 --logfile b1/build.log python-cogent_2024.5.7a1+dfsg-3.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/553802/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: architecture-is-64-bit, architecture-is-little-endian, cython3, debhelper-compat (= 13), dh-sequence-python3, flit, libjs-requirejs, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-chardet, python3-isort, python3-jupyter-sphinx-theme, python3-jupyterlab-server, python3-matplotlib, python3-nbsphinx, python3-numba, python3-numpy, python3-numpydoc, python3-pandas, python3-plotly, python3-pydata-sphinx-theme, python3-pytest, python3-pytest-cov, python3-pytest-xdist, python3-scipy, python3-scitrack, python3-sphinx, python3-sphinx-bootstrap-theme, python3-sphinx-design, python3-sphinx-gallery, python3-sphinxcontrib.bibtex, python3-stevedore, python3-tinydb, python3-tqdm, python3-typing-extensions dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on flit; however: Package flit is not installed. pbuilder-satisfydepends-dummy depends on libjs-requirejs; however: Package libjs-requirejs is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-chardet; however: Package python3-chardet is not installed. pbuilder-satisfydepends-dummy depends on python3-isort; however: Package python3-isort is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyter-sphinx-theme; however: Package python3-jupyter-sphinx-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyterlab-server; however: Package python3-jupyterlab-server is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-nbsphinx; however: Package python3-nbsphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-numba; however: Package python3-numba is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-numpydoc; however: Package python3-numpydoc is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-plotly; however: Package python3-plotly is not installed. pbuilder-satisfydepends-dummy depends on python3-pydata-sphinx-theme; however: Package python3-pydata-sphinx-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-cov; however: Package python3-pytest-cov is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-scitrack; however: Package python3-scitrack is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-bootstrap-theme; however: Package python3-sphinx-bootstrap-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-design; however: Package python3-sphinx-design is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-gallery; however: Package python3-sphinx-gallery is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.bibtex; however: Package python3-sphinxcontrib.bibtex is not installed. pbuilder-satisfydepends-dummy depends on python3-stevedore; however: Package python3-stevedore is not installed. pbuilder-satisfydepends-dummy depends on python3-tinydb; however: Package python3-tinydb is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-typing-extensions; however: Package python3-typing-extensions is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} flit{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-glyphicons-halflings{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} jupyter-sphinx-theme-common{a} libabsl20240722{a} libaom3{a} libarchive-zip-perl{a} libargon2-1{a} libavif16{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdav1d7{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhwloc15{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-bootstrap{a} libjs-bootstrap5{a} libjs-bootswatch{a} libjs-jquery{a} libjs-jquery-hotkeys{a} libjs-jquery-isonscreen{a} libjs-jquery-metadata{a} libjs-jquery-tablesorter{a} libjs-jquery-throttle-debounce{a} libjs-requirejs{a} libjs-sphinxdoc{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm19{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libnorm1t64{a} libnuma1{a} libopenjp2-7{a} libp11-kit0{a} libpfm4{a} libpgm-5.3-0t64{a} libpipeline1{a} libpng16-16t64{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsodium23{a} libssh2-1t64{a} libsvtav1enc2{a} libtasn1-6{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2-16{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libyuv0{a} libz3-4{a} libzmq5{a} libzopfli1{a} llvm-19{a} llvm-19-linker-tools{a} llvm-19-runtime{a} m4{a} man-db{a} media-types{a} netbase{a} node-fortawesome-fontawesome-free{a} node-popper2{a} openssl{a} pandoc{a} pandoc-data{a} po-debconf{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python-matplotlib-data{a} python-tinycss2-common{a} python3{a} python3-accessible-pygments{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-anyio{a} python3-argon2{a} python3-argon2-cffi-bindings{a} python3-arrow{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-bleach{a} python3-brotli{a} python3-bs4{a} python3-build{a} python3-certifi{a} python3-cffi{a} python3-cffi-backend{a} python3-chardet{a} python3-charset-normalizer{a} python3-click{a} python3-contourpy{a} python3-coverage{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-execnet{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fqdn{a} python3-fs{a} python3-html5lib{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-installer{a} python3-isoduration{a} python3-isort{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-json-pointer{a} python3-json5{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-jupyter-client{a} python3-jupyter-core{a} python3-jupyter-events{a} python3-jupyter-server{a} python3-jupyter-server-terminals{a} python3-jupyter-sphinx-theme{a} python3-jupyterlab-pygments{a} python3-jupyterlab-server{a} python3-kiwisolver{a} python3-latexcodec{a} python3-linkify-it{a} python3-llvmlite{a} python3-lxml{a} python3-lz4{a} python3-markdown-it{a} python3-markupsafe{a} python3-matplotlib{a} python3-mdit-py-plugins{a} python3-mdurl{a} python3-minimal{a} python3-mistune{a} python3-more-itertools{a} python3-mpmath{a} python3-myst-parser{a} python3-nbclient{a} python3-nbconvert{a} python3-nbformat{a} python3-nbsphinx{a} python3-numba{a} python3-numpy{a} python3-numpy-dev{a} python3-numpydoc{a} python3-overrides{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pandocfilters{a} python3-pbr{a} python3-pil{a} python3-pil.imagetk{a} python3-pip{a} python3-pkg-resources{a} python3-platformdirs{a} python3-plotly{a} python3-pluggy{a} python3-ply{a} python3-prometheus-client{a} python3-psutil{a} python3-ptyprocess{a} python3-pybtex{a} python3-pybtex-docutils{a} python3-pycparser{a} python3-pydata-sphinx-theme{a} python3-pygments{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pytest{a} python3-pytest-cov{a} python3-pytest-xdist{a} python3-pythonjsonlogger{a} python3-pytz{a} python3-referencing{a} python3-requests{a} python3-rfc3339-validator{a} python3-rfc3986-validator{a} python3-rich{a} python3-roman{a} python3-roman-numerals{a} python3-rpds-py{a} python3-scipy{a} python3-scitrack{a} python3-send2trash{a} python3-setuptools{a} python3-sniffio{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-bootstrap-theme{a} python3-sphinx-design{a} python3-sphinx-gallery{a} python3-sphinxcontrib.bibtex{a} python3-stevedore{a} python3-sympy{a} python3-tenacity{a} python3-terminado{a} python3-tinycss2{a} python3-tinydb{a} python3-tk{a} python3-tomli-w{a} python3-tornado{a} python3-tqdm{a} python3-traitlets{a} python3-typeguard{a} python3-typeshed{a} python3-typing-extensions{a} python3-tz{a} python3-uc-micro{a} python3-ufolib2{a} python3-uritemplate{a} python3-urllib3{a} python3-webcolors{a} python3-webencodings{a} python3-websocket{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3-zmq{a} python3-zopfli{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} x11-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: binfmt-support curl isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libhwloc-plugins libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules llvm-19-dev lynx numba-doc optipng publicsuffix python3-bottleneck python3-cssselect python3-gi python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-rfc3987 python3-tables shared-mime-info systemd wget xdg-user-dirs 0 packages upgraded, 334 newly installed, 0 to remove and 0 not upgraded. Need to get 246 MB of archives. After unpacking 1194 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.2-1 [1493 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.6 [2336 B] Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get: 59 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 66 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-roman all 5.1-1 [11.0 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 python3-pip all 25.2+dfsg-1 [1386 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 84 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.3-1 [131 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.5.0-1 [116 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.5+dfsg-1 [72.4 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-tomli-w all 1.2.0-1 [9100 B] Get: 90 http://deb.debian.org/debian unstable/main amd64 flit all 3.12.0-3 [96.5 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [163 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.4-1 [190 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 node-popper2 all 2.11.2-8 [100.0 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libjs-bootstrap5 all 5.3.8+dfsg-1 [460 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libjs-bootswatch all 3.3.7+dfsg2-1.3 [133 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libjs-bootstrap all 3.4.1+dfsg-6 [173 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-bootstrap-theme all 0.8.1+ds-1 [160 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 jupyter-sphinx-theme-common all 0.0.6+ds1-14 [12.8 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libargon2-1 amd64 0~20190702+dfsg-5 [21.2 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1916.20250814-1 [172 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.3.0-1 [135 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 114 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.1-2 [161 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.55-2 [88.1 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.12.2-1 [164 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-hotkeys all 0.2.0-1 [12.6 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 143 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-metadata all 12-4 [6532 B] Get: 144 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [184 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libjs-requirejs all 2.3.7+ds+~2.1.37-1 [196 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.7-6 [25.9 MB] Get: 153 http://deb.debian.org/debian unstable/main amd64 liblua5.4-0 amd64 5.4.8-1 [146 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1+b2 [221 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libpfm4 amd64 4.13.0+git106-g3e4031b-1 [372 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1+b1 [162 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.7-1 [1068 B] Get: 164 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-7 [248 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libsodium23 amd64 1.0.18-1+b2 [165 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libtbbbind-2-5 amd64 2022.1.0-2 [14.5 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libtbbmalloc2 amd64 2022.1.0-2 [54.8 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libtbb12 amd64 2022.1.0-2 [101 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.43-0.2 [155 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libzmq5 amd64 4.3.5-1+b3 [283 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 llvm-19-runtime amd64 1:19.1.7-6 [550 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 llvm-19-linker-tools amd64 1:19.1.7-6 [1261 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 llvm-19 amd64 1:19.1.7-6 [16.3 MB] Get: 182 http://deb.debian.org/debian unstable/main amd64 node-fortawesome-fontawesome-free all 6.7.2+ds1-1 [1521 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 pandoc amd64 3.1.11.1+ds-3 [26.4 MB] Get: 185 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.2-4 [36.2 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 6.20250414 [11.8 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.10.1+dfsg1-5 [2737 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python-tinycss2-common all 1.4.0-2 [44.7 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-accessible-pygments all 0.0.5-2 [1306 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.7-1 [1048 B] Get: 196 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.7-1 [1068 B] Get: 199 http://deb.debian.org/debian unstable/main amd64 python3-sniffio all 1.3.1-1 [7120 B] Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-anyio all 4.8.0-3 [63.6 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 python3-cffi-backend amd64 2.0.0~b1-1 [94.4 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 python3-ply all 3.11-9 [62.9 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-pycparser all 2.22-2 [78.0 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-cffi all 2.0.0~b1-1 [90.3 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-argon2-cffi-bindings amd64 25.1.0-2 [15.2 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-argon2 amd64 25.1.0-2 [18.2 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-typeshed all 0.0~git20241223.ea91db2-4 [1531 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-arrow all 1.3.0-1.1 [64.7 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.17.0-1 [117 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-webencodings all 0.5.1-5 [11.1 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-html5lib all 1.2-2 [92.1 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 python3-bleach all 6.2.0-1 [51.2 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 python3-soupsieve all 2.7-2 [39.0 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-bs4 all 4.13.5-1 [114 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 python3-click all 8.2.0+0.really.8.1.8-1 [95.4 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-2 [215 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-coverage amd64 7.8.2+dfsg1-1 [182 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-2 [9616 B] Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-execnet all 2.1.1-1 [40.2 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-fastjsonschema all 2.21.1-1 [22.4 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-8 [95.2 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 6.0.1-1 [1434 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.4+dfsg-1 [25.4 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 unicode-data all 16.0.0-1 [9197 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.57.0-2 [1457 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-fqdn all 1.5.1-2 [7592 B] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 245 http://deb.debian.org/debian unstable/main amd64 python3-isoduration all 20.11.0+git20211126.ae0bd61-2 [12.3 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 python3-isort all 6.0.1-1 [72.3 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 253 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 python3-json-pointer all 2.4-3 [14.6 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 python3-json5 all 0.10.0-1 [25.9 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 python3-rpds-py amd64 0.21.0-2+b1 [257 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 python3-referencing all 0.36.2-1 [23.7 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 260 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema all 4.19.2-6 [71.4 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-core all 5.7.2-5 [35.3 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 python3-psutil amd64 7.0.0-2 [220 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 python3-tornado amd64 6.4.2-3 [349 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 python3-zmq amd64 27.1.0-1 [189 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-client all 8.6.3-3 [92.4 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 python3-pythonjsonlogger all 3.3.0-1 [16.0 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 python3-rfc3339-validator all 0.1.4-2 [4060 B] Get: 269 http://deb.debian.org/debian unstable/main amd64 python3-rfc3986-validator all 0.1.1-2 [4884 B] Get: 270 http://deb.debian.org/debian unstable/main amd64 python3-mdurl all 0.1.2-1 [9444 B] Get: 271 http://deb.debian.org/debian unstable/main amd64 python3-uc-micro all 1.0.3-1 [5744 B] Get: 272 http://deb.debian.org/debian unstable/main amd64 python3-linkify-it all 2.0.3-1 [18.7 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 python3-markdown-it all 3.0.0-3 [59.5 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 python3-rich all 13.9.4-1 [203 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 python3-uritemplate all 4.1.1-3 [10.6 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 python3-webcolors all 1.13-1 [15.3 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-2 [137 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-events all 0.12.0-2 [19.2 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 python3-ptyprocess all 0.7.0-6 [14.5 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 python3-terminado all 0.18.1-1 [17.3 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-server-terminals all 0.5.3-3 [14.0 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 python3-tinycss2 all 1.4.0-2 [25.0 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Get: 284 http://deb.debian.org/debian unstable/main amd64 python3-mistune all 3.1.4-1 [35.7 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 python3-nbclient all 0.8.0-3 [62.3 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 python3-pandocfilters all 1.5.1-1 [23.7 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 python3-nbconvert all 7.16.6-1 [160 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 python3-overrides all 7.7.0-2 [14.2 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 python3-prometheus-client all 0.21.1+ds1-1 [44.9 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 python3-send2trash all 1.8.3-1 [15.8 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 python3-websocket all 1.8.0-2 [45.5 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-server all 2.15.0-1 [215 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 python3-mdit-py-plugins all 0.5.0-1 [33.4 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.2.3-6 [619 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 python3-roman-numerals all 3.1.0-2 [8740 B] Get: 297 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 3.0.1-1 [63.5 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.2.3-6 [477 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 python3-myst-parser all 4.0.1-1 [78.8 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 python3-nbsphinx all 0.9.5+ds-1 [39.9 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-sphinx-theme all 0.0.6+ds1-14 [2992 B] Get: 302 http://deb.debian.org/debian unstable/main amd64 python3-jupyterlab-server all 2.25.2-1 [50.9 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 python3-latexcodec all 3.0.0-1 [17.5 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 python3-llvmlite amd64 0.44.0-1 [231 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.7-1 [108 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.5-1 [9604 B] Get: 309 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 11.3.0-1 [81.1 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-5 [23.8 MB] Get: 312 http://deb.debian.org/debian unstable/main amd64 python3-numba amd64 0.61.2+dfsg-1 [1773 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 python3-numpydoc all 1.9.0-1 [52.3 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 python3-pytz all 2025.2-3 [152 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4595 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-9 [3097 kB] Get: 317 http://deb.debian.org/debian unstable/main amd64 python3-pbr all 6.1.1-2 [57.1 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2025.2-3 [4280 B] Get: 319 http://deb.debian.org/debian unstable/main amd64 python3-tenacity all 8.4.2+really8.4.1-2 [46.0 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 python3-plotly all 5.20.0+dfsg-1 [2726 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 python3-pybtex all 0.25.1-1 [75.2 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 python3-pybtex-docutils all 1.0.3-1 [8224 B] Get: 324 http://deb.debian.org/debian unstable/main amd64 python3-pydata-sphinx-theme all 0.16.1+dfsg-3 [917 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.4.2-1 [266 kB] Get: 326 http://deb.debian.org/debian unstable/main amd64 python3-pytest-cov all 5.0.0-1 [26.8 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 python3-pytest-xdist all 3.8.0-1 [45.7 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 python3-scitrack all 2024.10.8-1 [9420 B] Get: 329 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-design all 0.6.1-1 [883 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-gallery all 0.17.1-1 [401 kB] Get: 331 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.bibtex all 2.6.5-2 [33.2 kB] Get: 332 http://deb.debian.org/debian unstable/main amd64 python3-stevedore all 5.4.1-2 [20.9 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 python3-tinydb all 4.8.2-1 [29.1 kB] Get: 334 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.67.1-5 [90.8 kB] Fetched 246 MB in 9s (26.8 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20251 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21266 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.4+ds-1.2_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1.2) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../002-libblas3_3.12.1-7_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-7) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../003-libgfortran5_15.2.0-4_amd64.deb ... Unpacking libgfortran5:amd64 (15.2.0-4) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../004-liblapack3_3.12.1-7_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-7) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../005-python3-numpy_1%3a2.2.4+ds-1.2_amd64.deb ... Unpacking python3-numpy (1:2.2.4+ds-1.2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../006-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package openssl. 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Setting up x11-common (1:7.7+25) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libgcrypt20:amd64 (1.11.2-2) ... Setting up libqhull-r8.0:amd64 (2020.2-7) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up node-fortawesome-fontawesome-free (6.7.2+ds1-1) ... Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Setting up libjs-requirejs (2.3.7+ds+~2.1.37-1) ... Setting up libabsl20240722:amd64 (20240722.0-4) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up python-babel-localedata (2.17.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Sep 14 23:28:17 UTC 2025. Universal Time is now: Sun Sep 14 23:28:17 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (16.0.0-1) ... Setting up libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1+b1) ... Setting up autotools-dev (20240727.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpfm4:amd64 (4.13.0+git106-g3e4031b-1) ... Setting up libexpat1-dev:amd64 (2.7.1-2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libzopfli1 (1.0.3-3) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libsvtav1enc2:amd64 (2.3.0+dfsg-1) ... Setting up libjs-bootswatch (3.3.7+dfsg2-1.3) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (4.4.0-3) ... 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Setting up python3-jupyter-sphinx-theme (0.0.6+ds1-14) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-cogent_2024.5.7a1+dfsg-3_source.changes dpkg-buildpackage: info: source package python-cogent dpkg-buildpackage: info: source version 2024.5.7a1+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' #These files are rebuilt on-the-fly for f in `find -name '*.c'` ; do \ head -n 1 "$f" | grep -q '^/\* Generated by Cython' && rm "$f" ; \ done rm -rf build build-stamp rm -rf doc/_build dh_clean make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.13 with "build" module I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3 * Building wheel... Successfully built cogent3-2024.5.7a1-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' set -x; cd doc; PYTHONPATH=/build/reproducible-path/python-cogent-2024.5.7a1+dfsg http_proxy='127.0.0.1:9' /usr/bin/make html + cd doc + PYTHONPATH=/build/reproducible-path/python-cogent-2024.5.7a1+dfsg http_proxy=127.0.0.1:9 /usr/bin/make html make[2]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v8.2.3 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist WARNING: The config value `today' has type `date'; expected `str'. checking bibtex cache... out of date parsing bibtex file /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cogent3.bib... parsed 21 entries Writing evaluated template result to /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/_build/html/_static/nbsphinx-code-cells.css building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 176 source files that are out of date updating environment: [new config] 176 added, 0 changed, 0 removed reading sources... 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[ 31%] api/tree/classes/cogent3.core.tree.PhyloNode reading sources... [ 31%] api/tree/tree reading sources... [ 32%] api/util/deserialise/classes/cogent3.util.deserialise.register_deserialiser reading sources... [ 32%] api/util/deserialise/deserialise_object reading sources... [ 33%] app/app_cookbook/align-codon reading sources... [ 34%] app/app_cookbook/align-nucleotide reading sources... [ 34%] app/app_cookbook/align-protein reading sources... [ 35%] app/app_cookbook/index-align reading sources... [ 35%] app/app_cookbook/index-loaders reading sources... [ 36%] app/app_cookbook/index-sample reading sources... [ 36%] app/app_cookbook/index-writers reading sources... [ 37%] app/app_cookbook/load-aligned reading sources... [ 38%] app/app_cookbook/load-json reading sources... [ 38%] app/app_cookbook/load-tabular reading sources... [ 39%] app/app_cookbook/load-unaligned reading sources... [ 39%] app/app_cookbook/sample-concat reading sources... [ 40%] app/app_cookbook/sample-fixed-len reading sources... [ 40%] app/app_cookbook/sample-min-len reading sources... [ 41%] app/app_cookbook/sample-omit-bad reading sources... [ 41%] app/app_cookbook/sample-omit-degen reading sources... [ 42%] app/app_cookbook/sample-omit-duplicated reading sources... [ 43%] app/app_cookbook/sample-omit-gap reading sources... [ 43%] app/app_cookbook/sample-take-n-seqs reading sources... [ 44%] app/app_cookbook/sample-take-pos reading sources... [ 44%] app/app_cookbook/sample-take-seqs reading sources... [ 45%] app/app_cookbook/sample-trim-stops reading sources... [ 45%] app/app_cookbook/write-db reading sources... [ 46%] app/app_cookbook/write-json reading sources... [ 47%] app/app_cookbook/write-seqs reading sources... [ 47%] app/app_cookbook/write-tabular reading sources... [ 48%] app/app_overview/app-get reading sources... [ 48%] app/app_overview/app-help reading sources... [ 49%] app/app_overview/app-overview reading sources... [ 49%] app/app_overview/available-apps reading sources... [ 50%] app/app_overview/dstore reading sources... [ 51%] app/app_overview/not-completed reading sources... [ 51%] app/app_tutorials/evo-ancestral-states reading sources... [ 52%] app/app_tutorials/evo-dt-nuc-model reading sources... [ 52%] app/app_tutorials/evo-extract-model-stats reading sources... [ 53%] app/app_tutorials/evo-hypothesis reading sources... [ 53%] app/app_tutorials/evo-model reading sources... [ 54%] app/app_tutorials/evo-model-timehet reading sources... [ 55%] app/app_tutorials/evo-model-with-tree reading sources... [ 55%] app/app_tutorials/evo-natsel_neutral reading sources... [ 56%] app/app_tutorials/evo-natsel_sitehet reading sources... [ 56%] app/app_tutorials/evo-natsel_timehet reading sources... [ 57%] app/app_tutorials/evo-natsel_zhang reading sources... [ 57%] app/app_tutorials/evo-nstat-codon-model reading sources... [ 58%] app/app_tutorials/evo-tr-codon-model reading sources... [ 59%] app/app_tutorials/evo-tr-nuc-model reading sources... [ 59%] app/app_tutorials/index-evo-hypothesis reading sources... [ 60%] app/app_tutorials/index-evo-model reading sources... [ 60%] app/app_tutorials/index-evo-natsel reading sources... [ 61%] app/index reading sources... [ 61%] app/index-app reading sources... [ 62%] app/index-cookbook reading sources... [ 62%] app/index-custom reading sources... [ 63%] app/index-help reading sources... [ 64%] app/index-tutorials reading sources... [ 64%] app/user_function reading sources... [ 65%] community reading sources... [ 65%] cookbook/DNA_and_RNA_sequences reading sources... [ 66%] cookbook/alignments reading sources... [ 66%] cookbook/alphabet reading sources... [ 67%] cookbook/annotation_db reading sources... [ 68%] cookbook/building_alignments reading sources... [ 68%] cookbook/building_phylogenies reading sources... [ 69%] cookbook/calc_genetic_distance reading sources... [ 69%] cookbook/evo_modelling reading sources... [ 70%] cookbook/features reading sources... [ 70%] cookbook/genetic_code reading sources... [ 71%] cookbook/index reading sources... [ 72%] cookbook/loading_sequences reading sources... [ 72%] cookbook/loading_tabular reading sources... [ 73%] cookbook/manipulating_biological_data reading sources... [ 73%] cookbook/moltypes reading sources... [ 74%] cookbook/protein_sequences reading sources... [ 74%] cookbook/simple_trees reading sources... [ 75%] cookbook/tables reading sources... [ 76%] cookbook/union_dict reading sources... [ 76%] cookbook/useful_utilities reading sources... [ 77%] cookbook/what_codes reading sources... [ 77%] data_file_links reading sources... [ 78%] draw/aln/plot_aln-coevolution reading sources... [ 78%] draw/aln/plot_aln-dotplot-1 reading sources... [ 79%] draw/aln/plot_aln-dotplot-2 reading sources... [ 80%] draw/aln/plot_aln-dotplot-3 reading sources... [ 80%] draw/aln/plot_aln-gaps-per-seq reading sources... [ 81%] draw/aln/plot_aln-info-plot reading sources... [ 81%] draw/aln/plot_aln-seqlogo reading sources... [ 82%] draw/aln/plot_seq-features reading sources... [ 82%] draw/index reading sources... [ 83%] draw/tree/plot_tree-angular reading sources... [ 84%] draw/tree/plot_tree-circular reading sources... [ 84%] draw/tree/plot_tree-radial reading sources... [ 85%] draw/tree/plot_tree-square reading sources... [ 85%] draw/tree/plot_tree-support reading sources... [ 86%] examples/align_codons_to_protein reading sources... [ 86%] examples/calculate_UPGMA_cluster reading sources... [ 87%] examples/calculate_neigbourjoining_tree reading sources... [ 88%] examples/calculate_pairwise_distances reading sources... [ 88%] examples/codon_models reading sources... [ 89%] examples/coevolution reading sources... [ 89%] examples/empirical_protein_models reading sources... [ 90%] examples/hmm_par_heterogeneity reading sources... [ 90%] examples/index reading sources... [ 91%] examples/manipulating_tree_nodes reading sources... [ 91%] examples/neutral_test reading sources... [ 92%] examples/parallel reading sources... [ 93%] examples/parametric_bootstrap reading sources... [ 93%] examples/period_estimation reading sources... [ 94%] examples/phylo_by_ls reading sources... [ 94%] examples/rate_heterogeneity reading sources... [ 95%] examples/relative_rate reading sources... [ 95%] examples/scope_model_params_on_trees reading sources... [ 96%] examples/simple reading sources... [ 97%] examples/simulate_alignment reading sources... [ 97%] examples/testing_multi_loci reading sources... [ 98%] index reading sources... [ 98%] install reading sources... [ 99%] licenses reading sources... [ 99%] pycogent reading sources... [100%] templates/class WARNING: autodoc: failed to import function '__init__.available_apps' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.available_codes' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.available_models' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.available_moltypes' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.get_code' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.get_model' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.get_moltype' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_aligned_seqs' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_annotations' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_delimited' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_seq' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_table' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_tree' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.load_unaligned_seqs' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.make_aligned_seqs' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.make_seq' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.make_table' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.make_tree' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.make_unaligned_seqs' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.open_' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function '__init__.open_data_store' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alignment/alignment.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst SequenceCollection Alignment ArrayAlignment [docutils] WARNING: autodoc: failed to import class 'core.alignment.Alignment' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.alignment.ArrayAlignment' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.alignment.SequenceCollection' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alphabet/alphabet.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Alphabet [docutils] WARNING: autodoc: failed to import class 'core.alphabet.Alphabet' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation/annotation.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Feature [docutils] WARNING: autodoc: failed to import class 'core.annotation.Feature' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation_db/annotation_db.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst BasicAnnotationDb GffAnnotationDb GenbankAnnotationDb [docutils] WARNING: autodoc: failed to import class 'core.annotation_db.BasicAnnotationDb' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.annotation_db.GenbankAnnotationDb' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.annotation_db.GffAnnotationDb' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function 'app.composable.define_app' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'app.data_store.DataMember' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'app.data_store.DataStoreDirectory' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'app.data_store.ReadOnlyDataStoreZipped' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function 'app.io.register_datastore_reader' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'app.sqlite_data_store.DataStoreSqlite' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.genetic_code.GeneticCode' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/genetic_code/genetic_code.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst GeneticCode [docutils] WARNING: autodoc: failed to import class 'core.moltype.MolType' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/moltype/moltype.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst MolType [docutils] WARNING: autodoc: failed to import class 'core.sequence.DnaSequence' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.sequence.ProteinSequence' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'core.sequence.RnaSequence' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/sequence/sequence.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst DnaSequence RnaSequence ProteinSequence [docutils] WARNING: autodoc: failed to import class 'parse.table.FilteringParser' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'util.table.Columns' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import class 'util.table.Table' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/table.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Table Columns [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/table.rst:15: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst FilteringParser [docutils] WARNING: autodoc: failed to import class 'core.tree.PhyloNode' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/tree/tree.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst PhyloNode [docutils] WARNING: autodoc: failed to import class 'util.deserialise.register_deserialiser' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] WARNING: autodoc: failed to import function 'util.deserialise.deserialise_object' from module 'cogent3'; the following exception was raised: ['Traceback (most recent call last):\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 269, in import_object\n module = import_module(modname, try_reload=True)\n', ' File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 172, in import_module\n raise ModuleNotFoundError(msg, name=modname) # NoQA: TRY301\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', "ModuleNotFoundError: No module named 'cogent3'\n"] [autodoc.import_object] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") seqs = loader("data/SCA1-cds.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app codon_aligner = get_app("progressive_align", "codon") aligned = codon_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: nt_aligner = get_app("progressive_align", "codon", distance="paralinear") aligned = nt_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" codon_aligner = get_app("progressive_align", "codon", guide_tree=tree) aligned = codon_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: codon_aligner = get_app("progressive_align", "codon", guide_tree=tree, indel_rate=0.001, indel_length=0.01 ) aligned = codon_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: codon_aligner = get_app("progressive_align", "CNFHKY", guide_tree=tree, param_vals=dict(omega=0.1, kappa=3) ) aligned = codon_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligned.info [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") seqs = loader("data/SCA1-cds.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app nt_aligner = get_app("progressive_align", "nucleotide") aligned = nt_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: nt_aligner = get_app("progressive_align", "nucleotide", distance="TN93") aligned = nt_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = get_app("progressive_align", "nucleotide", guide_tree=tree) aligned = nt_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = get_app("progressive_align", "F81", guide_tree=tree) aligned = nt_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligned.info [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") to_aa = get_app("translate_seqs") process = loader + to_aa seqs = process("data/SCA1-cds.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app aa_aligner = get_app("progressive_align", "protein") aligned = aa_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aa_aligner = get_app("progressive_align", "protein", distance="paralinear") aligned = aa_aligner(seqs) aligned [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligned.info [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/index-sample.rst:6: WARNING: toctree contains reference to nonexisting document 'app/app_cookbook/sample-trim-stop' [toc.not_readable] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/index-writers.rst:5: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/brca1-bats.fasta") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_aligned_app = get_app("load_aligned", moltype="protein", format="phylip") aln = load_aligned_app("data/abglobin_aa.phylip") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:59: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") process = loader + cpos3 + writer [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process.apply_to(fasta_seq_dstore) print(result[0].read()[:50]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-json.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-json.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import get_app, open_data_store from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name # create lf object to write load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/primate_brca1.fasta") gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree") lf = gn_model_app(aln).lf out_dstore = open_data_store(path_to_dir, mode="w", suffix="json") # write with the same identifier as the write_json example write_json_app = get_app("write_json", data_store=out_dstore) data_member = write_json_app(lf, identifier="gn_params.json") path_to_dstore = data_member.data_store.source [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-json.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_json_app = get_app("load_json") lf = load_json_app(f"{path_to_dstore}/gn_params.json") lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_tsv_app = get_app("load_tabular", sep="\t") tsv_data = load_tsv_app("data/stats.tsv") tsv_data [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import NamedTemporaryFile tmpdir = NamedTemporaryFile(dir=".") path_to_csv_file = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app tsv_data.write(path_to_csv_file, sep=",") load_csv_app = get_app("load_tabular", sep=",") csv_data = load_csv_app(path_to_csv_file) csv_data [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="protein") seqs = load_unaligned_app("data/inseqs_protein.fasta") seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: out_dstore = open_data_store(path_to_dir, suffix="tsv", mode="w") load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="dna") jdist = get_app("jaccard_dist") writer = get_app("write_tabular", out_dstore, format="tsv") process = load_unaligned_app + jdist + writer [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process.apply_to(fasta_seq_dstore) print(result[1].read()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:6: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app concat_alns_app = get_app("concat", moltype="dna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln1 = make_aligned_seqs({"s1": "AAA", "s2": "CAA", "s3": "AAA"}, moltype="dna") aln2 = make_aligned_seqs({"s1": "GCG", "s2": "GGG", "s3": "GGT"}, moltype="dna") aln1 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = concat_alns_app([aln1, aln2]) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs, get_app concat_missing = get_app("concat", moltype="dna", intersect=False) aln3 = make_aligned_seqs({"s4": "GCG", "s5": "GGG"}, moltype="dna") result = concat_missing([aln1, aln3]) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app concat_delim = get_app("concat", join_seq="N", moltype="dna") result = concat_delim([aln1, aln2]) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:6: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="protein", format="phylip") aln = loader("data/abglobin_aa.phylip") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app first_20 = get_app("fixed_length", length=20) first_20(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app skip_10_take_20 = get_app("fixed_length", length=20, start=10) skip_10_take_20(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app random_20 = get_app("fixed_length", length=20, random=True) random_20(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", moltype="dna", format="fasta") aln = loader("data/SCA1-cds.fasta") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app over_240s = get_app("min_length", 240) aln_fltrd = over_240s(aln) aln_fltrd [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store dstore = open_data_store("data", suffix="fasta", limit=2) reader = get_app("load_aligned", format="fasta", moltype="dna") min_length = get_app("min_length", 300) out_dstore = open_data_store(path_to_dir, mode="w", suffix="fasta") writer = get_app("write_seqs", out_dstore) process = reader + min_length + writer result = process.apply_to(dstore) result.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-bad.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( { "s1": "---ACC---TT-", "s2": "---ACC---TT-", "s3": "---ACC---TT-", "s4": "--AACCG-GTT-", "s5": "--AACCGGGTTT", "s6": "AGAACCGGGTT-", "s7": "------------", }, moltype="dna", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-bad.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_frac_05 = get_app("omit_bad_seqs", gap_fraction=0.5) omit_frac_05(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-bad.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_quant_08 = get_app("omit_bad_seqs", quantile=0.8) omit_quant_08(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs({"s1": "ACGA-GACG", "s2": "GATGATGYT"}, moltype="dna") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_degens = get_app("omit_degenerates", moltype="dna") result = omit_degens(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_degens_keep_gaps = get_app("omit_degenerates", moltype="dna", gap_is_degen=False) result = omit_degens_keep_gaps(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_degenerates_app = get_app("omit_degenerates", moltype="dna", motif_length=2) result = omit_degenerates_app(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs data = { "a": "ACGT", "b": "ACG-", # identical to 'a' except has a gap "c": "ACGG", # duplicate "d": "ACGG", # duplicate "e": "AGTC", # unique } aln = make_aligned_seqs(data, moltype="dna") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_shorter_duplicate = get_app("omit_duplicated", moltype="dna", choose="longest") omit_shorter_duplicate(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_all_duplicates = get_app("omit_duplicated", moltype="dna", choose=None) omit_all_duplicates(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( { "s1": "ATCG", "s2": "ATYG", # matches s1 with ambiguity "s3": "GGTA", }, moltype="dna", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app app_dna = get_app("omit_duplicated", mask_degen=True, choose="longest", moltype="dna") app_dna(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:9: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs({"s1": "ACGA-GA-CG", "s2": "GATGATG-AT"}, moltype="dna") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_gap_pos_app = get_app("omit_gap_pos", moltype="dna") result = omit_gap_pos_app(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: omit_gap_pos_app = get_app("omit_gap_pos", allowed_frac=0.49, moltype="dna") result = omit_gap_pos_app(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: omit_gap_pos_app = get_app( "omit_gap_pos", allowed_frac=0, motif_length=3, moltype="dna" ) result = omit_gap_pos_app(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="dna") aln = loader("data/primate_brca1.fasta") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app first_3 = get_app("take_n_seqs", number=3) first_3(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app random_n = get_app("take_n_seqs", random=True, number=3, seed=1) random_n(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="dna") aln1 = loader("data/primate_brca1.fasta") aln2 = loader("data/brca1.fasta") aln1.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:64: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: fixed_choice = get_app("take_n_seqs", number=2, random=True, fixed_choice=True) result1 = fixed_choice(aln1).names result2 = fixed_choice(aln2).names result1 == result2 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs({"s1": "ACGACGACG", "s2": "GATGATGAT"}, moltype="dna") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app take_pos3 = get_app("take_codon_positions", 3, moltype="dna") result = take_pos3(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app take_pos12 = get_app("take_codon_positions", 1, 2, moltype="dna") result = take_pos12(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, make_aligned_seqs aln_ff = make_aligned_seqs({"s1": "GCAAGCGTTTAT", "s2": "GCTTTTGTCAAT"}) take_fourfold = get_app("take_codon_positions", fourfold_degenerate=True, moltype="dna") result = take_fourfold(aln_ff) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") process = loader + cpos3 + writer [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: out_dstore = process.apply_to(fasta_seq_dstore) out_dstore.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="dna") aln = loader("data/primate_brca1.fasta") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app greater_ape_selector = get_app("take_named_seqs", "Human", "Chimpanzee", "Gorilla") ape_aln = greater_ape_selector(aln) ape_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") select_seqs = get_app("take_named_seqs", "Human", "Rhesus", "Galago") process = loader + select_seqs hrg_aln = process("data/primate_brca1.fasta") hrg_aln.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app no_galagos = get_app("take_named_seqs", "Galago", negate=True) no_galago_aln = no_galagos(hrg_aln) no_galago_aln.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-trim-stops.rst:6: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ACGTAA---", "seq2": "ACGACA---", "seq3": "ACGCAATGA"}, moltype="dna", ) no_stops = get_app("trim_stop_codons", gc=1) no_stops(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store dstore = open_data_store("data", suffix="fasta", limit=2) reader = get_app("load_aligned", format="fasta", moltype="dna") min_length = get_app("min_length", 300) out_dstore = open_data_store(f"{path_to_dir}.sqlitedb", mode="w") writer = get_app("write_db", out_dstore) process = reader + min_length + writer result = process.apply_to(dstore) result.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: out_dstore is result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app # Load the alignment load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/primate_brca1.fasta") # Fit the GN model gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree") model_result = gn_model_app(aln) model_result.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store # Initialise the write_json app with a data store out_dstore = open_data_store(path_to_dir, mode="w", suffix="json") write_json_app = get_app("write_json", data_store=out_dstore) write_json_app(model_result.lf, identifier="gn_params.json") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/primate_brca1.fasta") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store seq_dstore = open_data_store(path_to_dir, suffix="phylip", mode="w") write_seqs_app = get_app("write_seqs", data_store=seq_dstore, format="phylip") result = write_seqs_app(aln) result.read()[:50] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_unaligned", format="fasta", moltype="dna") keep_translatable = get_app("select_translatable") translate = get_app("translate_seqs") writer = get_app("write_seqs", out_dstore, format="fasta") process = loader + keep_translatable + translate + writer [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process.apply_to(fasta_seq_dstore) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result.summary_not_completed [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app # load alignment load_aligned_app = get_app("load_aligned", moltype="dna") aln = load_aligned_app("data/primate_brca1.fasta") # fit GN model gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree") model_result = gn_model_app(aln) # tabulate the model result tabulator = get_app("tabulate_stats") model_result_tab = tabulator(model_result) motif_params = model_result_tab["motif params"] print(type(motif_params)) motif_params [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, mode="w", suffix="csv") write_tabular_app = get_app("write_tabular", data_store=out_dstore, format="csv") write_tabular_app(motif_params, identifier="gn_model_results.csv") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, mode="w", suffix="tsv") write_tabular_app = get_app("write_tabular", data_store=out_dstore, format="tsv") write_tabular_app(motif_params, identifier="gn_model_results.tsv") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store loader = get_app("load_unaligned", moltype="dna") jdist = get_app("jaccard_dist") out_dstore = open_data_store(path_to_dir, mode="w", suffix="tsv") writer = get_app("write_tabular", data_store=out_dstore, format="tsv") process = loader + jdist + writer in_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) result = process.apply_to(in_dstore) result.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-get.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app just_nucs = get_app("omit_degenerates", moltype="dna") just_nucs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-help.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import app_help app_help("omit_degenerates") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:95: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = loader("data/primate_brca1.fasta") just3rd = cpos3(data) m = writer(just3rd) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:138: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: process = loader + cpos3 + writer m = process("data/primate_brca1.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:148: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data", suffix="fasta", mode="r") result = process.apply_to(dstore) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:163: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_logs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:185: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result = process.apply_to(dstore, show_progress=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:205: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import shutil shutil.rmtree(path_to_dir, ignore_errors=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/available-apps.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_apps available_apps() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/available-apps.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: available_apps(name_filter="load") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import open_data_store dstore = open_data_store("data/raw.zip", suffix="fa", mode="r") print(dstore) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m = dstore[0] m [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:102: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for m in dstore[:5]: print(m) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m.read()[:20] # truncating [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data/demo-locked.sqlitedb") dstore.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.unlock(force=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.summary_logs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.logs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(dstore.logs[0].read()[:225]) # truncated for clarity [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import open_data_store in_dstore = open_data_store("data/raw.zip", suffix="fa") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore = open_data_store("translated.sqlitedb", mode="w") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:189: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app load = get_app("load_unaligned", moltype="dna") translate = get_app("translate_seqs") write = get_app("write_db", data_store=out_dstore) app = load + translate + write app [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore = app.apply_to(in_dstore) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:216: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.validate() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:222: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:232: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: len(out_dstore.not_completed) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:238: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.not_completed[:2] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:242: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib fn = pathlib.Path("translated.sqlitedb") fn.unlink() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:11: WARNING: download file not readable: /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/data/raw.zip [download.not_readable] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app reader = get_app("load_aligned", format="fasta") select_seqs = get_app("take_named_seqs", "Mouse", "Human") aln = reader("data/primate_brca1.fasta") result = select_seqs(aln) assert result == False result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.source [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.origin [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.message [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = reader("primate_brca1.fasta") result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: app = reader + select_seqs result = app("data/primate_brca1.fasta") result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = app("primate_brca1.fasta") result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta") aln = loader("data/primate_brca1.fasta") gn = get_app("model", "GN", tree="data/primate_brca1.tree") result = gn(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reconstuctor = get_app("ancestral_states") states_result = reconstuctor(result) states_result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: states_result["edge.0"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.tree.get_figure(contemporaneous=True).show(width=500, height=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = get_app("model", "BH", tree="data/primate_brca1.tree") result = model(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = result.tree fig = tree.get_figure() fig.scale_bar = "top right" fig.show(width=500, height=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = get_app("tabulate_stats") stats = tabulator(result) stats [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stats["edge motif motif2 params"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = get_app("model", "GN", tree="data/primate_brca1.tree") result = model(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = get_app("tabulate_stats") tabulated = tabulator(result) tabulated [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["edge params"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["global params"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["motif params"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") tree = "data/primate_brca1.tree" null = get_app("model", "GTR", tree=tree, optimise_motif_probs=True) alt = get_app("model", "GN", tree=tree, optimise_motif_probs=True) hyp = get_app("hypothesis", null, alt) result = hyp(aln) type(result) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.LR, result.df, result.pvalue [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") select_seqs = get_app("take_named_seqs", "Human", "Rhesus", "Galago") process = loader + select_seqs aln = process("data/primate_brca1.fasta") aln.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN") gn [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) type(fitted) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lnL, fitted.nfp [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.source [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.tree, fitted.alignment [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.total_length(length_as="paralinear") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN", split_codons=True) fitted = gn(aln) fitted [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted[3] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3 import get_app tree = load_tree("data/primate_brca1.tree") fig = tree.get_figure(contemporaneous=True) fig.style_edges( "Human", tip2="Orangutan", outgroup="Galago", line=dict(color="red") ) fig.show(width=500, height=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: time_het = get_app("model", "GN", tree=tree, time_het=[dict(tip_names=["Human", "Orangutan"], outgroup_name="Galago")], ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: loader = get_app("load_aligned", format="fasta") aln = loader("data/primate_brca1.fasta") result = time_het(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") aln.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3 import get_app tree = load_tree("data/primate_brca1.tree") gn = get_app("model", "GN", tree=tree) gn [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN", tree="data/primate_brca1.tree") gn [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) fitted [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") omega_eq_1 = get_app("natsel_neutral", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = omega_eq_1(aln) type(result) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") sites_differ = get_app("natsel_sitehet", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = sites_differ(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = result.alt.lf.get_bin_probs() bprobs[:, :20] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_timehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") hc_differ = get_app("natsel_timehet", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False, tip1="Human", tip2="Chimpanzee", ) result = hc_differ(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_timehet.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_zhang.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_zhang.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from IPython.core.display import HTML from numpy import array from cogent3 import make_table header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges'] data = {'Site Class': array(['0', '1', '2a', '2b'], dtype=' 1', '0 < omega0 < 1'], dtype=' AlignedSeqsType: return val[:index] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: first4 = up_to(index=4) first4 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=dict(a="GCAAGCGTTTAT", b="GCTTTTGTCAAT"), array_align=False, moltype="dna" ) result = first4(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from typing import Union from cogent3.app.composable import define_app from cogent3.app.typing import SeqsCollectionType, SerialisableType T = Union[SeqsCollectionType, SerialisableType] @define_app def rename_seqs(seqs: SeqsCollectionType) -> T: """upper case names""" return seqs.rename_seqs(lambda x: x.upper()) renamer = rename_seqs() result = renamer(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.composable import define_app from cogent3.app.typing import AlignedSeqsType, PairwiseDistanceType @define_app def get_dists(aln: AlignedSeqsType, calc="hamming") -> PairwiseDistanceType: return aln.distance_matrix(calc=calc, show_progress=False) percent_dist = get_dists(calc="pdist") result = percent_dist(aln) result [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT") my_seq.moltype.label [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq = make_seq("AGTACACTGGT", moltype="bytes") my_seq.moltype.label [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") rnaseq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", "my_gene", moltype="dna") my_seq type(my_seq) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq.name = "my_gene" my_seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq.complement() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq.rc() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("GCTTGGGAAAGTCAAATGGAA", name="s1", moltype="dna") pep = my_seq.get_translation() type(pep) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:144: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ACGTACGTACGTACGT", moltype="dna") rnaseq = my_seq.to_rna() rnaseq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:155: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") dnaseq = rnaseq.to_dna() dnaseq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:166: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq a = make_seq("AGTACACTGGT", moltype="dna") a.can_pair(a.complement()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: a.can_pair(a.rc()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") extra_seq = make_seq("CTGAC", moltype="dna") long_seq = my_seq + extra_seq long_seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:192: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq[1:6] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq("ATGATGATGATG", moltype="dna") pos3 = seq[2::3] assert str(pos3) == "GGGG" [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq("ATGATGATGATG", moltype="dna") indices = [(i, i + 2) for i in range(len(seq))[::3]] pos12 = seq.add_feature(biotype="pos12", name="pos12", spans=indices) pos12 = pos12.get_slice() assert str(pos12) == "ATATATAT" [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:227: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rnaseq.shuffle() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:234: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq s = make_seq("--AUUAUGCUAU-UAu--", moltype="rna") s.degap() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna") type(seqs) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = make_unaligned_seqs(dna, moltype="dna") type(seqs) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna", array_align=True) print(type(seqs)) seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/test.paml") seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_seqs = make_aligned_seqs( [("seq0", "ATG-AGT-AGG"), ("seq4", "ATGCC------")], moltype="dna" ) new_aln = aln.add_seqs(new_seqs) new_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:98: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, before_name="seq2") new_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:103: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, after_name="seq2") new_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:113: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) ref_aln = make_aligned_seqs( [("seq3", "ATAGGATG"), ("seq0", "ATG-AGCG"), ("seq4", "ATGCTGGG")], moltype="dna", ) new_aln = aln.add_from_ref_aln(ref_aln) new_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:135: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) new_aln = aln.get_degapped_relative_to("seq1") new_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:154: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", array_align=False, ) seq = aln.get_seq("seq1") seq.name type(seq) seq.is_gapped() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = aln.get_gapped_seq("seq1") seq.is_gapped() seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:187: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_unaligned_seqs fn = "data/long_testseqs.fasta" seqs = load_unaligned_seqs(fn, moltype="dna") my_seq = seqs.seqs[0] my_seq[:24] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(my_seq) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:200: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs(fn, moltype="dna") aln.seqs[0][:24] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:209: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/test.paml", moltype="dna") aln.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:216: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new = aln.take_seqs(["Human", "HowlerMon"]) new.names [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs from cogent3.core.alignment import Alignment seq = load_unaligned_seqs("data/test.paml", moltype="dna") seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:237: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = Alignment(seq) aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("a", "ACG---"), ("b", "CCTGGG")] aln = make_aligned_seqs(data=data) dna = aln.to_dna() dna [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.to_moltype("dna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:264: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("a", "ACG---"), ("b", "CCUGGG")] aln = make_aligned_seqs(data=data) rna = aln.to_rna() rna [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:275: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("x", "TYV"), ("y", "TE-")] aln = make_aligned_seqs(data=data) prot = aln.to_protein() prot [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:292: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") degapped = aln.degap() print(type(degapped)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:307: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} aln = make_aligned_seqs(data=dna, moltype="dna") aln.write("sample.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:317: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.write("sample", format="fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:323: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.io import remove_files remove_files(["sample", "sample.fasta"], error_on_missing=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:332: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/long_testseqs.fasta") aln = Alignment(seq) fasta_align = aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:344: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/test.paml") aln = Alignment(seq) got = aln.to_phylip() print(got) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:357: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/test.paml") aln = Alignment(seq) string_list = aln.to_dict().values() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:374: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs fn = "data/long_testseqs.fasta" aln = load_aligned_seqs(fn, moltype="dna") aln[:24] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:384: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3 import load_unaligned_seqs fn = "data/long_testseqs.fasta" seqs = load_unaligned_seqs(fn) seqs[:24] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:396: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/test.paml") column_four = aln[3] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:406: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") region = aln[50:70] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:416: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() type(col) list(col) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:430: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=False ) list(range(len(aln))[2::3]) indices = [(i, i + 1) for i in range(len(aln))[2::3]] indices [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:441: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pos3 = aln.add_feature(biotype="pos3", name="pos3", spans=indices) pos3 = pos3.get_slice() pos3 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:452: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=True ) pos3 = aln[2::3] pos3 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:472: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ACGTAA---", "seq2": "ACGACA---", "seq3": "ACGCAATGA"}, moltype="dna", ) new = aln.trim_stop_codons() new [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:485: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln = make_aligned_seqs( data={ "seq1": "ACGTAA---", "seq2": "ACGAC----", # terminal codon incomplete "seq3": "ACGCAATGA", }, moltype="dna", ) new = aln.trim_stop_codons(strict=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:504: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:519: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nucs = aln.no_degenerates() nucs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:526: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trinucs = aln.no_degenerates(motif_length=3) trinucs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:534: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") pos = aln.variable_positions() just_variable_aln = aln.take_positions(pos) just_variable_aln[:10] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:546: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") pos = aln.variable_positions() just_constant_aln = aln.take_positions(pos, negate=True) just_constant_aln[:10] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:560: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") variable_codons = aln.filtered( lambda x: len(set(map(tuple, x))) > 1, motif_length=3 ) just_variable_aln[:9] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:572: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = aln.to_type(array_align=False) variable_codons = aln.filtered(lambda x: len(set("".join(x))) > 1, motif_length=3) just_variable_aln[:9] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:586: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") aln.take_seqs(["Human", "Mouse"]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:595: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs(["Human", "Mouse"], negate=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:604: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) def no_N_chars(s): return "N" not in s aln.take_seqs_if(no_N_chars) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:624: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs_if(no_N_chars, negate=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:636: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) counts = aln.counts() counts [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:651: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.counts(motif_length=3) counts [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:656: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.counts(include_ambiguity=True) counts [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:670: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs() motif_probs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:680: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, load_aligned_seqs trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs(alphabet=trinuc_alphabet) for m in sorted(motif_probs, key=lambda x: motif_probs[x], reverse=True): print("%s %.3f" % (m, motif_probs[m])) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:694: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs(data=[("a", "AACAAC"), ("b", "AAGAAG")], moltype="dna") motif_probs = aln.get_motif_probs() assert motif_probs["T"] == 0.0 motif_probs = aln.get_motif_probs(pseudocount=1e-6) assert 0 < motif_probs["T"] <= 1e-6 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:706: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("a", "AACGTAAG"), ("b", "AACGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) motif_probs = aln.get_motif_probs(alphabet=dinuc_alphabet) assert motif_probs["AA"] == 0.25 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:716: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("my_seq", "AAAGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") my_seq = aln.get_seq("my_seq") my_seq.count("AA") "AAA".count("AA") "AAAA".count("AA") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:727: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq(moltype="dna", seq="AAAGTAAG") seq di_nucs = [seq[i : i + 2] for i in range(len(seq) - 1)] sum([nn == "AA" for nn in di_nucs]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:742: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() c1, c2 = list(col) c1, c2 list(filter(lambda x: x == "-", c1)) list(filter(lambda x: x == "-", c2)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") for column in aln[113:150].iter_positions(): ungapped = list(filter(lambda x: x == "-", column)) gap_fraction = len(ungapped) * 1.0 / len(column) print(gap_fraction) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:771: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGG-TG--"), ("seq2", "ATG-AGGTGATG"), ("seq3", "ATGAAG--GATG"), ], moltype="dna", ) seq_to_aln_map = aln.get_gapped_seq("seq1").gap_maps()[0] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:787: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq_to_aln_map[3] seq_to_aln_map[8] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:796: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_to_seq_map = aln.get_gapped_seq("seq1").gap_maps()[1] aln_to_seq_map[3] aln_to_seq_map[8] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:804: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError seq_pos = aln_to_seq_map[7] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:818: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) aln.omit_gap_runs(2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:832: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) aln.omit_gap_pos(0.40) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:846: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) filtered_aln = aln.omit_gap_seqs(0.50) filtered_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:861: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: filtered_aln.omit_gap_pos() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, PROTEIN print(DNA.alphabet) print(PROTEIN.alphabet) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: PROTEIN.alphabet.moltype == PROTEIN [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) print(dinuc_alphabet) trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) print(trinuc_alphabet) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = "TAGT" indices = DNA.alphabet.to_indices(seq) indices [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_indices([0, 2, 3, 0]) seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3.core.annotation_db import BasicAnnotationDb anno_db = BasicAnnotationDb() anno_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gff_db = load_annotations(path="data/mycoplasma-genitalium.gff") gff_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gb_db = load_annotations(path="data/mycoplasma-genitalium.gb") gb_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: summary = gff_db.describe summary [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:82: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: anno_db.add_feature( seqid="NC_000908", biotype="gene", name="interesting_gene", spans=[(1, 4)], strand="+", ) anno_db.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.add_feature( seqid="seq1", biotype="gene", name="interesting_gene", spans=[(1, 4)], strand="+", ) gff_db.describe[-2:, :] # showing just last two rows [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: mg_16s = list( gb_db.get_features_matching( name="MG_RS00775", biotype="gene", seqid="NC_000908" ) ) mg_16s [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogenes = list(gff_db.get_features_matching(biotype="pseudogene")) pseudogenes[:2] # showing just the first two [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: operon_cds = list( gff_db.get_features_matching(start=220600, end=229067, biotype="CDS") ) operon_cds [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:188: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: replication_records = list( gff_db.get_records_matching(attributes="replication", biotype="CDS") ) replication_records[0] # showing just the first match [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gb_db.num_matches(biotype="gene") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:215: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: total_genes = gb_db.count_distinct(biotype="gene", name=True) single_copy = total_genes[total_genes.columns["count"] == 1, :] len(single_copy) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:226: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: total_genes = gff_db.num_matches(biotype="gene") print("total genes: ", total_genes) genes = gff_db.count_distinct(biotype="gene", name=True) single_copy = genes[genes.columns["count"] == 1, :] print("single copy genes: ", len(single_copy)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:246: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: children = list(gff_db.get_feature_children(name="gene-MG_RS00035")) children [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: parents = list(gff_db.get_feature_parent(name="cds-WP_009885556.1")) parents [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:273: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.compatible(anno_db) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.compatible(gb_db) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: union_db = gb_db.union(anno_db) union_db.describe[-2:, :] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:307: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.update(anno_db) gff_db.describe[-2:, :] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:318: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3.core.annotation_db import GenbankAnnotationDb new_gb_db = GenbankAnnotationDb(source="m-genitalium-database.gbdb", db=anno_db) new_gb_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:331: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gff_db = load_annotations(path="data/mycoplasma-genitalium.gff") just_cds = gff_db.subset(biotype="CDS") just_cds.describe [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:354: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq seq1 = make_seq( "AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAGGGAACCCT", name="NC_000908", moltype="dna", ) seq1.annotation_db = anno_db seq1.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:376: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq gb_seq = load_seq("data/mycoplasma-genitalium.gb") gb_seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:389: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_seq = load_seq( "data/mycoplasma-genitalium.fa", annotation_path="data/mycoplasma-genitalium.gff", ) gff_seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:402: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq = load_seq( "data/mycoplasma-genitalium.fa", annotation_path="data/mycoplasma-genitalium.gff", label_to_name=lambda x: x.split()[0], ) seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:412: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib # clean up files path = pathlib.Path("m-genitalium-database.gbdb") path.unlink() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import tree_align [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") aln, tree = tree_align("HKY85", seqs, show_progress=False) aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = make_tree( "(((NineBande:0.013,Mouse:0.185):0.023,DogFaced:0.046):0.027,Human:0.034,HowlerMon:0.019)" ) params = {"kappa": 4.0} aln, tree = tree_align( "HKY85", seqs, tree=tree, param_vals=params, show_progress=False ) aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import tree_align seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") tree = make_tree( "((NineBande:0.058,Mouse:0.595):0.079,DogFaced:0.142,(HowlerMon:0.062,Human:0.103):0.079)" ) params = {"kappa": 4.0, "omega": 1.3} aln, tree = tree_align( "MG94HKY", seqs, tree=tree, param_vals=params, show_progress=False ) aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs from cogent3.align.progressive import tree_align from cogent3.evolve.models import get_model seqs = [ ( "hum", "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", ), ( "mus", "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", ), ("rat", "CTGAACAAGCAGCCACTTTCAAACAAGAAA"), ] unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") unaligned_DNA [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_DNA.get_translation() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aligned_aa_seqs = [ ("hum", "KQIQESSENGSLAARQERQAQVNLT"), ("mus", "KQIQESGESGSLAARQERQAQVNLT"), ("rat", "LNKQ------PLS---------NKK"), ] aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA, aa_to_codon=True) aligned_DNA [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = aln.quick_tree(calc="TN93", show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = aln.quick_tree(calc="TN93", bootstrap=100, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = dists.quick_tree(show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.phylo import nj aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = nj.nj(dists, show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo import nj dists = {("a", "b"): 2.7, ("c", "b"): 2.33, ("c", "a"): 0.73} tree = nj.nj(dists, show_progress=False) print(tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo.least_squares import WLS from cogent3.util.deserialise import deserialise_object dists = deserialise_object("data/dists_for_phylo.json") ls = WLS(dists) stat, tree = ls.trex(a=5, k=5, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve.models import F81 from cogent3.phylo.maximum_likelihood import ML aln = load_aligned_seqs("data/primate_brca1.fasta") ml = ML(F81(), aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_distances available_distances() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_distance_calculator, load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta") dist_calc = get_distance_calculator("tn93", alignment=aln) dist_calc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.run(show_progress=False) dists = dist_calc.get_pairwise_distances() dists [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.stderr [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_model, load_aligned_seqs from cogent3.evolve import distance aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") d = distance.EstimateDistances(aln, submodel=get_model("F81")) d.run(show_progress=False) dists = d.get_pairwise_distances() dists [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:82: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists.max_pair() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: dists[dists.max_pair()] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists.min_pair() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: dists[dists.min_pair()] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model hky = get_model("HKY85") print(hky) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("GTR", with_rate=True, distribution="gamma") print(sub_mod) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("CNFGTR", with_rate=True, distribution="gamma") print(sub_mod) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("JTT92", with_rate=True, distribution="gamma") print(sub_mod) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:80: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) aln = make_aligned_seqs( [("a", "ACGT"), ("b", "AC-T"), ("c", "ACGT"), ("d", "AC-T")] ) lf.set_alignment(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:112: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") print(tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule( "omega", tip_names=["Human", "Orangutan"], outgroup_name="Galago", clade=True, init=0.5, ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", is_constant=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1, lower=1e-9, upper=20.0) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:190: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_param_rule("length", upper=1.0) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:207: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, digits=2) lf.set_param_rule("bprobs", is_constant=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:222: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, sites_independent=False, digits=2) lf.set_param_rule("bprobs", is_constant=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:239: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:253: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, max_restarts=5, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=False, global_tolerance=1.0, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:265: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False, max_restarts=5, tolerance=1e-8) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:276: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) try: lf.optimise( show_progress=False, limit_action="raise", max_evaluations=10, return_calculator=True, ) except ArithmeticError as err: print(err) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:303: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model sm = get_model("GTR") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree) aln = load_aligned_seqs("data/primate_brca1.fasta") lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:321: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lnL = lf.lnL lnL [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:326: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nfp = lf.nfp nfp [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:338: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:344: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic(second_order=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:353: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_bic() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:367: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: a_g = lf.get_param_value("A/G") a_g [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human = lf.get_param_value("length", "Human") human [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:380: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mprobs = lf.get_motif_probs() mprobs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tables = lf.get_statistics(with_motif_probs=True, with_titles=True) tables[0] # just displaying the first [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:398: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) null_lnL = lf.lnL null_nfp = lf.nfp lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:423: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) lf.set_name("Alt Hypothesis") lf.optimise(local=True, show_progress=False) alt_lnL = lf.lnL alt_nfp = lf.nfp lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:434: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from scipy.stats.distributions import chi2 LR = 2 * (alt_lnL - null_lnL) # the likelihood ratio statistic df = alt_nfp - null_nfp # the test degrees of freedom p = chi2.sf(LR, df) print(f"LR={LR:.4f} ; df={df}; p={df:.4f}") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:450: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) sim_aln = lf.simulate_alignment() sim_aln[:60] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:478: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("HKY85") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) kappa_lo, kappa_mle, kappa_hi = lf.get_param_interval("kappa") print(f"lo={kappa_lo:.2f} ; mle={kappa_mle:.2f} ; hi={kappa_hi:.2f}") human_lo, human_mle, human_hi = lf.get_param_interval("length", "Human") print(f"lo={human_lo:.2f} ; mle={human_mle:.2f} ; hi={human_hi:.2f}") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:501: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model aln = make_aligned_seqs(data=dict(a="ACGG", b="ATAG", c="ATGG")) tree = make_tree(tip_names=aln.names) sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) json = lf.to_json() json[:60] # just truncating the displayed string [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:516: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.deserialise import deserialise_object newlf = deserialise_object(json) newlf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:542: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestors = lf.likely_ancestral_seqs() ancestors[:60] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:549: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestral_probs = lf.reconstruct_ancestral_seqs() ancestral_probs["root"][:5] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq # create an example sequence seq = make_seq( "GCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAA", name="seq1", moltype="dna", ) # Add a feature seq.add_feature(biotype="gene", name="a_gene", spans=[(12, 48)], seqid="seq1") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # Add a feature as a series seq.add_feature( biotype="cpgsite", name="a_cpgsite", spans=[(12, 18), (21, 29), (35, 48)], seqid="seq1", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # make demo alignment aln1 = make_aligned_seqs( data=[["seq1", "-AAACCCCCA"], ["seq2", "TTTT--TTTT"]], array_align=False ) # add feature to seq1 aln1.add_feature( seqid="seq1", biotype="exon", name="A", spans=[(3, 8)], on_alignment=False ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:84: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # make demo alignment aln1 = make_aligned_seqs( data=[["seq1", "-AAACCCCCA"], ["seq2", "TTTT--TTTT"]], array_align=False ) aln1.add_feature( biotype="exon", name="aligned_exon", spans=[(0, 8)], on_alignment=True, ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:108: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq from cogent3.core.annotation_db import BasicAnnotationDb # init empty db and add feature db = BasicAnnotationDb() db.add_feature(seqid="seq1", biotype="exon", name="C", spans=[(45, 48)]) # make demo seq s1 = make_seq( "AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAGGGAACCCT", name="seq1", moltype="dna" ) # assign db to sequence s1.annotation_db = db s1.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq %timeit load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:150: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: :hide-code: seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( filename="data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", moltype="dna", ) seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:189: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:209: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import load_seq loaded_seq = load_seq( "data/C-elegans-chromosome-I.fa", label_to_name=lambda x: x.split()[0], moltype="dna", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:220: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # loaded_seq = < loaded / created the seq> loaded_seq.annotate_from_gff("data/C-elegans-chromosome-I.gff") loaded_seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import make_seq sub_seq = make_seq( "GCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAAGACTAAGCCTAAGA", name="I", moltype="dna", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # sub_seq = sub_seq.annotate_from_gff("data/C-elegans-chromosome-I.gff", offset=600) sub_seq.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:254: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs brca1_aln = load_aligned_seqs( "data/primate_brca1.fasta", array_align=False, moltype="dna" ) brca1_aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:266: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: brca1_aln.annotate_from_gff("data/brca1_hsa_shortened.gff", seq_ids=["Human"]) brca1_aln.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:274: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: brca1_aln.get_seq("Human").annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:296: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") # note we wrap `get_features` in `list` as generator is returned gene = list(seq.get_features(name="WBGene00021661", biotype="gene")) gene [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:312: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS")) cds[:3] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:323: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: cds = list(seq.get_features(biotype="CDS", name="WBGene00021661")) cds [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") region_features = list(seq.get_features(start=10148, stop=26732)) region_features[:3] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:345: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: mRNA = list(seq.get_features(start=10148, stop=29322, biotype="mRNA"))[0] mRNA [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:358: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs # first load alignment and annotate the human seq aln = load_aligned_seqs( "data/primate_brca1.fasta", array_align=False, moltype="dna" ) aln.annotate_from_gff("data/brca1_hsa_shortened.gff", seq_ids=["Human"]) # query alignment providing seqid of interest human_exons = list(aln.get_features(biotype="exon", seqid="Human")) human_exons [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:383: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # add a feature to the alignment we created above on difference sequence aln.add_feature(biotype="gene", name="gene:101", spans=[(40, 387)], seqid="Rhesus") any_feature = list(aln.get_features(on_alignment=False)) any_feature [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:405: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # first we add the feature to the alignment aln.add_feature( biotype="pseudogene", name="pseudogene1", spans=[(420, 666)], on_alignment=True ) # query for features on the alignment aln_features = list(aln.get_features(on_alignment=True)) aln_features [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:426: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln3 = make_aligned_seqs( data=[["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], array_align=False, moltype="dna", ) exon = aln3.add_feature( seqid="x", biotype="exon", name="ex1", spans=[(0, 4)], on_alignment=False ) exon.get_slice() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:441: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln_exons = list(aln3.get_features(seqid="x", biotype="exon"))[0] aln_exons [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:451: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: exon.get_slice(allow_gaps=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:466: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) pseudogene = list(seq.get_features(start=10148, stop=26732, biotype="pseudogene"))[0] seq[pseudogene] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:484: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogene.get_slice() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:494: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") subseq = seq[25000:35000] fig = subseq.get_drawable(biotype=("gene", "mRNA", "CDS", "misc_RNA")) fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogene.get_coordinates() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:515: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS"))[0] exon_coords = cds.get_coordinates() exon_coords [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intron_coords = [] for i in range(len(exon_coords) - 1): intron_coords.append((exon_coords[i][1], exon_coords[i + 1][0])) intron_coords [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:540: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intron = seq.add_feature( biotype="intron", name="intron:Y74C9A.3.1", seqid="I", spans=intron_coords ) intron [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:553: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS")) union_cds = cds[0].union(cds[1:]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:572: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") genes = list(seq.get_features(biotype="gene")) genes = genes[0].union(genes[1:]) genes [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:584: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intergenic = genes.shadow() intergenic [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:592: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intergenic.get_slice() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:605: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") no_cds = seq.with_masked_annotations("CDS") no_cds[2575800:2575900] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:621: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]], moltype="dna", array_align=False, ) exon = aln.add_feature( seqid="x", biotype="exon", name="exon-be-gone", spans=[(0, 4)], on_alignment=False, ) aln.with_masked_annotations("exon", mask_char="?") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:642: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: rc = aln.rc() rc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:650: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: rc.with_masked_annotations("exon", mask_char="?") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:664: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) gene = list(seq.get_features(name="gene:WBGene00022276", biotype="gene"))[0] children = list(gene.get_children()) children [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:686: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: child = list(seq.get_features(name="transcript:Y74C9A.2a.3", biotype="mRNA"))[0] parent = list(child.get_parent()) parent [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:698: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False, moltype="dna", ) x, y = aln2.get_seq("x"), aln2.get_seq("y") x.annotation_db is y.annotation_db is aln2.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:711: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq = make_seq("CCCCCCCCCCCCCCCCCCCC", name="x", moltype="dna") match_exon = seq.add_feature(biotype="exon", name="A", spans=[(3, 8)]) aln2.copy_annotations(seq.annotation_db) aln2.annotation_db [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:721: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: copied = list(aln2.get_features(seqid="x", biotype="exon")) copied [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:732: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: unified = aln_exons.as_one_span() aln3[unified] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:743: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: plus = make_seq("CCCCCAAAAAAAAAATTTTTTTTTTAAAGG", moltype="dna") plus_rpt = plus.add_feature(biotype="blah", name="a", spans=[(5, 15), (25, 28)]) plus[plus_rpt] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:750: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: minus = plus.rc() minus [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: minus_rpt = list(minus.get_features(biotype="blah"))[0] minus[minus_rpt] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = { "s1": "GCTCATGCCAGCTCTTTACAGCATGAGAACA--AGT", "s2": "ACTCATGCCAACTCATTACAGCATGAGAACAGCAGT", "s3": "ACTCATGCCAGCTCATTACAGCATGAGAACAGCAGT", "s4": "ACTCATGCCAGCTCATTACAGCATGAGAACAGCAGT", "s5": "ACTCATGCCAGCTCAGTACAGCATGAGAACAGCAGT", } nt_seqs = make_aligned_seqs(data=data, moltype="dna") nt_seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_seqs.get_translation(gc=1, incomplete_ok=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") translations = standard_code.sixframes(seq) print(translations) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:62: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") stops_frame1 = standard_code.get_stop_indices(seq, start=0) stops_frame1 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stop_index = stops_frame1[0] seq[stop_index : stop_index + 3] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) standard_code["TTT"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: standard_code["A"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:95: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["TTT"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["A"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:115: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: targets = ["A", "C"] codons = [standard_code[aa] for aa in targets] codons [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: flat_list = sum(codons, []) flat_list [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(1) alphabet = gc.get_alphabet() print(alphabet) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:142: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna") codons = my_seq.get_in_motif_size(3) codons [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:155: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep = my_seq.get_translation() pep [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:163: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.core.alphabet import AlphabetError [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq seq = make_seq("ATGTGATGGTAA", name="s1", moltype="dna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:179: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AlphabetError pep = seq.get_translation() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep = seq.get_translation(include_stop=True) pep [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/mycoplasma-genitalium.fa", moltype="dna") seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = load_seq("data/brca1-bats.fasta", moltype="dna") seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna") type(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.info.source [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/long_testseqs.fasta", moltype="dna") type(seqs) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs( "https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/long_testseqs.fasta", moltype="dna", ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna", format="fasta") aln [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:101: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs protein_seqs = {"seq1": "DEKQL-RG", "seq2": "DDK--SRG"} proteins_loaded = make_aligned_seqs(protein_seqs) proteins_loaded.moltype proteins_loaded [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: proteins_loaded = make_aligned_seqs(protein_seqs, moltype="protein") proteins_loaded [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:123: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"} seqs_loaded = make_aligned_seqs(seqs) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:133: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"} seqs_loaded = make_aligned_seqs(seqs) seqs_loaded [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs DNA_seqs = { "sample1 Mus musculus": "AACCTGC--C", "sample2 Gallus gallus": "AAC-TGCAAC", } loaded_seqs = make_aligned_seqs( DNA_seqs, moltype="dna", label_to_name=lambda x: x.split()[0] ) loaded_seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs seqs = {"seq1": "AATCA", "seq2": "AATCGGA"} seqs = make_unaligned_seqs(data=seqs, moltype="dna") seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:184: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import MinimalFastaParser f = open("data/long_testseqs.fasta") seqs = [(name, seq) for name, seq in MinimalFastaParser(f)] seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:197: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import LabelParser def latin_to_common(latin): return {"Homo sapiens": "human", "Pan troglodtyes": "chimp"}[latin] label_parser = LabelParser( "%(species)s", [[1, "species", latin_to_common]], split_with=":" ) for label in ">abcd:Homo sapiens:misc", ">abcd:Pan troglodtyes:misc": label = label_parser(label) print(label, type(label)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:213: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import LabelParser, MinimalFastaParser fasta_data = [ ">gi|10047090|ref|NP_055147.1| small muscle protein, X-linked [Homo sapiens]", "MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGAKKLPGPAVNL", "SEIQNIKSELKYVPKAEQ", ">gi|10047092|ref|NP_037391.1| neuronal protein [Homo sapiens]", "MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLY", "PPGQEPIPKISESKMAFKQMEQISQFLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTKD", ] label_to_name = LabelParser( "%(ref)s", [[1, "gi", str], [3, "ref", str], [4, "description", str]], split_with="|", ) for name, seq in MinimalFastaParser(fasta_data, label_to_name=label_to_name): print(name) print(name.info.gi) print(name.info.description) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:54: WARNING: TODO entry found: add cross ref for description of Info class /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_moltypes available_moltypes() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_moltype dna = get_moltype("dna") dna [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.ambiguities [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.degenerates [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.complement("AGG") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = dna.make_seq("AGGCTT", name="seq1") seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rna = get_moltype("rna") rna.is_valid("ACGUACGUACGUACGU") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core import moltype as mt DNAgapped = mt.MolType( seq_constructor=mt.DnaSequence, motifset=mt.IUPAC_DNA_chars, ambiguities=mt.IUPAC_DNA_ambiguities, complements=mt.IUPAC_DNA_ambiguities_complements, pairs=mt.DnaStandardPairs, gaps=".", ) seq = DNAgapped.make_seq("ACG.") seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.sequence import DnaSequence DnaSequence.moltype = DNA [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq p = make_seq("THISISAPRQTEIN", "myProtein", moltype="protein") type(p) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: p [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq nuc = make_seq("TTTGCAAAC", moltype="dna") pep = nuc.get_translation() pep [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.write("data/temp.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") names = tr.get_node_names() names[:4] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: names[4:] names_nodes = tr.get_nodes_dict() names_nodes["Human"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_node_matching_name("Mouse") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tr.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: hu.name [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:70: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] type(hu) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(tr) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() for n in nodes.items(): print(n) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tr.iter_tips(): print(n) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for n in tr.iter_nontips(): print(n.get_newick()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") edges = tr.get_connecting_edges("edge.1", "Human") for edge in edges: print(edge.name) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] hu.distance(mu) hu.is_tip() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] lca = hu.last_common_ancestor(mu) lca [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:154: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(lca) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") for a in hu.ancestors(): print(a.name) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") node = tr.get_node_matching_name("edge.1") children = list(node.iter_tips()) + list(node.iter_nontips()) for child in children: print(child.name) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") dists = tr.get_distances() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human_dists = [names for names in dists if "Human" in names] for dist in human_dists: print(dist, dists[dist]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:204: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.max_tip_tip_distance() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tips = hu.tips_within_distance(0.2) for t in tips: print(t) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.rooted_at("edge.0").ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.root_at_midpoint().ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:254: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:261: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.rooted_with_tip("Mouse").ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:271: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.get_newick() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:278: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_newick(with_distances=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:285: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") xml = tr.get_xml() for line in xml.splitlines(): print(line) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:299: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:309: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.preorder(): print(t.get_newick()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:320: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.postorder(): print(t.get_newick()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for tip in tr.iter_nontips(): tip_names = tip.get_tip_names() print(tip_names) sub_tree = tr.get_sub_tree(tip_names) print(sub_tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:348: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.io import remove_files remove_files(["data/temp.tree", "data/temp.pdf"], error_on_missing=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:364: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree simple_tree_string = "(B:0.2,(D:0.4)E:0.5)F;" simple_tree = make_tree(simple_tree_string) print(simple_tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.prune() print(simple_tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:377: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:384: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = load_tree("data/test.tree") print(tr1.get_newick()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:391: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr2 = tr1.unrooted_deepcopy() print(tr2.get_newick()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:401: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tree_string = "(B:0.2,H:0.2,(C:0.3,D:0.4,E:0.1)F:0.5)G;" tr = make_tree(tree_string) print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:409: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.bifurcating().ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:422: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:429: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.balanced().ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:438: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr1 = make_tree("(B:0.2,(C:0.2,D:0.2)F:0.2)G;") tr2 = make_tree("((C:0.1,D:0.1)F:0.1,B:0.1)G;") tr1.same_topology(tr2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:467: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # Distance metrics for rooted trees from cogent3 import make_tree tr1 = make_tree(treestring="(a,(b,(c,(d,e))));") tr2 = make_tree(treestring="(e,(d,(c,(b,a))));") mc_distance = tr1.tree_distance(tr2, method="matching_cluster") # or method="mc" or method="matching" rooted_rf_distance = tr1.tree_distance(tr2, method="rooted_robinson_foulds") # or method="rrf" or method="rf" print("Matching Cluster Distance:", mc_distance) print("Rooted Robinson Foulds Distance:", rooted_rf_distance) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:481: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # Distance metrics for unrooted trees from cogent3 import make_tree tr1 = make_tree(treestring="(a,b,(c,(d,e)));") tr2 = make_tree(treestring="((a,c),(b,d),e);") lrm_distance = tr1.tree_distance(tr2, method="lin_rajan_moret") # or method="lrm" or method="matching" unrooted_rf_distance = tr1.tree_distance(tr2, method="unrooted_robinson_foulds") # or method="urf" or method="rf" print("Lin-Rajan-Moret Distance:", lrm_distance) print("Unrooted Robinson Foulds Distance:", unrooted_rf_distance) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:501: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.set_tip_distances() for t in tr.preorder(): print(t.name, t.TipDistance) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:517: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:524: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.scale_branch_lengths() print(tr) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:534: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:3,(C:2,D:4)F:5)G;") d, tips = tr.tip_to_tip_distances() for i, t in enumerate(tips): print(t.name, d[i]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:554: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr1 = make_tree("(B:2,(C:3,D:4)F:5)G;") tr2 = make_tree("(C:2,(B:3,D:4)F:5)G;") tr1.compare_by_tip_distances(tr2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table [docutils] cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv") [docutils] cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table [docutils] cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] [docutils] cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] [docutils] cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table [docutils] cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table [docutils] cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table [docutils] cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table [docutils] cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table [docutils] cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) [docutils] cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] [docutils] cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table [docutils] cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table [docutils] cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table [docutils] cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] [docutils] cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] [docutils] cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table [docutils] cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table [docutils] cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table [docutils] cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table [docutils] cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table [docutils] cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data, title="Sample title", legend="a legend") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table.title = "My title" table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") for row in table: print(row) break [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for row in table: print(row["Locus"]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3, 5], b=["a", "c", "d"]) table = make_table(data=data) table.shape[0] == 3 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.shape[1] == 2 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.columns [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Region"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:113: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for name in table.columns: print(name) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table[:2, "Region":] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:135: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table[:2, :1] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.format_column("Ratio", "%.1e") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", digits=1, space=2) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.space = " " table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table h = ["name", "A/C", "A/G", "A/T", "C/A"] rows = [["tardigrade", 0.0425, 0.1424, 0.0226, 0.0391]] wrap_table = make_table(header=h, data=rows, max_width=30) wrap_table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:184: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wrap_table = make_table(header=h, data=rows, max_width=30, index_name="name") wrap_table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:192: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data=dict(a=list(range(10)), b=list(range(10)))) table.head() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:199: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.head(2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail(1) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(random=3) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(head=2, tail=3) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:241: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.header) table = table.with_new_header("Ratio", "Stat") print(table.header) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:251: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:269: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table = table.with_new_column( "LargeCon", lambda r_v: r_v[0] == "Con" and r_v[1] > 10.0, columns=["Region", "Ratio"], ) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.array [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:292: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") locus = table.to_list("Locus") locus [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:300: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Locus"].tolist() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:311: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") rows = table.to_list(["Region", "Locus"]) rows [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:324: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.to_dict() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.columns.to_dict() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:342: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") df = table.to_pandas() df [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:350: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: df = table.to_pandas(categories="Region") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:359: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}, index_name="") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:364: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: contingency = table.to_categorical(["Ts", "Tv"]) contingency [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:369: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: g_test = contingency.G_independence() g_test [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:376: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}) contingency = table.to_categorical(["Ts", "Tv"], index_name="") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1 = load_table("data/stats.tsv") table2 = load_table("data/stats.tsv") table = table1.appended(None, table2) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:397: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1.title = "Data1" table2.title = "Data2" table = table1.appended("Data#", table2, title="") table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:409: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.summed("Ratio") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:416: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Ratio"].sum() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:425: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table all_numeric = make_table( header=["A", "B", "C"], data=[range(3), range(3, 6), range(6, 9), range(9, 12)] ) all_numeric [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:436: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:442: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed(col_sum=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:451: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed = make_table( header=["A", "B", "C"], data=[["*", 1, 2], [3, "*", 5], [6, 7, "*"]] ) mixed [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:460: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(strict=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:466: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(col_sum=False, strict=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:475: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") sub_table = table.filtered(lambda x: x < 10.0, columns="Ratio") sub_table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:483: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0") sub_table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:490: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0 and Region == 'NonCon'") sub_table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:500: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: big_numeric = all_numeric.filtered_by_column(lambda x: sum(x) > 20) big_numeric [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.sorted(columns="Ratio") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:516: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns="Ratio", reverse="Ratio") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:523: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns=["Region", "Ratio"], reverse="Ratio") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:530: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.to_list("Region") raw [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:539: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.to_list(["Locus", "Region"]) raw [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:548: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.distinct_values("Region") == set(["NonCon", "Con"]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:556: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.count("Region == 'NonCon' and Ratio > 1") == 1 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:566: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( data=dict(A=["a", "b", "b", "b", "a"], B=["c", "c", "c", "c", "d"]) ) unique = table.count_unique("A") type(unique) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:576: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:582: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique = table.count_unique(["A", "B"]) unique [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:587: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: r = unique.to_table() r [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:597: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rows = [ ["NP_004893", True], ["NP_005079", True], ["NP_005500", False], ["NP_055852", False], ] region_type = make_table(header=["Locus", "LargeCon"], data=rows) stats_table = load_table("data/stats.tsv") new = stats_table.joined(region_type, columns_self="Locus") new [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:617: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["#OTU ID", "14SK041", "14SK802"] rows = [ [-2920, "332", 294], [-1606, "302", 229], [-393, 141, 125], [-2109, 138, 120], ] table = make_table(header=header, rows=rows) table [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:633: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tp = table.transposed(new_column_name="sample", select_as_header="#OTU ID") tp [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:643: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="md") print(table) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:655: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="tex") print(table) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:667: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_markdown(justify="ccr")) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:675: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_latex(justify="ccr", label="tab:table1")) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:685: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst(csv_table=True)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:695: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:707: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_string(format="latex")) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:717: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: rows = [ ["1", 100, 101, 1.123], ["1", 101, 102, 1.123], ["1", 102, 103, 1.123], ["1", 103, 104, 1.123], ["1", 104, 105, 1.123], ["1", 105, 106, 1.123], ["1", 106, 107, 1.123], ["1", 107, 108, 1.123], ["1", 108, 109, 1], ["1", 109, 110, 1], ["1", 110, 111, 1], ["1", 111, 112, 1], ["1", 112, 113, 1], ["1", 113, 114, 1], ["1", 114, 115, 1], ["1", 115, 116, 1], ["1", 116, 117, 1], ["1", 117, 118, 1], ["1", 118, 119, 2], ["1", 119, 120, 2], ["1", 120, 121, 2], ["1", 150, 151, 2], ["1", 151, 152, 2], ["1", 152, 153, 2], ["1", 153, 154, 2], ["1", 154, 155, 2], ["1", 155, 156, 2], ["1", 156, 157, 2], ["1", 157, 158, 2], ["1", 158, 159, 2], ["1", 159, 160, 2], ["1", 160, 161, 2], ] bgraph = make_table(header=["chrom", "start", "end", "value"], rows=rows) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bgraph.head() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:762: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print( bgraph.to_string( format="bedgraph", name="test track", description="test of bedgraph", color=(255, 0, 0), digits=0, ) ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:777: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") straight_html = table.to_html() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:789: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.format.table import known_formats known_formats [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:798: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.write("stats_tab.tex", justify="ccr", label="tab:table1") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:807: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.write("stats_tab.txt", sep="\t") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:814: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib for name in ("stats_tab.txt", "stats_tab.tex"): p = pathlib.Path(name) if p.exists(): p.unlink() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.a [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data["a"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.d [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.b |= {"d": 25} data.b [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.union({"d": [25]}) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b {"c": 24, "d": [25]} [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data["k"] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AttributeError data.k [docutils] cookbook/union_dict.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.a [docutils] cookbook/union_dict.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data["a"] [docutils] cookbook/union_dict.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.d [docutils] cookbook/union_dict.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.b |= {"d": 25} data.b [docutils] cookbook/union_dict.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.union({"d": [25]}) [docutils] cookbook/union_dict.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b {"c": 24, "d": [25]} [docutils] cookbook/union_dict.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data["k"] [docutils] cookbook/union_dict.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AttributeError data.k [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy def DiffOmega(omega): def omega_from_S(S): omega_est = S / (1 - numpy.e ** (-1 * S)) return abs(omega - omega_est) ** 2 return omega_from_S omega = 0.1 f = DiffOmega(omega) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.optimisers import maximise, minimise S = minimise( f, # the function xinit=1.0, # the initial value bounds=(-100, 100), # [lower,upper] bounds for the parameter local=True, # just local optimisation, not Simulated Annealing show_progress=False, ) assert 0.0 <= f(S) < 1e-6 print("S=%.4f" % S) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3.util.misc import iterable my_var = 10 for i in my_var: print("will not work") for i in iterable(my_var): print(i) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import curry def foo(x, y): """Some function""" return x + y bar = curry(foo, 5) print(bar.__doc__) bar(10) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_iterable can_iter = [1, 2, 3, 4] cannot_iter = 1.234 is_iterable(can_iter) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_iterable(cannot_iter) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_char class foo: pass is_char("a") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char("ab") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:122: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char(foo()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:131: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import recursive_flatten l = [[[[1, 2], "abcde"], [5, 6]], [7, 8], [9, 10]] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: recursive_flatten(l) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import not_list_tuple not_list_tuple(1) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple([1]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple("ab") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import add_lowercase d = {"A": 5, "B": 6, "C": 7, "foo": 8, 42: "life"} add_lowercase(d) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:177: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from numpy import array from cogent3.util.misc import DistanceFromMatrix m = array([[1, 2, 3], [4, 5, 6], [7, 8, 9]]) f = DistanceFromMatrix(m) f(0, 0) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:187: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(1, 2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ClassChecker class not_okay(object): pass no = not_okay() class okay(object): pass o = okay() class my_dict(dict): pass md = my_dict() cc = ClassChecker(str, okay, dict) o in cc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:217: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: no in cc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 5 in cc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:225: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: {"a": 5} in cc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: "asasas" in cc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:233: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: md in cc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:242: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import Delegator class ListAndString(list, Delegator): def __init__(self, items, string): Delegator.__init__(self, string) for i in items: self.append(i) ls = ListAndString([1, 2, 3], "ab_cd") len(ls) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:255: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls[0] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.upper() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:263: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.split("_") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:272: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import FunctionWrapper f = FunctionWrapper(str) f [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(123) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:290: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.misc import ConstraintError [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:295: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ConstrainedDict d = ConstrainedDict({"a": 1, "b": 2, "c": 3}, constraint="abc") d [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:302: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ConstraintError d["d"] = 5 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:4: WARNING: duplicate label union_dict, other instance in /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/what_codes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/what_codes.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_codes available_codes() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/what_codes.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(4) gc [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/brca1.fasta", moltype="dna") aln = aln.no_degenerates(motif_length=3) aln = aln.get_translation() aln = aln[:100] # for compute speed in testing the documentation coevo = aln.coevolution(show_progress=False, drawable="heatmap") coevo.drawable.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-coevolution.png" coevo.drawable.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: coevo = aln.coevolution(show_progress=False, drawable="violin") coevo.drawable.show(width=300) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: coevo = aln.coevolution(show_progress=False, drawable="box") coevo.drawable.show(width=300) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:11: WARNING: TODO entry found: add citation for NMI /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/SCA1-cds.fasta", moltype="dna") draw = seqs.dotplot() draw.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-1.png" draw.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", window=8, threshold=8) draw.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True) draw.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True, title="SCA1", width=400) draw.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:11: WARNING: TODO entry found: Change dotplot ref to a citation /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_json") seqs = loader("data/tp53.json") dp = seqs.dotplot(name1="Macaque", name2="Marmoset", width=600) dp.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-2.png" dp.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: help(dp.remove_track) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dp.remove_track(left_track=True) dp.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs, get_app seqs = load_aligned_seqs("data/brca1.fasta", moltype="dna").degap() seqs = seqs.take_seqs( ["LeafNose", "FalseVamp", "RoundEare", "Sloth", "Anteater", "HairyArma"] ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligner = get_app("progressive_align", "nucleotide", indel_rate=1e-2, indel_length=1e-9) aln = aligner(seqs) dp = aln[2200:2500].dotplot("HairyArma", "RoundEare") dp.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-3.png" dp.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln[2300:2500] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligner = get_app("progressive_align", "nucleotide") aln = aligner(seqs) aln[2200:2500].dotplot("HairyArma", "RoundEare").show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln[2300:2500] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/brca1.fasta", moltype="dna") counts = aln.count_gaps_per_seq(unique=True) counts[10: 20] # limiting the width of the displayed output [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="bar") counts.drawable.show(width=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-gaps-per-seq.png" counts.drawable.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="violin") counts.drawable.show(width=300, height=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="box") counts.drawable.show(width=300, height=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_aligned_seqs, make_seq s1 = make_seq("TGATGTAAGGTAGTT", name="s1", moltype="dna") s2 = make_seq("--CTGGAAGGGT---", name="s2", moltype="dna") seqs = make_aligned_seqs(data=[s1, s2], array_align=False, moltype="dna") draw = seqs.information_plot(window=2, include_gap=True) draw.show(width=500, height=400) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/brca1.fasta", moltype="protein") fig = aln.information_plot(stat="median") fig.show(width=500, height=400) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-info-plot.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.parse import jaspar _, pwm = jaspar.read("data/tbp.jaspar") freqarr = pwm.to_freq_array() freqarr[:5] # illustrating the contents of the MotifFreqsArray [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: logo = freqarr.logo() logo.show(height=250, width=500) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-seqlogo.png" logo.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") l = aln[:311].seqlogo(height=300, width=500, wrap=60, vspace=0.05) l.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa = aln.get_translation(incomplete_ok=True)[:120] logo = aa.seqlogo(width=500, height=300, wrap=50, vspace=0.1) logo.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") seq [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = seq[25000:35000] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig = seq.get_drawable() fig.show(height=400, width=700) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig = seq.get_drawable(biotype=("gene", "CDS", "mRNA")) fig.show(height=300, width=650) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_seq-features.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure(style="angular", width=600, height=600) fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-angular.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure("circular", width=600, height=600) fig.scale_bar = "top right" fig.label_pad = 0.1 fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.style_edges( "AfricanEl", tip2="Manatee", legendgroup="Afrotheria", line=dict(color="magenta", width=2), ) fig.show(width=650, height=600) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.label_pad = 0.3 fig.show(width=650, height=600) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-circular.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:9: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure("radial", width=600, height=600) fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:19: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-radial.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.label_pad = 0.23 fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure(width=600, height=600) fig.scale_bar = "top right" fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-square.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.style_edges( "AfricanEl", tip2="Manatee", legendgroup="Afrotheria", line=dict(color="magenta"), ) fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() tree = reader("data/tree-with-support.json") fig = tree.get_figure(show_support=True, threshold=0.8) fig.scale_bar = None fig.show(width=500, height=400) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.support_xshift = 15 fig.support_yshift = 0 fig.show(width=500, height=400) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-support.png" fig.write(outpath) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = { "hum": "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", "mus": "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", "rat": "CTGAACAAGCAGCCACTTTCAAACAAGAAA", } unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") unaligned_DNA [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_aa = unaligned_DNA.get_translation() unaligned_aa [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_aa_seqs = { "hum": "KQIQESSENGSLAARQERQAQVNLT", "mus": "KQIQESGESGSLAARQERQAQVNLT", "rat": "LNKQ------PLS---------NKK", } aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA) aligned_DNA [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.cluster.UPGMA import upgma from cogent3.evolve import distance [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/test.paml") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster = upgma(d.get_pairwise_distances()) print(mycluster.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster.write("test_upgma.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_upgma.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.phylo import nj [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=get_model("HKY85")) d.run(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree = nj.nj(d.get_pairwise_distances(), show_progress=False) print(mytree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree.write("test_nj.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_nj.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) d.get_pairwise_distances() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d.write("dists_for_phylo.phylip", format="phylip") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os for file_name in "dists_for_phylo.phylip", "dists_for_phylo.pickle": os.remove(file_name) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:48: WARNING: TODO entry found: write out in json format /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tf = get_model("GY94") nf = get_model("MG94GTR") cnf = get_model("CNFGTR") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = load_tree("data/primate_brca1.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:64: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_param_rule("omega", is_constant=True, value=1.0) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: optimiser_args = dict( local=True, max_restarts=5, tolerance=1e-8, show_progress=False ) lf.set_alignment(aln) lf.optimise(**optimiser_args) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: neutral_lnL = lf.get_log_likelihood() neutral_nfp = lf.get_num_free_params() lf.set_param_rule("omega", is_constant=False) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from scipy.stats.distributions import chi2 LR = 2 * (non_neutral_lnL - neutral_lnL) df = non_neutral_nfp - neutral_nfp print(chi2.sf(LR, df)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:114: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Chimpanzee", "Human"], outgroup_name="Galago", clade=True ) lf.optimise(**optimiser_args) lf chimp_human_clade_lnL = lf.get_log_likelihood() chimp_human_clade_nfp = lf.get_num_free_params() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:124: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (chimp_human_clade_lnL - non_neutral_lnL) df = chimp_human_clade_nfp - non_neutral_nfp print(chi2.sf(LR, df)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:149: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: annot_tree = lf.get_annotated_tree() omega_mle = lf.get_param_value("omega") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf = cnf.make_likelihood_function( annot_tree, bins=["neutral", "adaptive"], digits=2, space=3 ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("omega", bin="neutral", upper=1, init=omega_mle) rate_lf.set_param_rule( "omega", bin="adaptive", lower=1 + epsilon, upper=100, init=1 + 2 * epsilon ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:179: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("bprobs", init=[1 - epsilon, epsilon]) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:185: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_alignment(aln) rate_lf.optimise(**optimiser_args) rate_lnL = rate_lf.get_log_likelihood() rate_nfp = rate_lf.get_num_free_params() LR = 2 * (rate_lnL - non_neutral_lnL) df = rate_nfp - non_neutral_nfp rate_lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(chi2.sf(LR, df)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pp = rate_lf.get_bin_probs() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from IPython.core.display import HTML from numpy import array from cogent3 import make_table header = ["Site Class", "Proportion", "Background Edges", "Foreground Edges"] data = { "Site Class": array(["0", "1", "2a", "2b"], dtype=" 1", "0 < omega0 < 1"], dtype=" 1.8: tips_to_delete.append(n) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/manipulating_tree_nodes.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tips_to_delete: n.parent.remove(n) complex_tree.prune() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/manipulating_tree_nodes.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(complex_tree.ascii_art(show_internal=False)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from scipy.stats.distributions import chi2 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree("data/test.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("MG94GTR") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=2) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(al) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(global_tolerance=1.0, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: at = lf.get_annotated_tree() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = chi2.sf(LR, df) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(f"Likelihood ratio statistic = {LR}") print(f"degrees-of-freedom = {df}") print(f"probability = {P}") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve import bootstrap from cogent3.evolve.models import HKY85 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_alt_function(): t = load_tree("data/test.tree") sm = HKY85() return sm.make_likelihood_function(t) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_null_function(): lf = create_alt_function() # set the local clock for humans & howler monkey lf.set_local_clock("Human", "HowlerMon") return lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP = bootstrap.EstimateProbability( create_null_function(), create_alt_function(), aln ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.set_num_replicates(5) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.run(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: p = estimateP.get_estimated_prob() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("%.2f, %.2f" % estimateP.get_observed_lnL()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import numpy numpy.random.seed(11) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy t = numpy.arange(0, 10, 0.1) n = numpy.random.randn(len(t)) nse = numpy.convolve(n, numpy.exp(-t / 0.05)) * 0.1 nse = nse[: len(t)] sig = numpy.sin(2 * numpy.pi * t) + nse [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import dft pwr, period = dft(sig) print(period) print(pwr) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pwr = abs(pwr) max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr pwr, period = auto_corr(sig) print(period) print(pwr) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s = ( "ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG" "GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT" "AATTTTTAACCGCGGAATTGCGTC" ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"]) symbols = seq_to_symbols(s) len(symbols) == len(s) symbols [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import ipdft powers, periods = ipdft(symbols) powers [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:123: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr, hybrid powers, periods = auto_corr(symbols) powers [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = hybrid(symbols) powers [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:139: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:151: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel pwr = goertzel(sig, 10) print(pwr) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = auto_corr(symbols) llim = 2 period5 = 5 - llim periods[period5] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers[period5] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel period = 4 power = goertzel(symbols, period) ipdft_powers, periods = ipdft(symbols) ipdft_power = abs(ipdft_powers[period - llim]) round(power, 6) == round(ipdft_power, 6) power [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:191: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: power = hybrid(symbols, period=period) power [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:204: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Goertzel goertzel_calc = Goertzel(len(sig), period=10) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap obs_stat, p = blockwise_bootstrap( sig, calc=goertzel_calc, block_size=10, num_reps=1000 ) print(obs_stat) print(p) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Hybrid hybrid_calculator = Hybrid(len(s), period=4) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"], length=len(s)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:248: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap stat, p = blockwise_bootstrap( s, calc=hybrid_calculator, block_size=10, num_reps=1000, seq_to_symbols=seq_to_symbols, ) print(stat) p < 0.1 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pickle from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.evolve.fast_distance import DistanceMatrix from cogent3.evolve.models import HKY85 al = load_aligned_seqs("data/long_testseqs.fasta") d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle from cogent3.phylo import least_squares [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: with open("dists_for_phylo.pickle", "rb") as f: dists = pickle.load(f) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls = least_squares.WLS(dists) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls_distance_matrix = least_squares.WLS(DistanceMatrix(dists)) ls_pairwise_matrix = least_squares.WLS(dists.to_dict()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: score, tree = ls.trex(a=5, k=1, show_progress=False) assert score < 1e-4 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trees = ls.trex(a=5, k=5, return_all=True, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:85: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(len(trees)) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls_stats = [tree[0] for tree in trees] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:103: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: t1 = trees[0][1].balanced() t2 = trees[1][1].balanced() print(t1.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(t2.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree query_tree = make_tree( "((Human:.2,DogFaced:.2):.3,(NineBande:.1, Mouse:.5):.2,HowlerMon:.1)" ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.evaluate_tree(query_tree) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:136: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls, t = ls.evaluate_topology(query_tree) assert "%.4f" % wls == "0.0084" [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:148: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("dists_for_phylo.pickle") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.substitution_model import TimeReversibleNucleotide [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide(equal_motif_probs=True) tree = load_tree("data/test.tree") lf = model.make_likelihood_function(tree) lf.set_param_rule("length", value=0.6, is_constant=True) aln1 = lf.simulate_alignment(sequence_length=10000) lf.set_param_rule("length", value=0.2, is_constant=True) aln2 = lf.simulate_alignment(sequence_length=10000) aln3 = aln1 + aln2 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="free" ) lf = model.make_likelihood_function(tree, bins=2, digits=2, space=3) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = [t for t in lf.get_statistics() if "bin" in t.title][0] bprobs [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="gamma" ) lf = model.make_likelihood_function(tree, bins=4) lf.set_param_rule("bprobs", is_constant=True) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from scipy.stats.distributions import chi2 [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree(filename="data/test.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("HKY85") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=3) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_local_clock("Human", "HowlerMon") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("clock") lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:84: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("non clock") lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = chi2.sf(LR, df) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("Likelihood ratio statistic = ", LR) print("degrees-of-freedom = ", df) print("probability = ", P) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import MG94HKY aln = load_aligned_seqs("data/long_testseqs.fasta") tree = load_tree("data/test.tree") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = MG94HKY() lf = sm.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tree.ascii_art()) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["DogFaced", "Mouse"], outgroup_name="Human", init=2.0, clade=True, ) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", init=1.0) lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=False, ) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=True, ) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, value=1.0, is_constant=True, ) lf.optimise(local=True, show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_constant=False, ) lf.optimise(local=True, show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:194: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_independent=True, ) lf.optimise(local=True, show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) lf.optimise(local=True, show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simple.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simple.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_tree from cogent3.evolve.models import get_model model = get_model("HKY85") aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") tree = make_tree(tip_names=aln.names) lf = model.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import sys from cogent3 import make_tree from cogent3.evolve.models import get_model [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: t = make_tree("(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);") [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("F81") lf = sm.make_likelihood_function(t) lf.set_constant_lengths() lf.set_motif_probs(dict(A=0.1, C=0.2, G=0.3, T=0.4)) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simulated = lf.simulate_alignment(sequence_length=1000) simulated [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_table, make_tree from cogent3.evolve.models import HKY85 from scipy.stats.distributions import chi2 from cogent3.recalculation.scope import ALL, EACH aln = load_aligned_seqs("data/long_testseqs.fasta") half = len(aln) // 2 aln1 = aln[:half] aln2 = aln[half:] [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: loci_names = ["1st-half", "2nd-half"] loci = [aln1, aln2] tree = make_tree(tip_names=aln.names) mod = HKY85() [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = mod.make_likelihood_function(tree, loci=loci_names, digits=2, space=3) lf.set_param_rule("length", is_independent=False) lf.set_param_rule("kappa", loci=ALL) lf.set_alignment(loci) lf.optimise(show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_lnL = lf.lnL all_nfp = lf.nfp lf.set_param_rule("kappa", loci=EACH) lf.optimise(show_progress=False) lf [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: each_lnL = lf.lnL each_nfp = lf.nfp LR = 2 * (each_lnL - all_lnL) df = each_nfp - all_nfp [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:62: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: make_table( header=["LR", "df", "p"], rows=[[LR, df, chi2.sf(LR, df)]], digits=2, space=3, ) [docutils] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/templates/class.rst:3: ERROR: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} [docutils] WARNING: invalid signature for autoclass ('{{ name }}') [autodoc] WARNING: don't know which module to import for autodocumenting '{{ name }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) [autodoc] looking for now-outdated files... none found pickling environment... done checking consistency... 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[ 65%] community writing output... [ 65%] cookbook/DNA_and_RNA_sequences writing output... [ 66%] cookbook/alignments writing output... [ 66%] cookbook/alphabet writing output... [ 67%] cookbook/annotation_db writing output... [ 68%] cookbook/building_alignments writing output... [ 68%] cookbook/building_phylogenies writing output... [ 69%] cookbook/calc_genetic_distance writing output... [ 69%] cookbook/evo_modelling writing output... [ 70%] cookbook/features writing output... [ 70%] cookbook/genetic_code writing output... [ 71%] cookbook/index writing output... [ 72%] cookbook/loading_sequences writing output... [ 72%] cookbook/loading_tabular writing output... [ 73%] cookbook/manipulating_biological_data writing output... [ 73%] cookbook/moltypes writing output... [ 74%] cookbook/protein_sequences writing output... [ 74%] cookbook/simple_trees writing output... [ 75%] cookbook/tables writing output... [ 76%] cookbook/union_dict writing output... [ 76%] cookbook/useful_utilities writing output... [ 77%] cookbook/what_codes writing output... [ 77%] data_file_links writing output... [ 78%] draw/aln/plot_aln-coevolution writing output... [ 78%] draw/aln/plot_aln-dotplot-1 writing output... [ 79%] draw/aln/plot_aln-dotplot-2 writing output... [ 80%] draw/aln/plot_aln-dotplot-3 writing output... [ 80%] draw/aln/plot_aln-gaps-per-seq writing output... [ 81%] draw/aln/plot_aln-info-plot writing output... [ 81%] draw/aln/plot_aln-seqlogo writing output... [ 82%] draw/aln/plot_seq-features writing output... [ 82%] draw/index writing output... [ 83%] draw/tree/plot_tree-angular writing output... [ 84%] draw/tree/plot_tree-circular writing output... [ 84%] draw/tree/plot_tree-radial writing output... [ 85%] draw/tree/plot_tree-square writing output... [ 85%] draw/tree/plot_tree-support writing output... [ 86%] examples/align_codons_to_protein writing output... [ 86%] examples/calculate_UPGMA_cluster writing output... [ 87%] examples/calculate_neigbourjoining_tree writing output... [ 88%] examples/calculate_pairwise_distances writing output... [ 88%] examples/codon_models writing output... [ 89%] examples/coevolution writing output... [ 89%] examples/empirical_protein_models writing output... [ 90%] examples/hmm_par_heterogeneity writing output... [ 90%] examples/index writing output... [ 91%] examples/manipulating_tree_nodes writing output... [ 91%] examples/neutral_test writing output... [ 92%] examples/parallel writing output... [ 93%] examples/parametric_bootstrap writing output... [ 93%] examples/period_estimation writing output... [ 94%] examples/phylo_by_ls writing output... [ 94%] examples/rate_heterogeneity writing output... [ 95%] examples/relative_rate writing output... [ 95%] examples/scope_model_params_on_trees writing output... [ 96%] examples/simple writing output... [ 97%] examples/simulate_alignment writing output... [ 97%] examples/testing_multi_loci writing output... [ 98%] index writing output... [ 98%] install writing output... [ 99%] licenses writing output... [ 99%] pycogent writing output... [100%] templates/class generating indices... genindex done copying linked files... copying notebooks ... writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 1169 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. make[2]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc' # remove superfluous files and dirs find doc/_build -name "*.doctree*" -delete rm -f doc/_build/html/_sources/COGENT_LICENSE.txt rm -f doc/_build/html/_static/jquery.js rm -f doc/_build/html/_static/underscore.js rm -rf doc/_build/html/_images/math/ make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: cp -r /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/tests/data /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build I: pybuild base:311: cd /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build; python3.13 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip' ============================= test session starts ============================== platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 rootdir: /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build configfile: pyproject.toml plugins: xdist-3.8.0, typeguard-4.4.4, cov-5.0.0, anyio-4.8.0 collected 11030 items / 4 deselected / 11026 selected tests/test_align/test_align.py ...............................X... 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[ 98%] tests/test_util/test_recode_alignment.py ............... [ 98%] tests/test_util/test_table.py ....F..................................... [ 99%] ............................................................... [ 99%] tests/test_util/test_transform.py ..... [ 99%] tests/test_util/test_union_dict.py ........... [ 99%] tests/test_util/test_warning.py ......................... [100%] =================================== FAILURES =================================== ____________________ TableTests.test_cast_str_to_numerical _____________________ self = def test_cast_str_to_numerical(self): """correctly converts a series of strings to numeric values""" d = arange(4, step=0.1) r = cast_str_to_numeric(d) assert_equal(d, r) with numpy.testing.suppress_warnings() as sup: # we know that converting to real loses imaginary > sup.filter(numpy.ComplexWarning) ^^^^^^^^^^^^^^^^^^^^ /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/tests/test_util/test_table.py:1769: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ attr = 'ComplexWarning' def __getattr__(attr): # Warn for expired attributes import warnings if attr == "linalg": import numpy.linalg as linalg return linalg elif attr == "fft": import numpy.fft as fft return fft elif attr == "dtypes": import numpy.dtypes as dtypes return dtypes elif attr == "random": import numpy.random as random return random elif attr == "polynomial": import numpy.polynomial as polynomial return polynomial elif attr == "ma": import numpy.ma as ma return ma elif attr == "ctypeslib": import numpy.ctypeslib as ctypeslib return ctypeslib elif attr == "exceptions": import numpy.exceptions as exceptions return exceptions elif attr == "testing": import numpy.testing as testing return testing elif attr == "matlib": import numpy.matlib as matlib return matlib elif attr == "f2py": import numpy.f2py as f2py return f2py elif attr == "typing": import numpy.typing as typing return typing elif attr == "rec": import numpy.rec as rec return rec elif attr == "char": import numpy.char as char return char elif attr == "array_api": raise AttributeError("`numpy.array_api` is not available from " "numpy 2.0 onwards", name=None) elif attr == "core": import numpy.core as core return core elif attr == "strings": import numpy.strings as strings return strings elif attr == "distutils": if 'distutils' in __numpy_submodules__: import numpy.distutils as distutils return distutils else: raise AttributeError("`numpy.distutils` is not available from " "Python 3.12 onwards", name=None) if attr in __future_scalars__: # And future warnings for those that will change, but also give # the AttributeError warnings.warn( f"In the future `np.{attr}` will be defined as the " "corresponding NumPy scalar.", FutureWarning, stacklevel=2) if attr in __former_attrs__: raise AttributeError(__former_attrs__[attr], name=None) if attr in __expired_attributes__: raise AttributeError( f"`np.{attr}` was removed in the NumPy 2.0 release. " f"{__expired_attributes__[attr]}", name=None ) if attr == "chararray": warnings.warn( "`np.chararray` is deprecated and will be removed from " "the main namespace in the future. Use an array with a string " "or bytes dtype instead.", DeprecationWarning, stacklevel=2) import numpy.char as char return char.chararray > raise AttributeError("module {!r} has no attribute " "{!r}".format(__name__, attr)) E AttributeError: module 'numpy' has no attribute 'ComplexWarning' /usr/lib/python3/dist-packages/numpy/__init__.py:414: AttributeError =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1533 /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1533: PytestConfigWarning: No files were found in testpaths; consider removing or adjusting your testpaths configuration. Searching recursively from the current directory instead. self.args, self.args_source = self._decide_args( tests/test_align/test_align.py: 1360 warnings tests/test_app/test_align.py: 550 warnings tests/test_app/test_dist.py: 90 warnings /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/maths/markov.py:35: DeprecationWarning: numpy.core is deprecated and has been renamed to numpy._core. The numpy._core namespace contains private NumPy internals and its use is discouraged, as NumPy internals can change without warning in any release. In practice, most real-world usage of numpy.core is to access functionality in the public NumPy API. If that is the case, use the public NumPy API. If not, you are using NumPy internals. If you would still like to access an internal attribute, use numpy._core.multiarray. matrix = numpy.core.multiarray.dot(matrix, matrix) tests/test_app/test_evo.py: 27 warnings tests/test_app/test_result.py: 3 warnings /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/evolve/likelihood_function.py:1064: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments. To learn more, see the migration guide https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword child_mprobs = numpy.dot(mprobs, psub) tests/test_app/test_evo.py: 27 warnings /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/maths/matrix_exponential_integration.py:102: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments. To learn more, see the migration guide https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword result = -dot(dot(p0, iexpm(t)), diag(Q)) tests/test_evolve/test_distance.py: 16900 warnings /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/maths/markov.py:35: DeprecationWarning: numpy.core is deprecated and has been renamed to numpy._core. The numpy._core namespace contains private NumPy internals and its use is discouraged, as NumPy internals can change without warning in any release. In practice, most real-world usage of numpy.core is to access functionality in the public NumPy API. If that is the case, use the public NumPy API. If not, you are using NumPy internals. If you would still like to access an internal attribute, use numpy._core.multiarray. tests/test_evolve/test_likelihood_function.py: 32 warnings tests/test_evolve/test_newq.py: 5 warnings tests/test_evolve/test_ns_substitution_model.py: 6 warnings /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/evolve/likelihood_function.py:1064: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments. To learn more, see the migration guide https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword tests/test_evolve/test_likelihood_function.py: 12 warnings /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/maths/matrix_exponential_integration.py:102: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments. To learn more, see the migration guide https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword tests/test_maths/test_stats/test_test.py::StatTests::test_t_two_sample_switch /usr/lib/python3/dist-packages/numpy/_core/_methods.py:223: RuntimeWarning: Degrees of freedom <= 0 for slice tests/test_util/test_deserialise.py::test_convert_annotation_to_annotation_db tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deser_annotated_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/cogent3/util/warning.py:226: DeprecationWarning: class Map is discontinued and will be removed in version 2024.6 reason='Replaced by IndelMap and FeatureMap' tests/test_util/test_dictarray.py::DictArrayTest::test_numpy_ops /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/tests/test_util/test_dictarray.py:145: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments. To learn more, see the migration guide https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword tests/test_util/test_dictarray.py::DictArrayTest::test_numpy_ops /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build/tests/test_util/test_dictarray.py:146: DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments. To learn more, see the migration guide https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_util/test_table.py::TableTests::test_cast_str_to_numerical = 1 failed, 11013 passed, 9 skipped, 4 deselected, 1 xfailed, 2 xpassed, 19022 warnings in 762.01s (0:12:42) = E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=1: cd /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.13_cogent3/build; python3.13 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip' dh_auto_test: error: pybuild --test -i python{version} -p 3.13 returned exit code 13 make: *** [debian/rules:20: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/553802 and its subdirectories python-cogent failed to build from source. removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/python-cogent_2024.5.7a1+dfsg-3.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/python-cogent_2024.5.7a1+dfsg-3.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/python-cogent_2024.5.7a1+dfsg-3.build1.log.gz' Sun Sep 14 23:49:38 UTC 2025 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 87.9% -- replaced with stdout INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-14 23:49:38] INFO: Starting at 2025-09-14 23:49:38.784621 [2025-09-14 23:49:38] INFO: Generating the pages of 1 package(s) [2025-09-14 23:49:39] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/python-cogent didn't produce a buildlog, even though it has been built. [2025-09-14 23:49:39] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/python-cogent_2024.5.7a1+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/python-cogent_2024.5.7a1+dfsg-3.diff.gz is missing [2025-09-14 23:49:39] INFO: Finished at 2025-09-14 23:49:39.084898, took: 0:00:00.300280 Sun Sep 14 23:49:39 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/python-cogent.html Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/python-cogent_2024.5.7a1+dfsg-3.rbuild.log: 87.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/python-cogent_2024.5.7a1+dfsg-3.rbuild.log.gz [2025-09-14 23:49:39] INFO: Starting at 2025-09-14 23:49:39.428936 [2025-09-14 23:49:39] INFO: Generating the pages of 1 package(s) [2025-09-14 23:49:39] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/python-cogent_2024.5.7a1+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/python-cogent_2024.5.7a1+dfsg-3.diff.gz is missing [2025-09-14 23:49:39] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/python-cogent_2024.5.7a1+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/python-cogent_2024.5.7a1+dfsg-3.diff.gz is missing [2025-09-14 23:49:39] INFO: Finished at 2025-09-14 23:49:39.713904, took: 0:00:00.284971 All cleanup done. Sun Sep 14 23:49:39 UTC 2025 - total duration: 0h 25m 35s. Sun Sep 14 23:49:39 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-nr94JM1Q, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 25min 36.294s CPU time consumed: 3.429s Memory peak: 46.5M (swap: 0B)