I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 13 17:09:00 -12 2026 I: pbuilder-time-stamp: 1776143340 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 [pybel_0.15.5-1.dsc] I: copying [./pybel_0.15.5.orig.tar.gz] I: copying [./pybel_0.15.5-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./pybel_0.15.5-1.dsc: unsupported subcommand dpkg-source: info: extracting pybel in pybel-0.15.5 dpkg-source: info: unpacking pybel_0.15.5.orig.tar.gz dpkg-source: info: unpacking pybel_0.15.5-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying not_testing_what_fails.patch dpkg-source: info: applying more_click_is_not_packaged.patch dpkg-source: info: applying remove_psycopg2-binary I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/719667/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=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='8521abf7d51c4bd190f5aea78a5fc05d' 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='719667' 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.xGJSeeCo/pbuilderrc_Xeed --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.xGJSeeCo/b1 --logfile b1/build.log pybel_0.15.5-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/719667/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: debhelper-compat (= 13), dh-sequence-python3, pybuild-plugin-pyproject, python3-all, python3-setuptools, python3-click-plugins, python3-humanize, python3-jinja2, python3-jsonschema, python3-networkx, python3-pandas, python3-pyparsing, python3-pystow, python3-pytest, python3-ratelimit, python3-requests-file, python3-sqlalchemy, python3-tabulate, python3-tqdm, python3-bioregistry, python3-bel-resources dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19783 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 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 pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-click-plugins; however: Package python3-click-plugins is not installed. pbuilder-satisfydepends-dummy depends on python3-humanize; however: Package python3-humanize is not installed. pbuilder-satisfydepends-dummy depends on python3-jinja2; however: Package python3-jinja2 is not installed. pbuilder-satisfydepends-dummy depends on python3-jsonschema; however: Package python3-jsonschema is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-pyparsing; however: Package python3-pyparsing is not installed. pbuilder-satisfydepends-dummy depends on python3-pystow; however: Package python3-pystow is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-ratelimit; however: Package python3-ratelimit is not installed. pbuilder-satisfydepends-dummy depends on python3-requests-file; however: Package python3-requests-file is not installed. pbuilder-satisfydepends-dummy depends on python3-sqlalchemy; however: Package python3-sqlalchemy is not installed. pbuilder-satisfydepends-dummy depends on python3-tabulate; however: Package python3-tabulate is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-bioregistry; however: Package python3-bioregistry is not installed. pbuilder-satisfydepends-dummy depends on python3-bel-resources; however: Package python3-bel-resources 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: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} pybuild-plugin-pyproject{a} python3{a} python3-all{a} python3-annotated-types{a} python3-attr{a} python3-autocommand{a} python3-bel-resources{a} python3-bioregistry{a} python3-build{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-click{a} python3-click-plugins{a} python3-curies{a} python3-dateutil{a} python3-dnspython{a} python3-email-validator{a} python3-greenlet{a} python3-humanize{a} python3-idna{a} python3-inflect{a} python3-iniconfig{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-multisplitby{a} python3-networkx{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pluggy{a} python3-pydantic{a} python3-pydantic-core{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pystow{a} python3-pytest{a} python3-pytz{a} python3-ratelimit{a} python3-referencing{a} python3-requests{a} python3-requests-file{a} python3-rpds-py{a} python3-setuptools{a} python3-sortedcontainers{a} python3-sqlalchemy{a} python3-tabulate{a} python3-toml{a} python3-tqdm{a} python3-trie{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-urllib3{a} python3-wheel{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-babel python3-bottleneck python3-bs4 python3-cryptography python3-fqdn python3-gdal python3-h2 python3-html5lib python3-httpcore python3-httpx python3-isoduration python3-json-pointer python3-lxml python3-matplotlib python3-numba python3-numexpr python3-odf python3-openpyxl python3-pydot python3-pygments python3-pygraphviz python3-rfc3339-validator python3-rfc3986-validator python3-rfc3987 python3-scipy python3-sqlalchemy-ext python3-tables python3-uritemplate python3-webcolors python3-yaml wget 0 packages upgraded, 115 newly installed, 0 to remove and 0 not upgraded. Need to get 68.9 MB of archives. After unpacking 331 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-2 [27.1 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 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-2 [28.1 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [138 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5084 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 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 2.13.0-1 [1420 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 43 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250308 [115 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.45.1-1 [56.7 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.2-1 [36.0 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 6.20250308 [11.7 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.2-2 [1044 B] Get: 61 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 python3-annotated-types all 0.7.0-1 [18.8 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.1.0-1 [68.7 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 python3-multisplitby all 0.0.1-6 [4688 B] Get: 66 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 67 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 python3-requests-file all 2.1.0-1 [6600 B] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-click all 8.2.0+0.really.8.1.8-1 [95.4 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-bel-resources all 0.0.3-4 [13.5 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-pydantic-core amd64 2.27.2-1+b2 [1502 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 python3-dnspython all 2.7.0-1 [164 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 python3-email-validator all 2.2.0-1 [31.6 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-pydantic amd64 2.10.6-1 [346 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-trie all 0.4.0+ds-1 [7640 B] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-curies all 0.9.0-1 [38.3 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.67.1-2 [91.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 python3-pystow all 0.5.5-1 [25.6 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 python3-bioregistry all 0.11.12-3 [3907 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 python3-click-plugins all 1.1.1-5 [10.1 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 python3-greenlet amd64 3.1.0-1+b2 [165 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-humanize all 4.12.1-1 [52.9 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 93 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.8.0-1 [724 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 99 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 python3-rpds-py amd64 0.21.0-2+b1 [257 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 python3-referencing all 0.35.1-2 [23.5 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 104 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema all 4.19.2-6 [71.4 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 106 http://deb.debian.org/debian unstable/main amd64 python3-pytz all 2025.1-3 [150 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2025.1-3 [4004 B] Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-8+b1 [4517 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-8 [3097 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.5-1 [250 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 python3-ratelimit all 2.2.1-2 [6108 B] Get: 114 http://deb.debian.org/debian unstable/main amd64 python3-sqlalchemy all 2.0.32+ds1-1 [1196 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Fetched 68.9 MB in 4s (15.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal: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 ... 19783 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... 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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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up python3-bel-resources (0.0.3-4) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up python3-jsonschema (4.19.2-6) ... Processing triggers for libc-bin (2.41-4) ... Processing triggers for ca-certificates (20241223) ... 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/pybel-0.15.5/ && 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 > ../pybel_0.15.5-1_source.changes dpkg-buildpackage: info: source package pybel dpkg-buildpackage: info: source version 0.15.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from pybel-0.15.5/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/pybel-0.15.5' dh_auto_clean rm -rf src/PyBEL.egg-info/ src/pybel.egg-info/ make[1]: Leaving directory '/build/reproducible-path/pybel-0.15.5' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --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/pybel-0.15.5/.pybuild/cpython3_3.13_pybel * Building wheel... running bdist_wheel running build running build_py creating build/lib/pybel copying src/pybel/grounding.py -> build/lib/pybel copying src/pybel/exceptions.py -> build/lib/pybel copying src/pybel/config.py -> build/lib/pybel copying src/pybel/language.py -> build/lib/pybel copying src/pybel/repository.py -> build/lib/pybel copying src/pybel/typing.py -> build/lib/pybel copying src/pybel/version.py -> build/lib/pybel copying src/pybel/tokens.py -> build/lib/pybel copying src/pybel/canonicalize.py -> build/lib/pybel copying src/pybel/__init__.py -> build/lib/pybel copying src/pybel/utils.py -> build/lib/pybel copying src/pybel/constants.py -> build/lib/pybel copying src/pybel/cli.py -> build/lib/pybel copying src/pybel/__main__.py -> build/lib/pybel creating build/lib/pybel/testing copying src/pybel/testing/mock_manager.py -> build/lib/pybel/testing copying src/pybel/testing/cases.py -> build/lib/pybel/testing copying src/pybel/testing/mocks.py -> build/lib/pybel/testing copying src/pybel/testing/__init__.py -> build/lib/pybel/testing copying src/pybel/testing/utils.py -> build/lib/pybel/testing copying src/pybel/testing/constants.py -> build/lib/pybel/testing copying src/pybel/testing/generate.py -> build/lib/pybel/testing creating build/lib/pybel/examples copying src/pybel/examples/various_example.py -> build/lib/pybel/examples copying src/pybel/examples/egf_example.py -> build/lib/pybel/examples copying src/pybel/examples/sialic_acid_example.py -> build/lib/pybel/examples copying src/pybel/examples/tloc_example.py -> build/lib/pybel/examples copying src/pybel/examples/__init__.py -> build/lib/pybel/examples copying src/pybel/examples/ampk_example.py -> build/lib/pybel/examples copying src/pybel/examples/statin_example.py -> build/lib/pybel/examples copying src/pybel/examples/vegf_example.py -> build/lib/pybel/examples copying src/pybel/examples/homology_example.py -> build/lib/pybel/examples copying src/pybel/examples/braf_example.py -> build/lib/pybel/examples creating build/lib/pybel/struct copying src/pybel/struct/getters.py -> build/lib/pybel/struct copying src/pybel/struct/__init__.py -> build/lib/pybel/struct copying src/pybel/struct/utils.py -> build/lib/pybel/struct copying src/pybel/struct/node_utils.py -> build/lib/pybel/struct copying src/pybel/struct/graph.py -> build/lib/pybel/struct copying src/pybel/struct/operations.py -> build/lib/pybel/struct creating build/lib/pybel/manager copying src/pybel/manager/cache_manager.py -> build/lib/pybel/manager copying src/pybel/manager/database_io.py -> build/lib/pybel/manager copying src/pybel/manager/base_manager.py -> build/lib/pybel/manager copying src/pybel/manager/exc.py -> build/lib/pybel/manager copying src/pybel/manager/models.py -> build/lib/pybel/manager copying src/pybel/manager/citation_utils.py -> build/lib/pybel/manager copying src/pybel/manager/lookup_manager.py -> build/lib/pybel/manager copying src/pybel/manager/__init__.py -> build/lib/pybel/manager copying src/pybel/manager/make_json_serializable.py -> build/lib/pybel/manager copying src/pybel/manager/utils.py -> build/lib/pybel/manager copying src/pybel/manager/query_manager.py -> build/lib/pybel/manager creating build/lib/pybel/resources copying src/pybel/resources/update_resources.py -> build/lib/pybel/resources copying src/pybel/resources/resources.py -> build/lib/pybel/resources copying src/pybel/resources/__init__.py -> build/lib/pybel/resources copying src/pybel/resources/constants.py -> build/lib/pybel/resources creating build/lib/pybel/parser copying src/pybel/parser/parse_concept.py -> build/lib/pybel/parser copying src/pybel/parser/parse_metadata.py -> build/lib/pybel/parser copying src/pybel/parser/__init__.py -> build/lib/pybel/parser copying src/pybel/parser/parse_bel.py -> build/lib/pybel/parser copying src/pybel/parser/baseparser.py -> build/lib/pybel/parser copying src/pybel/parser/utils.py -> build/lib/pybel/parser copying src/pybel/parser/constants.py -> build/lib/pybel/parser copying src/pybel/parser/parse_control.py -> build/lib/pybel/parser creating build/lib/pybel/dsl copying src/pybel/dsl/namespaces.py -> build/lib/pybel/dsl copying src/pybel/dsl/node_classes.py -> build/lib/pybel/dsl copying src/pybel/dsl/exc.py -> build/lib/pybel/dsl copying src/pybel/dsl/__init__.py -> build/lib/pybel/dsl copying src/pybel/dsl/constants.py -> build/lib/pybel/dsl copying src/pybel/dsl/edges.py -> build/lib/pybel/dsl creating build/lib/pybel/schema copying src/pybel/schema/__init__.py -> build/lib/pybel/schema creating build/lib/pybel/io copying src/pybel/io/neo4j.py -> build/lib/pybel/io copying src/pybel/io/umbrella_nodelink.py -> build/lib/pybel/io copying src/pybel/io/pykeen.py -> build/lib/pybel/io copying src/pybel/io/jgif.py -> build/lib/pybel/io copying src/pybel/io/exc.py -> build/lib/pybel/io copying src/pybel/io/extras.py -> build/lib/pybel/io copying src/pybel/io/nodelink.py -> build/lib/pybel/io copying src/pybel/io/gpickle.py -> build/lib/pybel/io copying src/pybel/io/line_utils.py -> build/lib/pybel/io copying src/pybel/io/graphdati.py -> build/lib/pybel/io copying src/pybel/io/spia.py -> build/lib/pybel/io copying src/pybel/io/biodati_client.py -> build/lib/pybel/io copying src/pybel/io/emmaa.py -> build/lib/pybel/io copying src/pybel/io/lines.py -> build/lib/pybel/io copying src/pybel/io/__init__.py -> build/lib/pybel/io copying src/pybel/io/bel_commons_client.py -> build/lib/pybel/io copying src/pybel/io/sbel.py -> build/lib/pybel/io copying src/pybel/io/utils.py -> build/lib/pybel/io copying src/pybel/io/aws.py -> build/lib/pybel/io copying src/pybel/io/indra.py -> build/lib/pybel/io copying src/pybel/io/hipathia.py -> build/lib/pybel/io copying src/pybel/io/graphml.py -> build/lib/pybel/io copying src/pybel/io/pynpa.py -> build/lib/pybel/io copying src/pybel/io/jinja_utils.py -> build/lib/pybel/io copying src/pybel/io/cx.py -> build/lib/pybel/io copying src/pybel/io/api.py -> build/lib/pybel/io copying src/pybel/io/fraunhofer_orientdb.py -> build/lib/pybel/io creating build/lib/pybel/struct/query copying src/pybel/struct/query/exc.py -> build/lib/pybel/struct/query copying src/pybel/struct/query/__init__.py -> build/lib/pybel/struct/query copying src/pybel/struct/query/constants.py -> build/lib/pybel/struct/query copying src/pybel/struct/query/seeding.py -> build/lib/pybel/struct/query copying src/pybel/struct/query/query.py -> build/lib/pybel/struct/query copying src/pybel/struct/query/selection.py -> build/lib/pybel/struct/query creating build/lib/pybel/struct/filters copying src/pybel/struct/filters/node_predicate_builders.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/typing.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/__init__.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/utils.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/node_filters.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/edge_predicates.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/edge_predicate_builders.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/edge_filters.py -> build/lib/pybel/struct/filters creating build/lib/pybel/struct/summary copying src/pybel/struct/summary/errors.py -> build/lib/pybel/struct/summary copying src/pybel/struct/summary/provenance.py -> build/lib/pybel/struct/summary copying src/pybel/struct/summary/edge_summary.py -> build/lib/pybel/struct/summary copying src/pybel/struct/summary/supersummary.py -> build/lib/pybel/struct/summary copying src/pybel/struct/summary/__init__.py -> build/lib/pybel/struct/summary copying src/pybel/struct/summary/node_summary.py -> build/lib/pybel/struct/summary creating build/lib/pybel/struct/mutation copying src/pybel/struct/mutation/induction_expansion.py -> build/lib/pybel/struct/mutation copying src/pybel/struct/mutation/__init__.py -> build/lib/pybel/struct/mutation copying src/pybel/struct/mutation/metadata.py -> build/lib/pybel/struct/mutation copying src/pybel/struct/mutation/utils.py -> build/lib/pybel/struct/mutation creating build/lib/pybel/struct/pipeline copying src/pybel/struct/pipeline/exc.py -> build/lib/pybel/struct/pipeline copying src/pybel/struct/pipeline/__init__.py -> build/lib/pybel/struct/pipeline copying src/pybel/struct/pipeline/decorators.py -> build/lib/pybel/struct/pipeline copying src/pybel/struct/pipeline/pipeline.py -> build/lib/pybel/struct/pipeline creating build/lib/pybel/struct/grouping copying src/pybel/struct/grouping/provenance.py -> build/lib/pybel/struct/grouping copying src/pybel/struct/grouping/__init__.py -> build/lib/pybel/struct/grouping copying src/pybel/struct/grouping/annotations.py -> build/lib/pybel/struct/grouping creating build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/activities.py -> build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/relations.py -> build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/types.py -> build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/__init__.py -> build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/modifications.py -> build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/utils.py -> build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/misc.py -> build/lib/pybel/struct/filters/node_predicates creating build/lib/pybel/struct/mutation/deletion copying src/pybel/struct/mutation/deletion/protein_rna_origins.py -> build/lib/pybel/struct/mutation/deletion copying src/pybel/struct/mutation/deletion/__init__.py -> build/lib/pybel/struct/mutation/deletion copying src/pybel/struct/mutation/deletion/deletion.py -> build/lib/pybel/struct/mutation/deletion creating build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/neighborhood.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/paths.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/random_subgraph.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/__init__.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/utils.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/annotations.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/upstream.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/citation.py -> build/lib/pybel/struct/mutation/induction creating build/lib/pybel/struct/mutation/inference copying src/pybel/struct/mutation/inference/transfer.py -> build/lib/pybel/struct/mutation/inference copying src/pybel/struct/mutation/inference/protein_rna_origins.py -> build/lib/pybel/struct/mutation/inference copying src/pybel/struct/mutation/inference/__init__.py -> build/lib/pybel/struct/mutation/inference creating build/lib/pybel/struct/mutation/expansion copying src/pybel/struct/mutation/expansion/neighborhood.py -> build/lib/pybel/struct/mutation/expansion copying src/pybel/struct/mutation/expansion/__init__.py -> build/lib/pybel/struct/mutation/expansion copying src/pybel/struct/mutation/expansion/upstream.py -> build/lib/pybel/struct/mutation/expansion creating build/lib/pybel/struct/mutation/collapse copying src/pybel/struct/mutation/collapse/protein_rna_origins.py -> build/lib/pybel/struct/mutation/collapse copying src/pybel/struct/mutation/collapse/collapse.py -> build/lib/pybel/struct/mutation/collapse copying src/pybel/struct/mutation/collapse/__init__.py -> build/lib/pybel/struct/mutation/collapse creating build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/location.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/fusion.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/truncation.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/variant.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/gene_modification.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/protein_modification.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/__init__.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/fragment.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/constants.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/protein_substitution.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/gene_substitution.py -> build/lib/pybel/parser/modifiers creating build/lib/pybel/io/tsv copying src/pybel/io/tsv/__init__.py -> build/lib/pybel/io/tsv copying src/pybel/io/tsv/converters.py -> build/lib/pybel/io/tsv copying src/pybel/io/tsv/api.py -> build/lib/pybel/io/tsv creating build/lib/pybel/io/jupyter copying src/pybel/io/jupyter/__init__.py -> build/lib/pybel/io/jupyter copying src/pybel/io/jupyter/inline.py -> build/lib/pybel/io/jupyter copying src/pybel/io/jupyter/visualization.py -> build/lib/pybel/io/jupyter copying src/pybel/io/jupyter/constants.py -> build/lib/pybel/io/jupyter creating build/lib/pybel/io/hetionet copying src/pybel/io/hetionet/__init__.py -> build/lib/pybel/io/hetionet copying src/pybel/io/hetionet/constants.py -> build/lib/pybel/io/hetionet copying src/pybel/io/hetionet/hetionet.py -> build/lib/pybel/io/hetionet copying src/pybel/io/hetionet/cli.py -> build/lib/pybel/io/hetionet copying src/pybel/io/hetionet/__main__.py -> build/lib/pybel/io/hetionet creating build/lib/pybel/io/triples copying src/pybel/io/triples/__init__.py -> build/lib/pybel/io/triples copying src/pybel/io/triples/converters.py -> build/lib/pybel/io/triples copying src/pybel/io/triples/api.py -> build/lib/pybel/io/triples running egg_info creating src/pybel.egg-info writing src/pybel.egg-info/PKG-INFO writing dependency_links to src/pybel.egg-info/dependency_links.txt writing entry points to src/pybel.egg-info/entry_points.txt writing requirements to src/pybel.egg-info/requires.txt writing top-level names to src/pybel.egg-info/top_level.txt writing manifest file 'src/pybel.egg-info/SOURCES.txt' reading manifest file 'src/pybel.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching 'scripts' no previously-included directories found matching 'notebooks' warning: no files found matching '*.bel' under directory 'src/pybel/testing/bel' warning: no files found matching '*.belanno' under directory 'src/pybel/testing/belanno' warning: no files found matching '*.belns' under directory 'src/pybel/testing/belns' warning: no previously-included files matching '*.py[cod]' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '*.dylib' found anywhere in distribution warning: no previously-included files matching '.DS_Store' found anywhere in distribution warning: no previously-included files matching '*.gpickle' found anywhere in distribution warning: no previously-included files found matching '.bumpversion.cfg' warning: no previously-included files found matching '.readthedocs.yml' warning: no previously-included files found matching '.flake8' warning: no previously-included files found matching 'tox.ini' warning: no previously-included files found matching 'CONTRIBUTING.md' warning: no previously-included files found matching 'CHANGELOG.rst' warning: no previously-included files found matching 'AUTHORS.rst' adding license file 'LICENSE' writing manifest file 'src/pybel.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybel.apps' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.apps' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybel.apps' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybel.apps' to be distributed and are already explicitly excluding 'pybel.apps' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybel.io.jupyter.templates' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.io.jupyter.templates' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybel.io.jupyter.templates' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybel.io.jupyter.templates' to be distributed and are already explicitly excluding 'pybel.io.jupyter.templates' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybel.schema.node_types' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.schema.node_types' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybel.schema.node_types' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybel.schema.node_types' to be distributed and are already explicitly excluding 'pybel.schema.node_types' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybel.schema.node_types.variants' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.schema.node_types.variants' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybel.schema.node_types.variants' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybel.schema.node_types.variants' to be distributed and are already explicitly excluding 'pybel.schema.node_types.variants' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybel.schema.node_types.variants.hgvs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.schema.node_types.variants.hgvs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybel.schema.node_types.variants.hgvs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybel.schema.node_types.variants.hgvs' to be distributed and are already explicitly excluding 'pybel.schema.node_types.variants.hgvs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybel.testing.resources.bel' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.testing.resources.bel' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybel.testing.resources.bel' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybel.testing.resources.bel' to be distributed and are already explicitly excluding 'pybel.testing.resources.bel' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybel.testing.resources.belanno' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.testing.resources.belanno' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybel.testing.resources.belanno' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybel.testing.resources.belanno' to be distributed and are already explicitly excluding 'pybel.testing.resources.belanno' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybel.testing.resources.belns' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.testing.resources.belns' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybel.testing.resources.belns' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybel.testing.resources.belns' to be distributed and are already explicitly excluding 'pybel.testing.resources.belns' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating build/lib/pybel/apps copying src/pybel/apps/parser.py -> build/lib/pybel/apps creating build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/Cytotoxic T-cell Signaling-2.0-Hs.json -> build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/isolated.bel -> build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/misordered.bel -> build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/obo.bel -> build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/slushy.bel -> build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/test_bel.bel -> build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/thorough.bel -> build/lib/pybel/testing/resources/bel creating build/lib/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/cell-line.belanno -> build/lib/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/confidence-1.0.0.belanno -> build/lib/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/mesh-diseases.belanno -> build/lib/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/species-taxonomy-id.belanno -> build/lib/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/test_an_1.belanno -> build/lib/pybel/testing/resources/belanno creating build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/chebi-names.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/disease-ontology.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/go-names.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/hgnc-names.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/mesh-names.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_1.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_1_updated.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_2.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_empty.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/schema/base_node.schema.json -> build/lib/pybel/schema copying src/pybel/schema/edge.schema.json -> build/lib/pybel/schema copying src/pybel/schema/entity.schema.json -> build/lib/pybel/schema copying src/pybel/schema/modifier.schema.json -> build/lib/pybel/schema creating build/lib/pybel/schema/node_types copying src/pybel/schema/node_types/base_abundance.schema.json -> build/lib/pybel/schema/node_types copying src/pybel/schema/node_types/fusion.schema.json -> build/lib/pybel/schema/node_types copying src/pybel/schema/node_types/fusion_range.schema.json -> build/lib/pybel/schema/node_types copying src/pybel/schema/node_types/list_abundance.schema.json -> build/lib/pybel/schema/node_types copying src/pybel/schema/node_types/reaction.schema.json -> build/lib/pybel/schema/node_types creating build/lib/pybel/schema/node_types/variants copying src/pybel/schema/node_types/variants/base_variant.schema.json -> build/lib/pybel/schema/node_types/variants copying src/pybel/schema/node_types/variants/fragment.schema.json -> build/lib/pybel/schema/node_types/variants copying src/pybel/schema/node_types/variants/gene_mod.schema.json -> build/lib/pybel/schema/node_types/variants copying src/pybel/schema/node_types/variants/protein_mod.schema.json -> build/lib/pybel/schema/node_types/variants creating build/lib/pybel/schema/node_types/variants/hgvs copying src/pybel/schema/node_types/variants/hgvs/base_hgvs.schema.json -> build/lib/pybel/schema/node_types/variants/hgvs copying src/pybel/schema/node_types/variants/hgvs/gene_hgvs.schema.json -> build/lib/pybel/schema/node_types/variants/hgvs copying src/pybel/schema/node_types/variants/hgvs/protein_hgvs.schema.json -> build/lib/pybel/schema/node_types/variants/hgvs copying src/pybel/schema/node_types/variants/hgvs/rna_hgvs.schema.json -> build/lib/pybel/schema/node_types/variants/hgvs creating build/lib/pybel/io/jupyter/templates copying src/pybel/io/jupyter/templates/graph_template.html -> build/lib/pybel/io/jupyter/templates copying src/pybel/io/jupyter/templates/pybel_jupyter.js -> build/lib/pybel/io/jupyter/templates copying src/pybel/io/jupyter/templates/pybel_vis.js -> build/lib/pybel/io/jupyter/templates installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/pybel creating build/bdist.linux-x86_64/wheel/pybel/testing copying build/lib/pybel/testing/mock_manager.py -> build/bdist.linux-x86_64/wheel/./pybel/testing copying build/lib/pybel/testing/cases.py -> build/bdist.linux-x86_64/wheel/./pybel/testing copying build/lib/pybel/testing/mocks.py -> build/bdist.linux-x86_64/wheel/./pybel/testing creating build/bdist.linux-x86_64/wheel/pybel/testing/resources creating build/bdist.linux-x86_64/wheel/pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/thorough.bel -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/misordered.bel -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/slushy.bel -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/isolated.bel -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/test_bel.bel -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/Cytotoxic T-cell Signaling-2.0-Hs.json -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/obo.bel -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel creating build/bdist.linux-x86_64/wheel/pybel/testing/resources/belanno copying build/lib/pybel/testing/resources/belanno/confidence-1.0.0.belanno -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belanno copying build/lib/pybel/testing/resources/belanno/test_an_1.belanno -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belanno copying build/lib/pybel/testing/resources/belanno/species-taxonomy-id.belanno -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belanno copying build/lib/pybel/testing/resources/belanno/cell-line.belanno -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belanno copying build/lib/pybel/testing/resources/belanno/mesh-diseases.belanno -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belanno creating build/bdist.linux-x86_64/wheel/pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/test_ns_1_updated.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/hgnc-names.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/mesh-names.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/test_ns_2.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/test_ns_1.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/disease-ontology.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/test_ns_empty.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/go-names.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/chebi-names.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/testing copying build/lib/pybel/testing/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/testing copying build/lib/pybel/testing/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/testing copying build/lib/pybel/testing/generate.py -> build/bdist.linux-x86_64/wheel/./pybel/testing copying build/lib/pybel/grounding.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/examples copying build/lib/pybel/examples/various_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/egf_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/sialic_acid_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/tloc_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/ampk_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/statin_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/vegf_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/homology_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/braf_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/exceptions.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/apps copying build/lib/pybel/apps/parser.py -> build/bdist.linux-x86_64/wheel/./pybel/apps copying build/lib/pybel/config.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/struct creating build/bdist.linux-x86_64/wheel/pybel/struct/query copying build/lib/pybel/struct/query/exc.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/query copying build/lib/pybel/struct/query/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/query copying build/lib/pybel/struct/query/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/query copying build/lib/pybel/struct/query/seeding.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/query copying build/lib/pybel/struct/query/query.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/query copying build/lib/pybel/struct/query/selection.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/query copying build/lib/pybel/struct/getters.py -> build/bdist.linux-x86_64/wheel/./pybel/struct copying build/lib/pybel/struct/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct creating build/bdist.linux-x86_64/wheel/pybel/struct/filters copying build/lib/pybel/struct/filters/node_predicate_builders.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters creating build/bdist.linux-x86_64/wheel/pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/activities.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/relations.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/types.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/modifications.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/misc.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/typing.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/filters/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/filters/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/filters/node_filters.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/filters/edge_predicates.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/filters/edge_predicate_builders.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/filters/edge_filters.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/struct creating build/bdist.linux-x86_64/wheel/pybel/struct/summary copying build/lib/pybel/struct/summary/errors.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/summary copying build/lib/pybel/struct/summary/provenance.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/summary copying build/lib/pybel/struct/summary/edge_summary.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/summary copying build/lib/pybel/struct/summary/supersummary.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/summary copying build/lib/pybel/struct/summary/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/summary copying build/lib/pybel/struct/summary/node_summary.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/summary copying build/lib/pybel/struct/node_utils.py -> build/bdist.linux-x86_64/wheel/./pybel/struct creating build/bdist.linux-x86_64/wheel/pybel/struct/mutation creating build/bdist.linux-x86_64/wheel/pybel/struct/mutation/deletion copying build/lib/pybel/struct/mutation/deletion/protein_rna_origins.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/deletion copying build/lib/pybel/struct/mutation/deletion/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/deletion copying build/lib/pybel/struct/mutation/deletion/deletion.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/deletion creating build/bdist.linux-x86_64/wheel/pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/neighborhood.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/paths.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/random_subgraph.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/annotations.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/upstream.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/citation.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction_expansion.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation creating build/bdist.linux-x86_64/wheel/pybel/struct/mutation/inference copying build/lib/pybel/struct/mutation/inference/transfer.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/inference copying build/lib/pybel/struct/mutation/inference/protein_rna_origins.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/inference copying build/lib/pybel/struct/mutation/inference/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/inference copying build/lib/pybel/struct/mutation/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation copying build/lib/pybel/struct/mutation/metadata.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation copying build/lib/pybel/struct/mutation/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation creating build/bdist.linux-x86_64/wheel/pybel/struct/mutation/expansion copying build/lib/pybel/struct/mutation/expansion/neighborhood.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/expansion copying build/lib/pybel/struct/mutation/expansion/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/expansion copying build/lib/pybel/struct/mutation/expansion/upstream.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/expansion creating build/bdist.linux-x86_64/wheel/pybel/struct/mutation/collapse copying build/lib/pybel/struct/mutation/collapse/protein_rna_origins.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/collapse copying build/lib/pybel/struct/mutation/collapse/collapse.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/collapse copying build/lib/pybel/struct/mutation/collapse/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/collapse creating build/bdist.linux-x86_64/wheel/pybel/struct/pipeline copying build/lib/pybel/struct/pipeline/exc.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/pipeline copying build/lib/pybel/struct/pipeline/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/pipeline copying build/lib/pybel/struct/pipeline/decorators.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/pipeline copying build/lib/pybel/struct/pipeline/pipeline.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/pipeline copying build/lib/pybel/struct/graph.py -> build/bdist.linux-x86_64/wheel/./pybel/struct creating build/bdist.linux-x86_64/wheel/pybel/struct/grouping copying build/lib/pybel/struct/grouping/provenance.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/grouping copying build/lib/pybel/struct/grouping/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/grouping copying build/lib/pybel/struct/grouping/annotations.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/grouping copying build/lib/pybel/struct/operations.py -> build/bdist.linux-x86_64/wheel/./pybel/struct copying build/lib/pybel/language.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/manager copying build/lib/pybel/manager/cache_manager.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/database_io.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/base_manager.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/exc.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/models.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/citation_utils.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/lookup_manager.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/make_json_serializable.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/query_manager.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/repository.py -> build/bdist.linux-x86_64/wheel/./pybel copying build/lib/pybel/typing.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/resources copying build/lib/pybel/resources/update_resources.py -> build/bdist.linux-x86_64/wheel/./pybel/resources copying build/lib/pybel/resources/resources.py -> build/bdist.linux-x86_64/wheel/./pybel/resources copying build/lib/pybel/resources/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/resources copying build/lib/pybel/resources/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/resources copying build/lib/pybel/version.py -> build/bdist.linux-x86_64/wheel/./pybel copying build/lib/pybel/tokens.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/parser creating build/bdist.linux-x86_64/wheel/pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/location.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/fusion.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/truncation.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/variant.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/gene_modification.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/protein_modification.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/fragment.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/protein_substitution.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/gene_substitution.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/parse_concept.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/parse_metadata.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/parse_bel.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/baseparser.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/parse_control.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/canonicalize.py -> build/bdist.linux-x86_64/wheel/./pybel copying build/lib/pybel/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/dsl copying build/lib/pybel/dsl/namespaces.py -> build/bdist.linux-x86_64/wheel/./pybel/dsl copying build/lib/pybel/dsl/node_classes.py -> build/bdist.linux-x86_64/wheel/./pybel/dsl copying build/lib/pybel/dsl/exc.py -> build/bdist.linux-x86_64/wheel/./pybel/dsl copying build/lib/pybel/dsl/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/dsl copying build/lib/pybel/dsl/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/dsl copying build/lib/pybel/dsl/edges.py -> build/bdist.linux-x86_64/wheel/./pybel/dsl copying build/lib/pybel/utils.py -> build/bdist.linux-x86_64/wheel/./pybel copying build/lib/pybel/constants.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/schema creating build/bdist.linux-x86_64/wheel/pybel/schema/node_types creating build/bdist.linux-x86_64/wheel/pybel/schema/node_types/variants creating build/bdist.linux-x86_64/wheel/pybel/schema/node_types/variants/hgvs copying build/lib/pybel/schema/node_types/variants/hgvs/rna_hgvs.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants/hgvs copying build/lib/pybel/schema/node_types/variants/hgvs/base_hgvs.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants/hgvs copying build/lib/pybel/schema/node_types/variants/hgvs/gene_hgvs.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants/hgvs copying build/lib/pybel/schema/node_types/variants/hgvs/protein_hgvs.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants/hgvs copying build/lib/pybel/schema/node_types/variants/gene_mod.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants copying build/lib/pybel/schema/node_types/variants/protein_mod.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants copying build/lib/pybel/schema/node_types/variants/fragment.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants copying build/lib/pybel/schema/node_types/variants/base_variant.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants copying build/lib/pybel/schema/node_types/fusion_range.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types copying build/lib/pybel/schema/node_types/base_abundance.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types copying build/lib/pybel/schema/node_types/reaction.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types copying build/lib/pybel/schema/node_types/fusion.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types copying build/lib/pybel/schema/node_types/list_abundance.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types copying build/lib/pybel/schema/edge.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema copying build/lib/pybel/schema/entity.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema copying build/lib/pybel/schema/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/schema copying build/lib/pybel/schema/base_node.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema copying build/lib/pybel/schema/modifier.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema creating build/bdist.linux-x86_64/wheel/pybel/io creating build/bdist.linux-x86_64/wheel/pybel/io/tsv copying build/lib/pybel/io/tsv/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/io/tsv copying build/lib/pybel/io/tsv/converters.py -> build/bdist.linux-x86_64/wheel/./pybel/io/tsv copying build/lib/pybel/io/tsv/api.py -> build/bdist.linux-x86_64/wheel/./pybel/io/tsv creating build/bdist.linux-x86_64/wheel/pybel/io/jupyter copying build/lib/pybel/io/jupyter/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter copying build/lib/pybel/io/jupyter/inline.py -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter creating build/bdist.linux-x86_64/wheel/pybel/io/jupyter/templates copying build/lib/pybel/io/jupyter/templates/pybel_jupyter.js -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter/templates copying build/lib/pybel/io/jupyter/templates/pybel_vis.js -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter/templates copying build/lib/pybel/io/jupyter/templates/graph_template.html -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter/templates copying build/lib/pybel/io/jupyter/visualization.py -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter copying build/lib/pybel/io/jupyter/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter creating build/bdist.linux-x86_64/wheel/pybel/io/hetionet copying build/lib/pybel/io/hetionet/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/io/hetionet copying build/lib/pybel/io/hetionet/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/io/hetionet copying build/lib/pybel/io/hetionet/hetionet.py -> build/bdist.linux-x86_64/wheel/./pybel/io/hetionet copying build/lib/pybel/io/hetionet/cli.py -> build/bdist.linux-x86_64/wheel/./pybel/io/hetionet copying build/lib/pybel/io/hetionet/__main__.py -> build/bdist.linux-x86_64/wheel/./pybel/io/hetionet copying build/lib/pybel/io/neo4j.py -> build/bdist.linux-x86_64/wheel/./pybel/io creating build/bdist.linux-x86_64/wheel/pybel/io/triples copying build/lib/pybel/io/triples/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/io/triples copying build/lib/pybel/io/triples/converters.py -> build/bdist.linux-x86_64/wheel/./pybel/io/triples copying build/lib/pybel/io/triples/api.py -> build/bdist.linux-x86_64/wheel/./pybel/io/triples copying build/lib/pybel/io/umbrella_nodelink.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/pykeen.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/jgif.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/exc.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/extras.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/nodelink.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/gpickle.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/line_utils.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/graphdati.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/spia.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/biodati_client.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/emmaa.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/lines.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/bel_commons_client.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/sbel.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/aws.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/indra.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/hipathia.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/graphml.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/pynpa.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/jinja_utils.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/cx.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/api.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/fraunhofer_orientdb.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/cli.py -> build/bdist.linux-x86_64/wheel/./pybel copying build/lib/pybel/__main__.py -> build/bdist.linux-x86_64/wheel/./pybel running install_egg_info Copying src/pybel.egg-info to build/bdist.linux-x86_64/wheel/./pybel-0.15.5.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/pybel-0.15.5.dist-info/WHEEL creating '/build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.13_pybel/.tmp-8ncp7u33/pybel-0.15.5-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'pybel/__init__.py' adding 'pybel/__main__.py' adding 'pybel/canonicalize.py' adding 'pybel/cli.py' adding 'pybel/config.py' adding 'pybel/constants.py' adding 'pybel/exceptions.py' adding 'pybel/grounding.py' adding 'pybel/language.py' adding 'pybel/repository.py' adding 'pybel/tokens.py' adding 'pybel/typing.py' adding 'pybel/utils.py' adding 'pybel/version.py' adding 'pybel/apps/parser.py' adding 'pybel/dsl/__init__.py' adding 'pybel/dsl/constants.py' adding 'pybel/dsl/edges.py' adding 'pybel/dsl/exc.py' adding 'pybel/dsl/namespaces.py' adding 'pybel/dsl/node_classes.py' adding 'pybel/examples/__init__.py' adding 'pybel/examples/ampk_example.py' adding 'pybel/examples/braf_example.py' adding 'pybel/examples/egf_example.py' adding 'pybel/examples/homology_example.py' adding 'pybel/examples/sialic_acid_example.py' adding 'pybel/examples/statin_example.py' adding 'pybel/examples/tloc_example.py' adding 'pybel/examples/various_example.py' adding 'pybel/examples/vegf_example.py' adding 'pybel/io/__init__.py' adding 'pybel/io/api.py' adding 'pybel/io/aws.py' adding 'pybel/io/bel_commons_client.py' adding 'pybel/io/biodati_client.py' adding 'pybel/io/cx.py' adding 'pybel/io/emmaa.py' adding 'pybel/io/exc.py' adding 'pybel/io/extras.py' adding 'pybel/io/fraunhofer_orientdb.py' adding 'pybel/io/gpickle.py' adding 'pybel/io/graphdati.py' adding 'pybel/io/graphml.py' adding 'pybel/io/hipathia.py' adding 'pybel/io/indra.py' adding 'pybel/io/jgif.py' adding 'pybel/io/jinja_utils.py' adding 'pybel/io/line_utils.py' adding 'pybel/io/lines.py' adding 'pybel/io/neo4j.py' adding 'pybel/io/nodelink.py' adding 'pybel/io/pykeen.py' adding 'pybel/io/pynpa.py' adding 'pybel/io/sbel.py' adding 'pybel/io/spia.py' adding 'pybel/io/umbrella_nodelink.py' adding 'pybel/io/utils.py' adding 'pybel/io/hetionet/__init__.py' adding 'pybel/io/hetionet/__main__.py' adding 'pybel/io/hetionet/cli.py' adding 'pybel/io/hetionet/constants.py' adding 'pybel/io/hetionet/hetionet.py' adding 'pybel/io/jupyter/__init__.py' adding 'pybel/io/jupyter/constants.py' adding 'pybel/io/jupyter/inline.py' adding 'pybel/io/jupyter/visualization.py' adding 'pybel/io/jupyter/templates/graph_template.html' adding 'pybel/io/jupyter/templates/pybel_jupyter.js' adding 'pybel/io/jupyter/templates/pybel_vis.js' adding 'pybel/io/triples/__init__.py' adding 'pybel/io/triples/api.py' adding 'pybel/io/triples/converters.py' adding 'pybel/io/tsv/__init__.py' adding 'pybel/io/tsv/api.py' adding 'pybel/io/tsv/converters.py' adding 'pybel/manager/__init__.py' adding 'pybel/manager/base_manager.py' adding 'pybel/manager/cache_manager.py' adding 'pybel/manager/citation_utils.py' adding 'pybel/manager/database_io.py' adding 'pybel/manager/exc.py' adding 'pybel/manager/lookup_manager.py' adding 'pybel/manager/make_json_serializable.py' adding 'pybel/manager/models.py' adding 'pybel/manager/query_manager.py' adding 'pybel/manager/utils.py' adding 'pybel/parser/__init__.py' adding 'pybel/parser/baseparser.py' adding 'pybel/parser/constants.py' adding 'pybel/parser/parse_bel.py' adding 'pybel/parser/parse_concept.py' adding 'pybel/parser/parse_control.py' adding 'pybel/parser/parse_metadata.py' adding 'pybel/parser/utils.py' adding 'pybel/parser/modifiers/__init__.py' adding 'pybel/parser/modifiers/constants.py' adding 'pybel/parser/modifiers/fragment.py' adding 'pybel/parser/modifiers/fusion.py' adding 'pybel/parser/modifiers/gene_modification.py' adding 'pybel/parser/modifiers/gene_substitution.py' adding 'pybel/parser/modifiers/location.py' adding 'pybel/parser/modifiers/protein_modification.py' adding 'pybel/parser/modifiers/protein_substitution.py' adding 'pybel/parser/modifiers/truncation.py' adding 'pybel/parser/modifiers/variant.py' adding 'pybel/resources/__init__.py' adding 'pybel/resources/constants.py' adding 'pybel/resources/resources.py' adding 'pybel/resources/update_resources.py' adding 'pybel/schema/__init__.py' adding 'pybel/schema/base_node.schema.json' adding 'pybel/schema/edge.schema.json' adding 'pybel/schema/entity.schema.json' adding 'pybel/schema/modifier.schema.json' adding 'pybel/schema/node_types/base_abundance.schema.json' adding 'pybel/schema/node_types/fusion.schema.json' adding 'pybel/schema/node_types/fusion_range.schema.json' adding 'pybel/schema/node_types/list_abundance.schema.json' adding 'pybel/schema/node_types/reaction.schema.json' adding 'pybel/schema/node_types/variants/base_variant.schema.json' adding 'pybel/schema/node_types/variants/fragment.schema.json' adding 'pybel/schema/node_types/variants/gene_mod.schema.json' adding 'pybel/schema/node_types/variants/protein_mod.schema.json' adding 'pybel/schema/node_types/variants/hgvs/base_hgvs.schema.json' adding 'pybel/schema/node_types/variants/hgvs/gene_hgvs.schema.json' adding 'pybel/schema/node_types/variants/hgvs/protein_hgvs.schema.json' adding 'pybel/schema/node_types/variants/hgvs/rna_hgvs.schema.json' adding 'pybel/struct/__init__.py' adding 'pybel/struct/getters.py' adding 'pybel/struct/graph.py' adding 'pybel/struct/node_utils.py' adding 'pybel/struct/operations.py' adding 'pybel/struct/utils.py' adding 'pybel/struct/filters/__init__.py' adding 'pybel/struct/filters/edge_filters.py' adding 'pybel/struct/filters/edge_predicate_builders.py' adding 'pybel/struct/filters/edge_predicates.py' adding 'pybel/struct/filters/node_filters.py' adding 'pybel/struct/filters/node_predicate_builders.py' adding 'pybel/struct/filters/typing.py' adding 'pybel/struct/filters/utils.py' adding 'pybel/struct/filters/node_predicates/__init__.py' adding 'pybel/struct/filters/node_predicates/activities.py' adding 'pybel/struct/filters/node_predicates/misc.py' adding 'pybel/struct/filters/node_predicates/modifications.py' adding 'pybel/struct/filters/node_predicates/relations.py' adding 'pybel/struct/filters/node_predicates/types.py' adding 'pybel/struct/filters/node_predicates/utils.py' adding 'pybel/struct/grouping/__init__.py' adding 'pybel/struct/grouping/annotations.py' adding 'pybel/struct/grouping/provenance.py' adding 'pybel/struct/mutation/__init__.py' adding 'pybel/struct/mutation/induction_expansion.py' adding 'pybel/struct/mutation/metadata.py' adding 'pybel/struct/mutation/utils.py' adding 'pybel/struct/mutation/collapse/__init__.py' adding 'pybel/struct/mutation/collapse/collapse.py' adding 'pybel/struct/mutation/collapse/protein_rna_origins.py' adding 'pybel/struct/mutation/deletion/__init__.py' adding 'pybel/struct/mutation/deletion/deletion.py' adding 'pybel/struct/mutation/deletion/protein_rna_origins.py' adding 'pybel/struct/mutation/expansion/__init__.py' adding 'pybel/struct/mutation/expansion/neighborhood.py' adding 'pybel/struct/mutation/expansion/upstream.py' adding 'pybel/struct/mutation/induction/__init__.py' adding 'pybel/struct/mutation/induction/annotations.py' adding 'pybel/struct/mutation/induction/citation.py' adding 'pybel/struct/mutation/induction/neighborhood.py' adding 'pybel/struct/mutation/induction/paths.py' adding 'pybel/struct/mutation/induction/random_subgraph.py' adding 'pybel/struct/mutation/induction/upstream.py' adding 'pybel/struct/mutation/induction/utils.py' adding 'pybel/struct/mutation/inference/__init__.py' adding 'pybel/struct/mutation/inference/protein_rna_origins.py' adding 'pybel/struct/mutation/inference/transfer.py' adding 'pybel/struct/pipeline/__init__.py' adding 'pybel/struct/pipeline/decorators.py' adding 'pybel/struct/pipeline/exc.py' adding 'pybel/struct/pipeline/pipeline.py' adding 'pybel/struct/query/__init__.py' adding 'pybel/struct/query/constants.py' adding 'pybel/struct/query/exc.py' adding 'pybel/struct/query/query.py' adding 'pybel/struct/query/seeding.py' adding 'pybel/struct/query/selection.py' adding 'pybel/struct/summary/__init__.py' adding 'pybel/struct/summary/edge_summary.py' adding 'pybel/struct/summary/errors.py' adding 'pybel/struct/summary/node_summary.py' adding 'pybel/struct/summary/provenance.py' adding 'pybel/struct/summary/supersummary.py' adding 'pybel/testing/__init__.py' adding 'pybel/testing/cases.py' adding 'pybel/testing/constants.py' adding 'pybel/testing/generate.py' adding 'pybel/testing/mock_manager.py' adding 'pybel/testing/mocks.py' adding 'pybel/testing/utils.py' adding 'pybel/testing/resources/bel/Cytotoxic T-cell Signaling-2.0-Hs.json' adding 'pybel/testing/resources/bel/isolated.bel' adding 'pybel/testing/resources/bel/misordered.bel' adding 'pybel/testing/resources/bel/obo.bel' adding 'pybel/testing/resources/bel/slushy.bel' adding 'pybel/testing/resources/bel/test_bel.bel' adding 'pybel/testing/resources/bel/thorough.bel' adding 'pybel/testing/resources/belanno/cell-line.belanno' adding 'pybel/testing/resources/belanno/confidence-1.0.0.belanno' adding 'pybel/testing/resources/belanno/mesh-diseases.belanno' adding 'pybel/testing/resources/belanno/species-taxonomy-id.belanno' adding 'pybel/testing/resources/belanno/test_an_1.belanno' adding 'pybel/testing/resources/belns/chebi-names.belns' adding 'pybel/testing/resources/belns/disease-ontology.belns' adding 'pybel/testing/resources/belns/go-names.belns' adding 'pybel/testing/resources/belns/hgnc-names.belns' adding 'pybel/testing/resources/belns/mesh-names.belns' adding 'pybel/testing/resources/belns/test_ns_1.belns' adding 'pybel/testing/resources/belns/test_ns_1_updated.belns' adding 'pybel/testing/resources/belns/test_ns_2.belns' adding 'pybel/testing/resources/belns/test_ns_empty.belns' adding 'pybel-0.15.5.dist-info/LICENSE' adding 'pybel-0.15.5.dist-info/METADATA' adding 'pybel-0.15.5.dist-info/WHEEL' adding 'pybel-0.15.5.dist-info/entry_points.txt' adding 'pybel-0.15.5.dist-info/top_level.txt' adding 'pybel-0.15.5.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built pybel-0.15.5-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.13_pybel/build; python3.13 -m pytest --ignore=tests/test_grounding.py -k ' not test_seeding and not test_import and not test_manager_graph and not test_insert_namespace_persistent and not test_parse_metadata and not test_bel_simple and not test_bel_thorough and not test_update_matrix_activation and not test_update_matrix_activation_phosphorylation and not test_update_matrix_activation_ubiquination and not test_update_matrix_association and not test_update_matrix_expression and not test_update_matrix_inhibition and not test_update_matrix_inhibition_phosphorylation and not test_update_matrix_inhibition_ubiquination and not test_update_matrix_pmods and not test_update_matrix_repression and not test_reset_citation and not test_set_regex and not test_get_random_path ' ============================= test session starts ============================== platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 rootdir: /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.13_pybel/build configfile: pyproject.toml plugins: typeguard-4.4.2 collected 727 items / 171 deselected / 556 selected tests/test_bel_repository.py . [ 0%] tests/test_canonicalization.py .......................... [ 4%] tests/test_dsl.py ........................ [ 9%] tests/test_io/test_hipathia/test_export.py .... [ 9%] tests/test_io/test_hipathia/test_hipathia.py . [ 10%] tests/test_io/test_jgif.py . [ 10%] tests/test_io/test_jupyter.py .. [ 10%] tests/test_io/test_pynpa.py ..... [ 11%] tests/test_io/test_spia.py ... [ 12%] tests/test_io/test_triples.py .. [ 12%] tests/test_io/test_umbrella_nodelink.py .. [ 12%] tests/test_manager/test_citation_utils.py ........ssssss. [ 15%] tests/test_manager/test_connection.py .......... [ 17%] tests/test_manager/test_manager_definitions.py .. [ 17%] tests/test_manager/test_manager_drop.py .......... [ 19%] tests/test_manager/test_manager_model.py ....... [ 20%] tests/test_parse/test_parse_bel.py ..................................... [ 27%] ............................................ [ 35%] tests/test_parse/test_parse_bel_relations.py ........................... [ 40%] ........ [ 41%] tests/test_parse/test_parse_bel_variants.py ............................ [ 46%] .......... [ 48%] tests/test_parse/test_parse_control.py ................................. [ 54%] [ 54%] tests/test_parse/test_parse_identifier.py .................... [ 57%] tests/test_parse/test_parse_utils.py .......... [ 59%] tests/test_parse/test_user_api.py .... [ 60%] tests/test_schema.py ........... [ 62%] tests/test_struct/test_filters/test_edge_predicate_builders.py .... [ 63%] tests/test_struct/test_filters/test_edge_predicates.py . [ 63%] tests/test_struct/test_filters/test_node_predicate_builders.py ....... [ 64%] tests/test_struct/test_filters/test_node_predicates.py ................. [ 67%] ............... [ 70%] tests/test_struct/test_filters/test_node_selection.py . [ 70%] tests/test_struct/test_filters/test_struct_filters.py .................. [ 73%] .... [ 74%] tests/test_struct/test_getters.py . [ 74%] tests/test_struct/test_grouping.py ... [ 75%] tests/test_struct/test_node_utils.py .... [ 75%] tests/test_struct/test_query/test_mocks.py ... [ 76%] tests/test_struct/test_query/test_query.py ................. [ 79%] tests/test_struct/test_query/test_struct_pipeline.py ............ [ 81%] tests/test_struct/test_struct_graph.py .......... [ 83%] tests/test_struct/test_struct_operations.py ....................... [ 87%] tests/test_struct/test_summary/test_errors.py .. [ 87%] tests/test_struct/test_summary/test_provenance.py . [ 88%] tests/test_struct/test_summary/test_struct_summary_edges.py ...... [ 89%] tests/test_struct/test_summary/test_summary_nodes.py .......... [ 91%] tests/test_struct/test_transformations/test_collapse.py ...... [ 92%] tests/test_struct/test_transformations/test_deletions.py ......... [ 93%] tests/test_struct/test_transformations/test_expansion.py .... [ 94%] tests/test_struct/test_transformations/test_induction.py .......... [ 96%] tests/test_struct/test_transformations/test_metadata.py ... [ 96%] tests/test_struct/test_transformations/test_random.py ...... [ 97%] tests/test_struct/test_transformations/test_transfer.py ... [ 98%] tests/test_tokens.py . [ 98%] tests/test_utils.py ........ [100%] =============================== warnings summary =============================== pybel/io/api.py:9 /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.13_pybel/build/pybel/io/api.py:9: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import iter_entry_points pybel/manager/models.py:91 /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.13_pybel/build/pybel/manager/models.py:91: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) Base = declarative_base() pybel/schema/__init__.py:30 /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.13_pybel/build/pybel/schema/__init__.py:30: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need. RESOLVER = jsonschema.RefResolver(base_uri=schema_uri, referrer=__file__) tests/test_io/test_spia.py::TestSpia::test_spia_matrix_complexes tests/test_io/test_spia.py::TestSpia::test_spia_matrix_composites /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.13_pybel/build/pybel/io/spia.py:178: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy spia_matrices["activation"][u_name][v_name] = 1 tests/test_io/test_spia.py::TestSpia::test_spia_matrix_complexes tests/test_io/test_spia.py::TestSpia::test_spia_matrix_composites /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.13_pybel/build/pybel/io/spia.py:174: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy spia_matrices["activation_phosphorylation"][u_name][v_name] = 1 tests/test_io/test_spia.py::TestSpia::test_spia_matrix_complexes tests/test_io/test_spia.py::TestSpia::test_spia_matrix_composites /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.13_pybel/build/pybel/io/spia.py:193: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy spia_matrices["inhibition"][u_name][v_name] = 1 tests/test_manager/test_manager_definitions.py: 1 warning tests/test_manager/test_manager_drop.py: 23 warnings /usr/lib/python3/dist-packages/sqlalchemy/sql/schema.py:3594: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC). return util.wrap_callable(lambda ctx: fn(), fn) # type: ignore tests/test_manager/test_manager_drop.py::TestReconstituteNodeTuples::test_simple /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.13_pybel/build/pybel/manager/cache_manager.py:421: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) network = self.session.query(Network).get(network_id) tests/test_manager/test_manager_model.py::TestNetwork::test_dump tests/test_manager/test_manager_model.py::TestNetwork::test_network tests/test_manager/test_manager_model.py::TestNetwork::test_to_json /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.13_pybel/build/tests/test_manager/test_manager_model.py:33: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC). self.created = datetime.datetime.utcnow() tests/test_parse/test_parse_bel.py: 82 warnings tests/test_parse/test_parse_bel_relations.py: 2 warnings /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.13_pybel/build/pybel/struct/graph.py:913: DeprecationWarning: use node.as_bel() warnings.warn("use node.as_bel()", DeprecationWarning) tests/test_struct/test_struct_graph.py: 1778 warnings /usr/lib/python3/dist-packages/bioregistry/schema_utils.py:61: PydanticDeprecatedSince20: The `parse_obj` method is deprecated; use `model_validate` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.10/migration/ return {prefix: Resource.parse_obj(value) for prefix, value in data.items()} tests/test_struct/test_struct_graph.py: 7112 warnings /usr/lib/python3/dist-packages/bioregistry/schema/struct.py:648: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.10/migration/ return self.dict().get(metaprefix) or dict() -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======== 550 passed, 6 skipped, 171 deselected, 9011 warnings in 21.47s ======== create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/pybel-0.15.5' dh_auto_install I: pybuild plugin_pyproject:178: Copying package built for python3.13 to destdir # eliminate lintian warning for d in $(find /build/reproducible-path/pybel-0.15.5/debian/python3-pybel/usr/lib -maxdepth 1 -type d -name "python3.*"); \ do \ chmod -x $d/dist-packages/pybel/testing/resources/bel/*.json ; \ done find debian -type f -name graph_template.html \ | xargs sed -i \ -e 's;https://cdn[js]*\..*/jquery.min.js;file:///usr/share/javascript/jquery/jquery.min.js;g' \ -e 's;https://cdn[js]*\..*/d3.min.js;file:///usr/share/javascript/d3/d3.min.js;g' \ make[1]: Leaving directory '/build/reproducible-path/pybel-0.15.5' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pybel' in '../python3-pybel_0.15.5-1_all.deb'. dpkg-genbuildinfo --build=binary -O../pybel_0.15.5-1_amd64.buildinfo dpkg-genchanges --build=binary -O../pybel_0.15.5-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from pybel-0.15.5/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration 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/719667 and its subdirectories I: Current time: Mon Apr 13 17:13:17 -12 2026 I: pbuilder-time-stamp: 1776143597