I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 12 18:26:09 -12 2026 I: pbuilder-time-stamp: 1776061569 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: using eatmydata during job I: Copying source file I: copying [python-cobra_0.29.1-1.dsc] I: copying [./python-cobra_0.29.1.orig.tar.gz] I: copying [./python-cobra_0.29.1-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-cobra_0.29.1-1.dsc: unsupported subcommand dpkg-source: info: extracting python-cobra in python-cobra-0.29.1 dpkg-source: info: unpacking python-cobra_0.29.1.orig.tar.gz dpkg-source: info: unpacking python-cobra_0.29.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying mathjax.patch dpkg-source: info: applying xfail_test_show_versions.patch dpkg-source: info: applying ignore_tests.patch dpkg-source: info: applying 32-bit-test.patch dpkg-source: info: applying no_future_dependency.patch dpkg-source: info: applying remove-appdirs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/118571/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='f49f58b59ab546f4ad7df146aa6514d3' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='118571' 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.V4u3CTIv/pbuilderrc_sit3 --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.V4u3CTIv/b1 --logfile b1/build.log python-cobra_0.29.1-1.dsc' SUDO_GID='112' SUDO_UID='107' 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 ionos16-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) 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/118571/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: i386 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, libglpk-dev, python3-dev, python3-setuptools, python3-depinfo, python3-importlib-resources, python3-numpy, python3-optlang (>= 1.7.0-1~), python3-ruamel.yaml, python3-pandas, python3-pip, python3-pipdeptree, python3-requests, python3-swiglpk (>= 5.0.8-1~), python3-tabulate, python3-sbml5, cython3, python3-pytest, python3-pytest-benchmark, python3-pytest-mock, python3-jsonschema, libsbml5-dev, python3-matplotlib, python3-platformdirs, python3-diskcache, python3-httpx, python3-pydantic, python3-rich dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19769 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 libglpk-dev; however: Package libglpk-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-depinfo; however: Package python3-depinfo is not installed. pbuilder-satisfydepends-dummy depends on python3-importlib-resources; however: Package python3-importlib-resources is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-optlang (>= 1.7.0-1~); however: Package python3-optlang is not installed. pbuilder-satisfydepends-dummy depends on python3-ruamel.yaml; however: Package python3-ruamel.yaml is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-pip; however: Package python3-pip is not installed. pbuilder-satisfydepends-dummy depends on python3-pipdeptree; however: Package python3-pipdeptree is not installed. pbuilder-satisfydepends-dummy depends on python3-requests; however: Package python3-requests is not installed. pbuilder-satisfydepends-dummy depends on python3-swiglpk (>= 5.0.8-1~); however: Package python3-swiglpk is not installed. pbuilder-satisfydepends-dummy depends on python3-tabulate; however: Package python3-tabulate is not installed. pbuilder-satisfydepends-dummy depends on python3-sbml5; however: Package python3-sbml5 is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-benchmark; however: Package python3-pytest-benchmark is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-mock; however: Package python3-pytest-mock is not installed. pbuilder-satisfydepends-dummy depends on python3-jsonschema; however: Package python3-jsonschema is not installed. pbuilder-satisfydepends-dummy depends on libsbml5-dev; however: Package libsbml5-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-platformdirs; however: Package python3-platformdirs is not installed. pbuilder-satisfydepends-dummy depends on python3-diskcache; however: Package python3-diskcache is not installed. pbuilder-satisfydepends-dummy depends on python3-httpx; however: Package python3-httpx is not installed. pbuilder-satisfydepends-dummy depends on python3-pydantic; however: Package python3-pydantic is not installed. pbuilder-satisfydepends-dummy depends on python3-rich; however: Package python3-rich 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} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libamd3{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libbrotli1{a} libbtf2{a} libcamd3{a} libccolamd3{a} libcholmod5{a} libcolamd3{a} libcxsparse4{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libglpk-dev{a} libglpk40{a} libgmp-dev{a} libgmpxx4ldbl{a} libgpg-error0{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libklu2{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldl3{a} liblerc4{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libopenjp2-7{a} libparu1{a} libpipeline1{a} libpng16-16t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} librbio4{a} libreadline8t64{a} libsbml5-dev{a} libsbml5t64{a} libsharpyuv0{a} libspex3{a} libspqr4{a} libsuitesparse-dev{a} libsuitesparse-mongoose3{a} libsuitesparseconfig7{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libumfpack6{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} python-matplotlib-data{a} python3{a} python3-annotated-types{a} python3-anyio{a} python3-attr{a} python3-autocommand{a} python3-brotli{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-click{a} python3-contourpy{a} python3-cpuinfo{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-depinfo{a} python3-dev{a} python3-diskcache{a} python3-dnspython{a} python3-email-validator{a} python3-fonttools{a} python3-fs{a} python3-h11{a} python3-httpcore{a} python3-httpx{a} python3-idna{a} python3-importlib-resources{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-markdown-it{a} python3-matplotlib{a} python3-mdurl{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-numpy-dev{a} python3-optlang{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pip{a} python3-pipdeptree{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pydantic{a} python3-pydantic-core{a} python3-pygments{a} python3-pyparsing{a} python3-pytest{a} python3-pytest-benchmark{a} python3-pytest-mock{a} python3-pytz{a} python3-referencing{a} python3-requests{a} python3-rich{a} python3-rpds-py{a} python3-ruamel.yaml{a} python3-ruamel.yaml.clib{a} python3-sbml5{a} python3-scipy{a} python3-setuptools{a} python3-sniffio{a} python3-swiglpk{a} python3-sympy{a} python3-tabulate{a} python3-tk{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-unicodedata2{a} python3-urllib3{a} python3-wheel{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} x11-common{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl isympy-common javascript-common libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libgraphblas-dev libltdl-dev libmail-sendmail-perl lynx python3-bottleneck python3-bs4 python3-cryptography python3-cssselect python3-elasticsearch python3-fqdn python3-freezegun python3-graphviz python3-h2 python3-html5lib python3-isoduration python3-jinja2 python3-json-pointer python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-pygal python3-rfc3339-validator python3-rfc3986-validator python3-rfc3987 python3-tables python3-uritemplate python3-webcolors python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 217 newly installed, 0 to remove and 0 not upgraded. Need to get 164 MB of archives. After unpacking 682 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.13-minimal i386 3.13.2-1 [859 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.13.2-2 [27.1 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 libffi8 i386 3.4.7-1 [21.4 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libpython3.13-stdlib i386 3.13.2-1 [1985 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 python3.13 i386 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.13.2-2 [10.1 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 python3 i386 3.13.2-2 [28.1 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 python3-numpy-dev i386 1:2.2.3+ds-5 [146 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.1-2 [150 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-17 [735 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.1-2 [2198 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:2.2.3+ds-5 [5060 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 openssl i386 3.4.1-1 [1432 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 ca-certificates all 20241223 [164 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.23.1-1 [245 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-7 [1199 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.4-5 [96.5 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-7 [301 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 automake all 1:1.17-3 [862 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 autopoint all 0.23.1-1 [770 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 libtcl8.6 i386 8.6.16+dfsg-1 [1103 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b7 [299 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.47-1 [289 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-2.1 [318 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-2.1 [402 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.10-2 [337 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.10-2 [834 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b4 [28.8 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 libxft2 i386 2.3.6-1+b4 [55.3 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b3 [52.5 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+24 [217 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libxss1 i386 1:1.2.3-1+b3 [17.3 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libtk8.6 i386 8.6.16-1 [834 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 tk8.6-blt2.5 i386 2.5.3+dfsg-8 [618 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 blt i386 2.5.3+dfsg-8 [5984 B] Get: 58 http://deb.debian.org/debian unstable/main i386 cython3 i386 3.0.11+dfsg-2+b1 [2467 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libtool all 2.5.4-4 [539 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 65 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-1 [458 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-6 [9582 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 gettext i386 0.23.1-1 [1714 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20250308 [115 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 fonts-lyx all 2.4.3-1 [190 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libsuitesparseconfig7 i386 1:7.10.1+dfsg-1 [32.5 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libamd3 i386 1:7.10.1+dfsg-1 [51.9 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libblas-dev i386 3.12.1-2 [162 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libbtf2 i386 1:7.10.1+dfsg-1 [34.3 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libcamd3 i386 1:7.10.1+dfsg-1 [49.5 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libccolamd3 i386 1:7.10.1+dfsg-1 [51.7 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libcolamd3 i386 1:7.10.1+dfsg-1 [44.0 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libcholmod5 i386 1:7.10.1+dfsg-1 [742 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libcxsparse4 i386 1:7.10.1+dfsg-1 [110 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.23-1+b1 [48.4 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libexpat1-dev i386 2.6.4-1 [165 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.16-1 [27.0 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libgpg-error0 i386 1.51-3 [87.3 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libgcrypt20 i386 1.11.0-7 [799 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.83.5-1 [1583 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libltdl7 i386 2.5.4-4 [417 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libglpk40 i386 5.0-1+b2 [422 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-3 [329 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libgmp-dev i386 2:6.3.0+dfsg-3 [661 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libklu2 i386 1:7.10.1+dfsg-1 [104 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libldl3 i386 1:7.10.1+dfsg-1 [33.6 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libsuitesparse-mongoose3 i386 1:7.10.1+dfsg-1 [63.5 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 libumfpack6 i386 1:7.10.1+dfsg-1 [331 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 librbio4 i386 1:7.10.1+dfsg-1 [53.8 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libspqr4 i386 1:7.10.1+dfsg-1 [176 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libspex3 i386 1:7.10.1+dfsg-1 [78.6 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libparu1 i386 1:7.10.1+dfsg-1 [90.7 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 liblapack-dev i386 3.12.1-2 [4458 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libsuitesparse-dev i386 1:7.10.1+dfsg-1 [1728 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libglpk-dev i386 5.0-1+b2 [511 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 10.2.0-1 [504 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 libimagequant0 i386 2.18.0-1+b2 [36.0 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3.1 [170 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.16-2 [171 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 libopenjp2-7 i386 2.5.3-2 [216 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 libpython3.13 i386 3.13.2-1 [2199 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 libpython3.13-dev i386 3.13.2-1 [5181 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 libpython3-dev i386 3.13.2-2 [10.3 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 libqhull-r8.0 i386 2020.2-6+b2 [259 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 libraqm0 i386 0.10.2-1 [14.6 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 libsbml5t64 i386 5.20.4+dfsg-0.1 [2302 kB] Get: 125 http://deb.debian.org/debian unstable/main i386 libsbml5-dev i386 5.20.4+dfsg-0.1 [3360 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.5.0-0.1 [115 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.5.0-0.1 [329 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 libwebpdemux2 i386 1.5.0-0.1 [114 kB] Get: 130 http://deb.debian.org/debian unstable/main i386 libwebpmux3 i386 1.5.0-0.1 [127 kB] Get: 131 http://deb.debian.org/debian unstable/main i386 libxslt1.1 i386 1.1.35-1.1+b1 [243 kB] Get: 132 http://deb.debian.org/debian unstable/main i386 python-matplotlib-data all 3.8.3-7 [2735 kB] Get: 133 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 134 http://deb.debian.org/debian unstable/main i386 python3-annotated-types all 0.7.0-1 [18.8 kB] Get: 135 http://deb.debian.org/debian unstable/main i386 python3-idna all 3.10-1 [42.0 kB] Get: 136 http://deb.debian.org/debian unstable/main i386 python3-sniffio all 1.3.1-1 [7120 B] Get: 137 http://deb.debian.org/debian unstable/main i386 python3-anyio all 4.8.0-2 [63.6 kB] Get: 138 http://deb.debian.org/debian unstable/main i386 python3-attr all 25.1.0-1 [68.7 kB] Get: 139 http://deb.debian.org/debian unstable/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 140 http://deb.debian.org/debian unstable/main i386 python3-brotli i386 1.1.0-2+b7 [318 kB] Get: 141 http://deb.debian.org/debian unstable/main i386 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 142 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 143 http://deb.debian.org/debian unstable/main i386 python3-charset-normalizer i386 3.4.1-1+b1 [127 kB] Get: 144 http://deb.debian.org/debian unstable/main i386 python3-click all 8.2.0+0.really.8.1.8-1 [95.4 kB] Get: 145 http://deb.debian.org/debian unstable/main i386 python3-contourpy i386 1.3.1-1+b1 [223 kB] Get: 146 http://deb.debian.org/debian unstable/main i386 python3-cpuinfo all 9.0.0+git20221119-3 [23.5 kB] Get: 147 http://deb.debian.org/debian unstable/main i386 python3-cycler all 0.12.1-1 [9496 B] Get: 148 http://deb.debian.org/debian unstable/main i386 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 149 http://deb.debian.org/debian unstable/main i386 python3-decorator all 5.1.1-5 [15.1 kB] Get: 150 http://deb.debian.org/debian unstable/main i386 python3-depinfo i386 2.2.0-3 [11.6 kB] Get: 151 http://deb.debian.org/debian unstable/main i386 python3.13-dev i386 3.13.2-1 [505 kB] Get: 152 http://deb.debian.org/debian unstable/main i386 python3-dev i386 3.13.2-2 [26.1 kB] Get: 153 http://deb.debian.org/debian unstable/main i386 python3-diskcache all 5.6.3-1 [34.4 kB] Get: 154 http://deb.debian.org/debian unstable/main i386 python3-dnspython all 2.7.0-1 [164 kB] Get: 155 http://deb.debian.org/debian unstable/main i386 python3-email-validator all 2.2.0-1 [31.6 kB] Get: 156 http://deb.debian.org/debian unstable/main i386 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 157 http://deb.debian.org/debian unstable/main i386 python3-fs all 2.4.16-7 [95.2 kB] Get: 158 http://deb.debian.org/debian unstable/main i386 python3-lxml i386 5.3.1-1+b1 [1257 kB] Get: 159 http://deb.debian.org/debian unstable/main i386 python3-lz4 i386 4.4.0+dfsg-1+b1 [25.5 kB] Get: 160 http://deb.debian.org/debian unstable/main i386 python3-scipy i386 1.15.2-2 [16.4 MB] Get: 161 http://deb.debian.org/debian unstable/main i386 python3-mpmath all 1.3.0-1 [419 kB] Get: 162 http://deb.debian.org/debian unstable/main i386 python3-sympy all 1.13.3-5 [4148 kB] Get: 163 http://deb.debian.org/debian unstable/main i386 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 164 http://deb.debian.org/debian unstable/main i386 python3-unicodedata2 i386 15.1.0+ds-1+b4 [298 kB] Get: 165 http://deb.debian.org/debian unstable/main i386 unicode-data all 15.1.0-1 [8547 kB] Get: 166 http://deb.debian.org/debian unstable/main i386 python3-fonttools i386 4.55.3-2+b1 [1442 kB] Get: 167 http://deb.debian.org/debian unstable/main i386 python3-h11 all 0.14.0-1 [50.1 kB] Get: 168 http://deb.debian.org/debian unstable/main i386 python3-httpcore all 1.0.7-1 [44.7 kB] Get: 169 http://deb.debian.org/debian unstable/main i386 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 170 http://deb.debian.org/debian unstable/main i386 python3-mdurl all 0.1.2-1 [9444 B] Get: 171 http://deb.debian.org/debian unstable/main i386 python3-markdown-it all 3.0.0-2 [62.5 kB] Get: 172 http://deb.debian.org/debian unstable/main i386 python3-rich all 13.9.4-1 [203 kB] Get: 173 http://deb.debian.org/debian unstable/main i386 python3-httpx all 0.28.1-1 [76.2 kB] Get: 174 http://deb.debian.org/debian unstable/main i386 python3-zipp all 3.21.0-1 [10.6 kB] Get: 175 http://deb.debian.org/debian unstable/main i386 python3-importlib-resources all 6.5.2-1 [24.2 kB] Get: 176 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 177 http://deb.debian.org/debian unstable/main i386 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 178 http://deb.debian.org/debian unstable/main i386 python3-inflect all 7.3.1-2 [32.4 kB] Get: 179 http://deb.debian.org/debian unstable/main i386 python3-iniconfig all 1.1.1-2 [6396 B] Get: 180 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 181 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 182 http://deb.debian.org/debian unstable/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 183 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 75.8.0-1 [724 kB] Get: 184 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 185 http://deb.debian.org/debian unstable/main i386 python3-rpds-py i386 0.21.0-2+b1 [275 kB] Get: 186 http://deb.debian.org/debian unstable/main i386 python3-referencing all 0.35.1-2 [23.5 kB] Get: 187 http://deb.debian.org/debian unstable/main i386 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 188 http://deb.debian.org/debian unstable/main i386 python3-jsonschema all 4.19.2-6 [71.4 kB] Get: 189 http://deb.debian.org/debian unstable/main i386 python3-kiwisolver i386 1.4.7-3+b1 [69.7 kB] Get: 190 http://deb.debian.org/debian unstable/main i386 python3-pil i386 11.1.0-5+b1 [518 kB] Get: 191 http://deb.debian.org/debian unstable/main i386 python3.13-tk i386 3.13.2-1 [104 kB] Get: 192 http://deb.debian.org/debian unstable/main i386 python3-tk i386 3.13.2-1 [9516 B] Get: 193 http://deb.debian.org/debian unstable/main i386 python3-pil.imagetk i386 11.1.0-5+b1 [81.9 kB] Get: 194 http://deb.debian.org/debian unstable/main i386 python3-pyparsing all 3.1.2-1 [146 kB] Get: 195 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.2-1 [55.3 kB] Get: 196 http://deb.debian.org/debian unstable/main i386 python3-matplotlib i386 3.8.3-7+b1 [23.0 MB] Get: 197 http://deb.debian.org/debian unstable/main i386 python3-swiglpk i386 5.0.10-2+b2 [65.2 kB] Get: 198 http://deb.debian.org/debian unstable/main i386 python3-optlang all 1.8.2-3 [5376 kB] Get: 199 http://deb.debian.org/debian unstable/main i386 python3-pytz all 2025.1-3 [150 kB] Get: 200 http://deb.debian.org/debian unstable/main i386 python3-tz all 2025.1-3 [4004 B] Get: 201 http://deb.debian.org/debian unstable/main i386 python3-pandas-lib i386 2.2.3+dfsg-8+b1 [4307 kB] Get: 202 http://deb.debian.org/debian unstable/main i386 python3-pandas all 2.2.3+dfsg-8 [3097 kB] Get: 203 http://deb.debian.org/debian unstable/main i386 python3-wheel all 0.45.1-1 [56.7 kB] Get: 204 http://deb.debian.org/debian unstable/main i386 python3-pip all 25.0+dfsg-1 [1454 kB] Get: 205 http://deb.debian.org/debian unstable/main i386 python3-pipdeptree i386 2.2.0-3 [20.6 kB] Get: 206 http://deb.debian.org/debian unstable/main i386 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 207 http://deb.debian.org/debian unstable/main i386 python3-pydantic-core i386 2.27.2-1+b2 [1454 kB] Get: 208 http://deb.debian.org/debian unstable/main i386 python3-pydantic i386 2.10.6-1 [346 kB] Get: 209 http://deb.debian.org/debian unstable/main i386 python3-pytest all 8.3.5-1 [250 kB] Get: 210 http://deb.debian.org/debian unstable/main i386 python3-pytest-benchmark all 5.1.0-1 [44.4 kB] Get: 211 http://deb.debian.org/debian unstable/main i386 python3-pytest-mock all 3.14.0-2 [18.3 kB] Get: 212 http://deb.debian.org/debian unstable/main i386 python3-urllib3 all 2.3.0-1 [114 kB] Get: 213 http://deb.debian.org/debian unstable/main i386 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 214 http://deb.debian.org/debian unstable/main i386 python3-ruamel.yaml.clib i386 0.2.12+ds-1+b1 [137 kB] Get: 215 http://deb.debian.org/debian unstable/main i386 python3-ruamel.yaml all 0.18.10+ds-1 [147 kB] Get: 216 http://deb.debian.org/debian unstable/main i386 python3-sbml5 i386 5.20.4+dfsg-0.1 [3553 kB] Get: 217 http://deb.debian.org/debian unstable/main i386 python3-tabulate all 0.9.0-1 [45.9 kB] Fetched 164 MB in 1s (117 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:i386. (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 ... 19769 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_i386.deb ... Unpacking libpython3.13-minimal:i386 (3.13.2-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_i386.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:i386 (3.13.2-1) ... Setting up libexpat1:i386 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20103 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.2-2_i386.deb ... Unpacking python3-minimal (3.13.2-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libffi8:i386. Preparing to unpack .../4-libffi8_3.4.7-1_i386.deb ... Unpacking libffi8:i386 (3.4.7-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../6-libreadline8t64_8.2-6_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:i386. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_i386.deb ... Unpacking libpython3.13-stdlib:i386 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_i386.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:i386. 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Setting up libjbig0:i386 (2.1-6.1+b2) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Apr 13 06:26:50 UTC 2026. Universal Time is now: Mon Apr 13 06:26:50 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up libbtf2:i386 (1:7.10.1+dfsg-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.1-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libgmpxx4ldbl:i386 (2:6.3.0+dfsg-3) ... Setting up libexpat1-dev:i386 (2.6.4-1) ... Setting up libjpeg62-turbo:i386 (1:2.1.5-3.1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libfribidi0:i386 (1.0.16-1) ... Setting up libimagequant0:i386 (2.18.0-1+b2) ... Setting up libunistring5:i386 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:i386 (1.6.47-1) ... Setting up python3-numpy-dev:i386 (1:2.2.3+ds-5) ... Setting up libtcl8.6:i386 (8.6.16+dfsg-1) ... Setting up autopoint (0.23.1-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libltdl7:i386 (2.5.4-4) ... Setting up libgfortran5:i386 (14.2.0-17) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:i386 (1.5.0-0.1) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:i386 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:i386 (4.5.1+git230720-5) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up libsuitesparseconfig7:i386 (1:7.10.1+dfsg-1) ... Setting up libopenjp2-7:i386 (2.5.3-2) ... Setting up libx11-6:i386 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.8.3-7) ... Setting up openssl (3.4.1-1) ... Setting up libwebpmux3:i386 (1.5.0-0.1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up libblas-dev:i386 (3.12.1-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:i386 (3.12.1-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libgmp-dev:i386 (2:6.3.0+dfsg-3) ... Setting up libamd3:i386 (1:7.10.1+dfsg-1) ... Setting up libxrender1:i386 (1:0.9.10-1.1+b4) ... Setting up libtool (2.5.4-4) ... Setting up libcolamd3:i386 (1:7.10.1+dfsg-1) ... Setting up libsbml5t64:i386 (5.20.4+dfsg-0.1) ... Setting up libspex3:i386 (1:7.10.1+dfsg-1) ... Setting up libsuitesparse-mongoose3:i386 (1:7.10.1+dfsg-1) ... Setting up fontconfig-config (2.15.0-2.1) ... Setting up libwebpdemux2:i386 (1.5.0-0.1) ... Setting up libcxsparse4:i386 (1:7.10.1+dfsg-1) ... Setting up libxext6:i386 (2:1.3.4-1+b3) ... Setting up libcamd3:i386 (1:7.10.1+dfsg-1) ... Setting up libsbml5-dev (5.20.4+dfsg-0.1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libglib2.0-0t64:i386 (2.83.5-1) ... No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:i386 (2.13.3+dfsg-1) ... Setting up libglpk40:i386 (5.0-1+b2) ... Setting up librbio4:i386 (1:7.10.1+dfsg-1) ... Setting up liblapack-dev:i386 (3.12.1-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up libccolamd3:i386 (1:7.10.1+dfsg-1) ... Setting up libreadline8t64:i386 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libxslt1.1:i386 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:i386 (10.2.0-1) ... Setting up libxss1:i386 (1:1.2.3-1+b3) ... Setting up libfontconfig1:i386 (2.15.0-2.1) ... Setting up libpython3.13-stdlib:i386 (3.13.2-1) ... Setting up libpython3-stdlib:i386 (3.13.2-2) ... Setting up libpython3.13:i386 (3.13.2-1) ... Setting up libcholmod5:i386 (1:7.10.1+dfsg-1) ... Setting up libxft2:i386 (2.3.6-1+b4) ... Setting up libspqr4:i386 (1:7.10.1+dfsg-1) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:i386 (8.6.16-1) ... Setting up python3 (3.13.2-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-click (8.2.0+0.really.8.1.8-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-wheel (0.45.1-1) ... Setting up python3.13-tk (3.13.2-1) ... Setting up python3-annotated-types (0.7.0-1) ... Setting up python3-sbml5 (5.20.4+dfsg-0.1) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-fs (2.4.16-7) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up libklu2:i386 (1:7.10.1+dfsg-1) ... Setting up python3-brotli (1.1.0-2+b7) ... Setting up libraqm0:i386 (0.10.2-1) ... Setting up libpython3.13-dev:i386 (3.13.2-1) ... Setting up python3-mdurl (0.1.2-1) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.7-3+b1) ... Setting up python3-idna (3.10-1) ... Setting up cython3 (3.0.11+dfsg-2+b1) ... Setting up python3-h11 (0.14.0-1) ... Setting up python3-depinfo (2.2.0-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pip (25.0+dfsg-1) ... Setting up python3-cpuinfo (9.0.0+git20221119-3) ... Setting up python3-numpy (1:2.2.3+ds-5) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-markdown-it (3.0.0-2) ... Setting up python3-rpds-py (0.21.0-2+b1) ... Setting up libumfpack6:i386 (1:7.10.1+dfsg-1) ... Setting up python3-lxml:i386 (5.3.1-1+b1) ... Setting up python3-dnspython (2.7.0-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-contourpy (1.3.1-1+b1) ... Setting up python3-email-validator (2.2.0-1) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-diskcache (5.6.3-1) ... Setting up python3-pipdeptree (2.2.0-3) ... Setting up python3-swiglpk (5.0.10-2+b2) ... Setting up dh-python (6.20250308) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-httpcore (1.0.7-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sniffio (1.3.1-1) ... Setting up python3-sympy (1.13.3-5) ... Setting up python3-attr (25.1.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... Setting up python3-scipy (1.15.2-2) ... Setting up libpython3-dev:i386 (3.13.2-2) ... Setting up python3-pydantic-core (2.27.2-1+b2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-anyio (4.8.0-2) ... Setting up python3-importlib-resources (6.5.2-1) ... Setting up python3-rich (13.9.4-1) ... Setting up python3-lz4 (4.4.0+dfsg-1+b1) ... Setting up python3-charset-normalizer (3.4.1-1+b1) ... Setting up python3.13-dev (3.13.2-1) ... Setting up python3-pytest (8.3.5-1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b4) ... Setting up blt (2.5.3+dfsg-8) ... Setting up python3-pandas-lib:i386 (2.2.3+dfsg-8+b1) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3-ruamel.yaml.clib (0.2.12+ds-1+b1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-tk:i386 (3.13.2-1) ... Setting up debhelper (13.24.1) ... Setting up python3-pytz (2025.1-3) ... Setting up libparu1:i386 (1:7.10.1+dfsg-1) ... Setting up python3-tz (2025.1-3) ... Setting up python3-pil:i386 (11.1.0-5+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pandas (2.2.3+dfsg-8) ... Setting up python3-httpx (0.28.1-1) ... Setting up python3-pil.imagetk:i386 (11.1.0-5+b1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pydantic (2.10.6-1) ... Setting up python3-dev (3.13.2-2) ... Setting up python3-requests (2.32.3+dfsg-4) ... Setting up python3-ruamel.yaml (0.18.10+ds-1) ... Setting up python3-pytest-mock (3.14.0-2) ... Setting up python3-referencing (0.35.1-2) ... Setting up python3-optlang (1.8.2-3) ... /usr/lib/python3/dist-packages/optlang/matrix_interface.py:60: SyntaxWarning: invalid escape sequence '\m' """A representation of the convex optimizatgion problem in standard form. /usr/lib/python3/dist-packages/optlang/tests/data/parse_the_final_netlib_results.py:34: SyntaxWarning: invalid escape sequence '\*' OBJ_REGEX = re.compile('\* Objvalue : -?\d+/\d+') /usr/lib/python3/dist-packages/optlang/tests/test_cplex_interface.py:222: SyntaxWarning: invalid escape sequence '\s' self.assertRegexpMatches(str(self.model), '\s*Dummy_\d+:\s*y \+ z \+ 2\.333 x - .* = -300') Setting up python3-pytest-benchmark (5.1.0-1) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up python3-setuptools (75.8.0-1) ... Setting up libsuitesparse-dev:i386 (1:7.10.1+dfsg-1) ... Setting up libglpk-dev:i386 (5.0-1+b2) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up python3-jsonschema (4.19.2-6) ... Setting up python3-fonttools (4.55.3-2+b1) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-7+b1) ... 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/python-cobra-0.29.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-cobra_0.29.1-1_source.changes dpkg-buildpackage: info: source package python-cobra dpkg-buildpackage: info: source version 0.29.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-cobra-0.29.1' dh_auto_clean I: pybuild base:311: python3.13 setup.py clean running clean removing '/build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it rm -f cobra/solvers/cglpk.c rm -rf .pytest_cache make[1]: Leaving directory '/build/reproducible-path/python-cobra-0.29.1' 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 I: pybuild base:311: python3.13 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra copying src/cobra/exceptions.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra copying src/cobra/__init__.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra creating /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io copying src/cobra/io/dict.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io copying src/cobra/io/__init__.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io copying src/cobra/io/sbml.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io copying src/cobra/io/mat.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io copying src/cobra/io/json.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io copying src/cobra/io/yaml.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io creating /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/summary copying src/cobra/summary/metabolite_summary.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/summary copying src/cobra/summary/reaction_summary.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/summary copying src/cobra/summary/summary.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/summary copying src/cobra/summary/__init__.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/summary copying src/cobra/summary/model_summary.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/summary creating /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/util copying src/cobra/util/process_pool.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/util copying src/cobra/util/util.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/util copying src/cobra/util/context.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/util copying src/cobra/util/__init__.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/util copying src/cobra/util/solver.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/util copying src/cobra/util/array.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/util creating /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/model.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/configuration.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/group.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/metabolite.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/singleton.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/reaction.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/species.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/formula.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/__init__.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/dictlist.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/gene.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/solution.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core copying src/cobra/core/object.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core creating /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/sampling copying src/cobra/sampling/__init__.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/sampling copying src/cobra/sampling/core.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/sampling copying src/cobra/sampling/sampling.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/sampling copying src/cobra/sampling/hr_sampler.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/sampling copying src/cobra/sampling/achr.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/sampling copying src/cobra/sampling/optgp.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/sampling creating /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/parsimonious.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/helpers.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/deletion.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/reaction.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/variability.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/loopless.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/room.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/__init__.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/fastcc.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/gapfilling.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/geometric.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/phenotype_phase_plane.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis copying src/cobra/flux_analysis/moma.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/flux_analysis creating /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/manipulation copying src/cobra/manipulation/delete.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/manipulation copying src/cobra/manipulation/__init__.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/manipulation copying src/cobra/manipulation/annotate.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/manipulation copying src/cobra/manipulation/modify.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/manipulation copying src/cobra/manipulation/validate.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/manipulation creating /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/data copying src/cobra/data/__init__.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/data creating /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/medium copying src/cobra/medium/minimal_medium.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/medium copying src/cobra/medium/__init__.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/medium copying src/cobra/medium/annotations.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/medium copying src/cobra/medium/boundary_types.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/medium creating /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io/web copying src/cobra/io/web/load.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io/web copying src/cobra/io/web/cobrapy_repository.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io/web copying src/cobra/io/web/abstract_model_repository.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io/web copying src/cobra/io/web/__init__.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io/web copying src/cobra/io/web/bigg_models_repository.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io/web copying src/cobra/io/web/biomodels_repository.py -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io/web copying src/cobra/data/mini.mat -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/data copying src/cobra/data/mini.yml -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/data copying src/cobra/data/mini.json -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/data copying src/cobra/data/iJO1366.xml.gz -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/data copying src/cobra/data/salmonella.xml.gz -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/data copying src/cobra/data/mini_cobra.xml -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/data copying src/cobra/data/textbook.xml.gz -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/data copying src/cobra/io/schema_v1.json -> /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/io dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build; python3.13 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 benchmark: 5.1.0 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000) rootdir: /build/reproducible-path/python-cobra-0.29.1 configfile: tox.ini plugins: benchmark-5.1.0, mock-3.14.0, anyio-4.8.0, typeguard-4.4.2 collected 553 items tests/test_core/test_configuration.py ...E.E [ 1%] tests/test_core/test_core_reaction.py ....EEE.EEssEEEEEEEEEEEEEEEEEEEEEE [ 7%] EEEEEEEEEEE...EEEEExEEEEEEE [ 12%] tests/test_core/test_dictlist.py ...................... [ 16%] tests/test_core/test_formula.py ..... [ 16%] tests/test_core/test_gene.py E [ 17%] tests/test_core/test_gpr.py F....FFFFFFFFFFFFFFFFxFFx................... [ 25%] .............EE..........E [ 29%] tests/test_core/test_group.py E. [ 30%] tests/test_core/test_metabolite.py .EEssEssE [ 31%] tests/test_core/test_model.py EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE [ 39%] EEEEEEEEEEEsEEsEssE [ 42%] tests/test_core/test_solution.py Ess [ 43%] tests/test_flux_analysis/test_deletion.py EEEEEEEE.. [ 45%] tests/test_flux_analysis/test_fastcc.py EFFE [ 45%] tests/test_flux_analysis/test_geometric.py E. [ 46%] tests/test_flux_analysis/test_moma.py E [ 46%] tests/test_flux_analysis/test_parsimonious.py EE [ 46%] tests/test_flux_analysis/test_reaction.py E [ 47%] tests/test_flux_analysis/test_room.py EEEE [ 47%] tests/test_flux_analysis/test_variability.py EEEEEEE [ 49%] tests/test_flux_analysis/test_deletion.py sss [ 49%] tests/test_flux_analysis/test_moma.py s [ 49%] tests/test_flux_analysis/test_deletion.py EEEEE. [ 50%] tests/test_flux_analysis/test_gapfilling.py E [ 50%] tests/test_flux_analysis/test_helpers.py EEE [ 51%] tests/test_flux_analysis/test_loopless.py ...E. [ 52%] tests/test_flux_analysis/test_phenotype_phase_plane.py EEEEEE [ 53%] tests/test_flux_analysis/test_variability.py EEEEEEE [ 54%] tests/test_io/test_annotation.py .. [ 55%] tests/test_io/test_annotation_format.py .. [ 55%] tests/test_io/test_io_order.py EEEEEEEEEEEEEEEEEEEEEEEEEEE [ 60%] tests/test_io/test_json.py .... [ 61%] tests/test_io/test_mat.py ....E..ssss.... [ 63%] tests/test_io/test_notes.py . [ 64%] tests/test_io/test_pickle.py .. [ 64%] tests/test_io/test_sbml.py .ssss............xxxx.x.x..s........E.... [ 71%] tests/test_io/test_web/test_load.py ..ssssE [ 73%] tests/test_io/test_yaml.py .x [ 73%] tests/test_manipulation/test_annotate.py E [ 73%] tests/test_manipulation/test_delete.py EEEEEFF [ 74%] tests/test_manipulation/test_modify.py EEE [ 75%] tests/test_manipulation/test_validate.py EE [ 75%] tests/test_medium/test_boundary_types.py EEEE.EEE.EE [ 77%] tests/test_medium/test_minimal_medium.py EEEEEEEEEE [ 79%] tests/test_sampling/test_achr.py EEEEEE [ 80%] tests/test_sampling/test_optgp.py EEEEEE [ 81%] tests/test_sampling/test_sampling.py EEEEEEEEFE [ 83%] tests/test_summary/test_metabolite_summary.py EEEEEEEEEEEEEEEEE [ 86%] tests/test_summary/test_model_summary.py EEEEEEEEEEEEEEE [ 89%] tests/test_summary/test_reaction_summary.py EEEEEEEEEEEEEEEEEEEE [ 92%] tests/test_util/test_array.py EE [ 93%] tests/test_util/test_context.py .E. [ 93%] tests/test_util/test_process_pool.py ............... [ 96%] tests/test_util/test_solver.py ...EEEEEEEEEEEs [ 99%] tests/test_util/test_util.py ...x [100%] ==================================== ERRORS ==================================== ___________________ ERROR at setup of test_default_tolerance ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe944beb0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_tolerance_assignment __________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe92d3280> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_gpr_modification ____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9237118> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_gpr_modification_with_context _____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe92a2550> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_gene_knock_out _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe93acb68> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_str_from_model _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe928c6b8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_add_metabolite_from_solved_model[glpk] _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9285988> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_add_metabolite_benchmark[glpk] _____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9237f28> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_add_metabolite_benchmark[cplex] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe915e280> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_add_metabolite_benchmark[gurobi] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9aa3d48> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_add_metabolite _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe94e2208> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________ ERROR at setup of test_subtract_metabolite_benchmark[glpk] __________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9158730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________ ERROR at setup of test_subtract_metabolite_benchmark[cplex] __________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe913a820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________ ERROR at setup of test_subtract_metabolite_benchmark[gurobi] _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe92ddb68> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________ ERROR at setup of test_subtract_metabolite[glpk] _______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe910e550> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________ ERROR at setup of test_subtract_metabolite[cplex] _______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe917c0a0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________ ERROR at setup of test_subtract_metabolite[gurobi] ______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9110118> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_mass_balance ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe92c1370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_build_from_string ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9144a78> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_bounds_setter _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9a79898> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________________ ERROR at setup of test_copy __________________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe93cc4d8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________________ ERROR at setup of test_iadd __________________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe93fb910> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_iadd_with_context ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe93cd820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________________ ERROR at setup of test_add __________________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe93c9a78> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________________ ERROR at setup of test_radd __________________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe93c1820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________________ ERROR at setup of test_mul __________________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe93c30a0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________________ ERROR at setup of test_sub __________________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9a9b910> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_removal_from_model_retains_bounds ___________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9a92118> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_set_bounds_scenario_1 _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9a7aa78> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_set_bounds_scenario_2 _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9aada78> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_set_bounds_scenario_3 _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9a81118> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_set_bounds_scenario_4 _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9a94d48> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_set_upper_before_lower_bound_to_0 ___________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9a8a028> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_change_bounds _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9a8bdc0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_make_irreversible ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe951b7a8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_make_reversible ____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9529208> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_make_irreversible_irreversible_to_the_other_side ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe953fa78> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_make_lhs_irreversible_reversible ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe953c6b8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_model_less_reaction __________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe953d370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________________ ERROR at setup of test_knockout ________________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe953ba78> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_irrev_reaction_set_negative_lb _____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9520190> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __ ERROR at setup of test_twist_irrev_right_to_left_reaction_to_left_to_right __ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe924d640> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_set_lb_higher_than_ub_sets_ub_to_new_lb ________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9242b68> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_set_ub_lower_than_lb_sets_lb_to_new_ub _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9254730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_add_metabolites_combine_true ______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9253988> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_reaction_imul _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9252370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_remove_from_model ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe925ba00> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_change_id_is_reflected_in_solver ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe92555c8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_repr_html_ _______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe927b2f8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_compartment_changes __________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9348a00> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_gpr_serialization ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9374460> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_gpr_serialization_backwards_compatibility _______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe93630a0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_repr_html_ _______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9110730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_gpr_symbolism_benchmark ________________ large_once = @pytest.fixture(scope="function") def large_model(large_once: Model) -> Model: """Provide function-level fixture for ecoli model.""" > return large_once.copy() tests/conftest.py:101: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe8502dc0> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_gpr_equality_benchmark _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a86640> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_gpr_from_as_symbolic_equality _____________ large_once = @pytest.fixture(scope="function") def large_model(large_once: Model) -> Model: """Provide function-level fixture for ecoli model.""" > return large_once.copy() tests/conftest.py:101: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe9aad5c8> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_group_add_elements ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8aa24d8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_formula_element_setting ________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b58988> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_set_id[glpk] ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a68b68> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_remove_from_model[glpk] ________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86b32f8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_repr_html_ _______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c7b190> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_add_metabolite _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe85437a8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_remove_metabolite_subtractive _____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe88cf5c8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_remove_metabolite_destructive _____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87e1eb0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_compartments ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a53640> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_model_remove_reaction _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b99eb0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_reaction_remove ____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a5f730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_reaction_delete ____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8796190> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_remove_gene ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a4a910> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_group_model_reaction_association ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87d7730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________ ERROR at setup of test_group_members_add_to_model _______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8afea00> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_group_loss_of_elements _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8829898> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_exchange_reactions ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe85f1208> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________ ERROR at setup of test_add_boundary[exchange-exchange-EX_] __________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8836be0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_add_boundary[demand-demand-DM_] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a1c820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________ ERROR at setup of test_add_boundary[sink-sink-SK_] ______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8cd42f8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______ ERROR at setup of test_add_boundary_context[exchange-exchange-EX_] ______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a066b8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_add_boundary_context[demand-demand-DM_] ________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe858a3e8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________ ERROR at setup of test_add_boundary_context[sink-sink-SK_] __________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8ac7b68> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_add_existing_boundary[exchange-exchange] ________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86197a8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________ ERROR at setup of test_add_existing_boundary[demand-demand] __________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe85e5730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_add_existing_boundary[sink-sink] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a93cd0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_copy_benchmark[optlang-glpk] ______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a02af0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_copy_benchmark_large_model[optlang-glpk] ________ large_once = @pytest.fixture(scope="function") def large_model(large_once: Model) -> Model: """Provide function-level fixture for ecoli model.""" > return large_once.copy() tests/conftest.py:101: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe87a0eb0> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________________ ERROR at setup of test_copy __________________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8cfa820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_copy_with_groups ____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe88c5370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_deepcopy_benchmark ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b2a460> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________________ ERROR at setup of test_deepcopy ________________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c8e7a8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_add_reaction_orphans __________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8bf32f8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_merge_models ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86ab3e8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_change_objective_benchmark[optlang-glpk] ________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe862a820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_get_objective_direction ________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe85f15c8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_set_objective_direction ________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8ada280> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_slim_optimize _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87c5d48> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_optimize[optlang-glpk] _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c5a550> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_change_objective ____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe887c028> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_problem_properties ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8619730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_solution_data_frame __________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8874550> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_context_manager ____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86225c8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_objective_coefficient_reflects_changed_objective ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87ce0a0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____ ERROR at setup of test_change_objective_through_objective_coefficient _____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe88f4460> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_transfer_objective ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87964d8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_model_from_other_model _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a13b68> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_add_reactions _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86d6be0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_add_reactions_single_existing _____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a71730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_add_reactions_duplicate ________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe85b23e8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____ ERROR at setup of test_all_objects_point_to_all_other_correct_objects _____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8996820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_objects_point_to_correct_other_after_copy _______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87d7820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_remove_reactions ____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe89e8640> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________________ ERROR at setup of test_objective _______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8bcf460> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_change_objective_with_context _____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8866820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_set_reaction_objective _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c61c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________ ERROR at setup of test_set_reaction_objective_str _______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe889c820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________ ERROR at setup of test_invalid_objective_raises ________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe860b898> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________ ERROR at setup of test_no_change_for_same_solver _______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe893c3e8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_invalid_solver_change_raises ______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8cca640> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_copy_preserves_existing_solution[glpk] _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8ada190> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_repr_html_ _______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe89a3e38> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_solution_contains_only_reaction_specific_values[glpk] _ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe867ca78> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_single_gene_deletion_fba_benchmark[glpk] ________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8ba4988> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_single_gene_deletion_fba[glpk] _____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8cfa460> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_single_gene_deletion_linear_moma_benchmark[glpk] ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c72a00> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_single_gene_deletion_linear_moma[glpk] _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b16dc0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_single_gene_deletion_room_benchmark[glpk] _______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c14028> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_single_gene_deletion_linear_room_benchmark[glpk] ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe866b3e8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_single_reaction_deletion_benchmark[glpk] ________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe882f3e8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_single_reaction_deletion[glpk] _____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86a2640> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_fastcc_benchmark[glpk] _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8723280> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_fastcc_against_fva_nonblocked_rxns[glpk] ________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe88b90a0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_geometric_fba_benchmark[glpk] _____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b99be0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________ ERROR at setup of test_linear_moma_sanity[glpk] ________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8874550> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_pfba_benchmark[glpk] __________________ large_once = @pytest.fixture(scope="function") def large_model(large_once: Model) -> Model: """Provide function-level fixture for ecoli model.""" > return large_once.copy() tests/conftest.py:101: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe8d00550> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_pfba[glpk] _______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8ba4820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_assess[glpk] ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8d99820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_room_sanity[glpk-True-0.03-0.001] ___________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87a0a00> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________ ERROR at setup of test_room_sanity[glpk-False-0.03-0.001] ___________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8716208> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_room_sanity[glpk-True-0.1-0.01] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe881ae38> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_room_sanity[glpk-False-0.1-0.01] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8920730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_flux_variability_benchmark[glpk] ____________ large_once = @pytest.fixture(scope="function") def large_model(large_once: Model) -> Model: """Provide function-level fixture for ecoli model.""" > return large_once.copy() tests/conftest.py:101: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe8619f28> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________ ERROR at setup of test_pfba_flux_variability[glpk] ______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8890b68> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_flux_variability[glpk] _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe859e0a0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_parallel_flux_variability[glpk] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8cef7a8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_flux_variability_loopless_benchmark[glpk] _______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe89a3be0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_flux_variability_loopless[glpk] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8d8b820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_find_blocked_reactions[glpk] ______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8ada898> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_double_gene_deletion_benchmark _____________ large_once = @pytest.fixture(scope="function") def large_model(large_once: Model) -> Model: """Provide function-level fixture for ecoli model.""" > return large_once.copy() tests/conftest.py:101: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe87e14d8> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_double_gene_deletion __________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a68be0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________ ERROR at setup of test_double_gene_knockout_bug ________________ large_once = @pytest.fixture(scope="function") def large_model(large_once: Model) -> Model: """Provide function-level fixture for ecoli model.""" > return large_once.copy() tests/conftest.py:101: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe8df8460> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________ ERROR at setup of test_double_reaction_deletion_benchmark ___________ large_once = @pytest.fixture(scope="function") def large_model(large_once: Model) -> Model: """Provide function-level fixture for ecoli model.""" > return large_once.copy() tests/conftest.py:101: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe8b225c8> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________ ERROR at setup of test_double_reaction_deletion ________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe85e50a0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_gapfilling _______________________ medium_model = @pytest.fixture(scope="function") def salmonella(medium_model: Model) -> Model: """Provide function-level fixture for salmonella model.""" > return medium_model.copy() tests/conftest.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe89e0988> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_normalize_cutoff ____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a86190> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_normalize_cutoff_with_specified_cutoff_above_default __ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87e82f8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_normalize_cutoff_with_specified_cutoff_below_default __ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe88d9028> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________ ERROR at setup of test_loopless_solution_fluxes ________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a68a78> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_envelope_one ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8d08370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_envelope_multi_reaction_objective ___________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe85663e8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_multi_variable_envelope[variables0-30] _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87a9dc0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_multi_variable_envelope[variables1-20] _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c0aa00> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_multi_variable_envelope[variables2-10] _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b3b6b8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_envelope_two ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86020a0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_loopless_pfba_fva ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86fe820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_fva_data_frame _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe882fbe0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_fva_infeasible _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8cb65c8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_fva_minimization ____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8905640> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________ ERROR at setup of test_find_blocked_reactions_solver_none ___________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe88747a8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_essential_genes ____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8bb9910> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_essential_reactions __________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b70550> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[metabolites-minimized_shuffle-read_sbml_model-write_sbml_model-.xml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[metabolites-minimized_shuffle-load_json_model-save_json_model-.json] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[metabolites-minimized_shuffle-load_yaml_model-save_yaml_model-.yml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[metabolites-minimized_reverse-read_sbml_model-write_sbml_model-.xml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[metabolites-minimized_reverse-load_json_model-save_json_model-.json] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[metabolites-minimized_reverse-load_yaml_model-save_yaml_model-.yml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[reactions-minimized_reverse-read_sbml_model-write_sbml_model-.xml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[reactions-minimized_reverse-load_json_model-save_json_model-.json] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[reactions-minimized_reverse-load_yaml_model-save_yaml_model-.yml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[reactions-minimized_shuffle-read_sbml_model-write_sbml_model-.xml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[reactions-minimized_shuffle-load_json_model-save_json_model-.json] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[reactions-minimized_shuffle-load_yaml_model-save_yaml_model-.yml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[reactions-minimized_sorted-read_sbml_model-write_sbml_model-.xml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[reactions-minimized_sorted-load_json_model-save_json_model-.json] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[reactions-minimized_sorted-load_yaml_model-save_yaml_model-.yml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[metabolites-minimized_sorted-read_sbml_model-write_sbml_model-.xml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[metabolites-minimized_sorted-load_json_model-save_json_model-.json] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[metabolites-minimized_sorted-load_yaml_model-save_yaml_model-.yml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[genes-minimized_sorted-read_sbml_model-write_sbml_model-.xml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[genes-minimized_sorted-load_json_model-save_json_model-.json] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[genes-minimized_sorted-load_yaml_model-save_yaml_model-.yml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[genes-minimized_reverse-read_sbml_model-write_sbml_model-.xml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[genes-minimized_reverse-load_json_model-save_json_model-.json] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[genes-minimized_reverse-load_yaml_model-save_yaml_model-.yml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[genes-minimized_shuffle-read_sbml_model-write_sbml_model-.xml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[genes-minimized_shuffle-load_json_model-save_json_model-.json] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_io_order[genes-minimized_shuffle-load_yaml_model-save_yaml_model-.yml] _ small_model = @pytest.fixture(scope="module") def minimized_shuffle(small_model: Model) -> Model: """Generate a minimal shuffled model for I/O order tests.""" > model = small_model.copy() tests/test_io/test_io_order.py:27: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b01c58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_large_bounds ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe89c6550> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________________ ERROR at setup of test_gprs __________________________ large_once = @pytest.fixture(scope="function") def large_model(large_once: Model) -> Model: """Provide function-level fixture for ecoli model.""" > return large_once.copy() tests/conftest.py:101: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe91de2f8> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_local_load _______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9ac5208> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_sbo_annotation _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8ca7be0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________ ERROR at setup of test_prune_unused_metabolites_output_type __________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8d00d48> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_prune_unused_metabolites_sanity ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe85f1118> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________ ERROR at setup of test_prune_unused_reactions_output_type ___________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe88365c8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_prune_unused_rxns_functionality ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b22e38> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_gene_knockout _____________________ medium_model = @pytest.fixture(scope="function") def salmonella(medium_model: Model) -> Model: """Provide function-level fixture for salmonella model.""" > return medium_model.copy() tests/conftest.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe8de96b8> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_escape_ids _______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86a2910> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_rename_genes ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87bb460> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________ ERROR at setup of test_rename_genes_with_context _______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe858a0a0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_validate_mass_balance _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8d1b910> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_validate_formula_compartment ______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8853118> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_find_external_compartment_single ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe867c730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_find_external_compartment_multi ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe896bdc0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______ ERROR at setup of test_find_external_popular_reconstructions[C_e] _______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8ce76b8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_find_external_popular_reconstructions[e0] _______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe88b9a00> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_find_boundary_types_exchange ______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8920370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________ ERROR at setup of test_find_boundary_types_demand _______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8cb6460> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________ ERROR at setup of test_find_boundary_types_sink ________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86dfdc0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_is_boundary_type ____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8dc5118> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_bad_exchange ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe85d9370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_minimal_medium_linear _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8aba910> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_minimal_medium_linear_benchmark ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b8e730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_minimal_medium_mip ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c14dc0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_minimal_medium_mip_benchmark ______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe89615c8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_minimal_medium_alternative_mip _____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b32cd0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_minimal_medium_exports _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c9e4d8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_minimal_medium_open_exchanges _____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe88424d8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_model_medium ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8934910> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_medium_does_not_affect_reactant_exports ________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8e3c2f8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_medium_does_not_affect_product_exports _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe887c5c8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_achr_init_benchmark __________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8aa2730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_achr_sample_benchmark _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe88b37a8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_validate_wrong_sample _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8bc85c8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________________ ERROR at setup of test_sampling ________________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe890fc58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_batch_sampling _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8d6d208> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_variables_samples ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8ac75c8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_optgp_init_benchmark __________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87fac58> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________ ERROR at setup of test_optgp_sample_benchmark _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8d49118> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________________ ERROR at setup of test_sampling ________________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b70820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ ERROR at setup of test_batch_sampling _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe897b4d8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ ERROR at setup of test_variables_samples ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8699820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________________ ERROR at setup of test_reproject _______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8e5ab68> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_single_achr ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8ae8cd0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_single_optgp ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8cfa898> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_multi_optgp ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe88537a8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_wrong_method ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8bda190> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_fixed_seed _______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c8eaf0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_equality_constraint __________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86eb3e8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_inequality_constraint _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8e625c8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_inhomogeneous_sanity __________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a5fd48> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_single_point_space ___________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8e82550> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______ ERROR at setup of test_metabolite_summary_interface[optlang-glpk] _______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c82d48> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_metabolite_summary_to_frame[optlang-glpk] _______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe89757a8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __ ERROR at setup of test_metabolite_summary_to_string[optlang-glpk-kwargs0] ___ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8baf6b8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __ ERROR at setup of test_metabolite_summary_to_string[optlang-glpk-kwargs1] ___ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8af5370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __ ERROR at setup of test_metabolite_summary_to_string[optlang-glpk-kwargs2] ___ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86fe370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __ ERROR at setup of test_metabolite_summary_to_string[optlang-glpk-kwargs3] ___ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8836af0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __ ERROR at setup of test_metabolite_summary_to_string[optlang-glpk-kwargs4] ___ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8cb6d48> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_metabolite_summary_to_html[optlang-glpk-kwargs0] ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8edd370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_metabolite_summary_to_html[optlang-glpk-kwargs1] ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8690370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_metabolite_summary_to_html[optlang-glpk-kwargs2] ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe9399820> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_metabolite_summary_to_html[optlang-glpk-kwargs3] ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8f44cd0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________ ERROR at setup of test_q8_producing_summary[optlang-glpk] ___________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a93af0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________ ERROR at setup of test_q8_consuming_summary[optlang-glpk] ___________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe863f7a8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________ ERROR at setup of test_fdp_production_with_fva[optlang-glpk] _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8d116b8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_metabolite_summary_flux_in_context[optlang-glpk-q8_c] _ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe881a640> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_metabolite_summary_flux_in_context[optlang-glpk-fdp_c] _ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8619eb0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_metabolite_summary_flux_in_context[optlang-glpk-atp_c] _ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe86352f8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________ ERROR at setup of test_model_summary_interface[optlang-glpk] _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe887c988> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________ ERROR at setup of test_model_summary_to_frame[optlang-glpk] __________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe88423e8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____ ERROR at setup of test_model_summary_to_string[optlang-glpk-kwargs0] _____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8e975c8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____ ERROR at setup of test_model_summary_to_string[optlang-glpk-kwargs1] _____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8db4550> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____ ERROR at setup of test_model_summary_to_string[optlang-glpk-kwargs2] _____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8e5a190> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____ ERROR at setup of test_model_summary_to_string[optlang-glpk-kwargs3] _____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8cefbe0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____ ERROR at setup of test_model_summary_to_string[optlang-glpk-kwargs4] _____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8dbc3e8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______ ERROR at setup of test_model_summary_to_html[optlang-glpk-kwargs0] ______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b0ca78> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______ ERROR at setup of test_model_summary_to_html[optlang-glpk-kwargs1] ______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87b3eb0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______ ERROR at setup of test_model_summary_to_html[optlang-glpk-kwargs2] ______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe85b23e8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______ ERROR at setup of test_model_summary_to_html[optlang-glpk-kwargs3] ______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8d1bcd0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _ ERROR at setup of test_model_summary_to_frame_previous_solution[optlang-glpk] _ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8961370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_model_summary_flux[optlang-glpk] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe89e8190> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_model_summary_fva[optlang-glpk] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8765cd0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______ ERROR at setup of test_model_summary_flux_in_context[optlang-glpk] ______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b3b730> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_reaction_summary_interface[optlang-glpk] ________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe872a640> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_reaction_summary_to_frame[optlang-glpk] ________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8af5118> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_reaction_summary_to_string[optlang-glpk-kwargs0] ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8597a00> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_reaction_summary_to_string[optlang-glpk-kwargs1] ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8ea8898> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_reaction_summary_to_string[optlang-glpk-kwargs2] ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8afe208> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_reaction_summary_to_string[optlang-glpk-kwargs3] ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8e484d8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___ ERROR at setup of test_reaction_summary_to_string[optlang-glpk-kwargs4] ____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe975ba78> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____ ERROR at setup of test_reaction_summary_to_html[optlang-glpk-kwargs0] _____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8ab2dc0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____ ERROR at setup of test_reaction_summary_to_html[optlang-glpk-kwargs1] _____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c61e38> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____ ERROR at setup of test_reaction_summary_to_html[optlang-glpk-kwargs2] _____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe889c2f8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____ ERROR at setup of test_reaction_summary_to_html[optlang-glpk-kwargs3] _____ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8796f28> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_reaction_summary_flux[ACALD-0.0] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8f62190> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_reaction_summary_flux[FUM-5.06] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c14208> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ ERROR at setup of test_reaction_summary_flux[PFK-7.48] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8f7ba78> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______ ERROR at setup of test_reaction_summary_flux_fva[ACALD--1.27-0.0] _______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8d52a78> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_reaction_summary_flux_fva[FUM-0.79-7.38] ________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87c5b68> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_reaction_summary_flux_fva[PFK-2.58-16.38] _______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe855e640> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________ ERROR at setup of test_reaction_summary_flux_in_context[ACALD] ________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8a53370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________ ERROR at setup of test_reaction_summary_flux_in_context[FUM] _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c82898> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________ ERROR at setup of test_reaction_summary_flux_in_context[PFK] _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b8e4d8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_dense_matrix ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c14eb0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_sparse_matrix _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe976ee38> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_get_context ______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe867c550> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ ERROR at setup of test_choose_solver _____________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8e97898> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ ERROR at setup of test_linear_reaction_coefficients ______________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe913abe0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________ ERROR at setup of test_fail_non_linear_reaction_coefficients _________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87a9af0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_add_remove _______________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8996028> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _________________ ERROR at setup of test_add_remove_in_context _________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8b703e8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ ERROR at setup of test_absolute_expression __________________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8d8b7a8> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______ ERROR at setup of test_fix_objective_as_constraint[optlang-glpk] _______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8c9e370> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __ ERROR at setup of test_fix_objective_as_constraint_minimize[optlang-glpk] ___ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8d6dbe0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________ ERROR at setup of test_add_lp_feasibility[optlang-glpk] ____________ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe8eaecd0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______ ERROR at setup of test_add_lexicographic_constraints[optlang-glpk] ______ small_model = @pytest.fixture(scope="function") def model(small_model: Model) -> Model: """Provide function-level fixture for textbook model.""" > return small_model.copy() tests/conftest.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('b0351 or b1241'), memo = {} func = args = . at 0xe87e8be0> state = {'_genes': {'b0351', 'b1241'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ ERROR at setup of test_time_limit _______________________ large_once = @pytest.fixture(scope="function") def large_model(large_once: Model) -> Model: """Provide function-level fixture for ecoli model.""" > return large_once.copy() tests/conftest.py:101: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe8a93820> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError =================================== FAILURES =================================== ___________________________________ test_gpr ___________________________________ def test_gpr() -> None: """Test GPR instance creation and basic usage.""" gpr1 = GPR() assert len(gpr1.genes) == 0 gpr1.update_genes() assert len(gpr1.genes) == 0 assert gpr1.to_string() == "" assert gpr1.eval() > gpr2 = gpr1.copy() tests/test_core/test_gpr.py:25: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe9366208> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ test_and_gpr[a & b-2-gpr_genes0-a and b] ___________________ gpr_input = 'a & b', num_genes = 2, gpr_genes = {'a', 'b'} gpr_output_string = 'a and b' @pytest.mark.parametrize( "gpr_input, num_genes, gpr_genes, gpr_output_string", [ ("a & b", 2, {"a", "b"}, "a and b"), ("a and b", 2, {"a", "b"}, "a and b"), pytest.param( "a AND b", 2, {"a", "b"}, "a and b", marks=pytest.mark.filterwarnings ), ("a & b & c", 3, {"a", "b", "c"}, "(a and b) and c"), ("a and b and c", 3, {"a", "b", "c"}, "a and b and c"), ], ) def test_and_gpr(gpr_input, num_genes, gpr_genes, gpr_output_string) -> None: """Test 'and' GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in powerset_ne(gpr_genes): assert not gpr1.eval(ko_genes) assert gpr1.body > gpr1.copy() tests/test_core/test_gpr.py:92: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a and b'), memo = {} func = args = . at 0xe93c3dc0> state = {'_genes': {'a', 'b'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ test_and_gpr[a and b-2-gpr_genes1-a and b] __________________ gpr_input = 'a and b', num_genes = 2, gpr_genes = {'a', 'b'} gpr_output_string = 'a and b' @pytest.mark.parametrize( "gpr_input, num_genes, gpr_genes, gpr_output_string", [ ("a & b", 2, {"a", "b"}, "a and b"), ("a and b", 2, {"a", "b"}, "a and b"), pytest.param( "a AND b", 2, {"a", "b"}, "a and b", marks=pytest.mark.filterwarnings ), ("a & b & c", 3, {"a", "b", "c"}, "(a and b) and c"), ("a and b and c", 3, {"a", "b", "c"}, "a and b and c"), ], ) def test_and_gpr(gpr_input, num_genes, gpr_genes, gpr_output_string) -> None: """Test 'and' GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in powerset_ne(gpr_genes): assert not gpr1.eval(ko_genes) assert gpr1.body > gpr1.copy() tests/test_core/test_gpr.py:92: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a and b'), memo = {} func = args = . at 0xe9366e38> state = {'_genes': {'a', 'b'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError __________________ test_and_gpr[a AND b-2-gpr_genes2-a and b] __________________ gpr_input = 'a AND b', num_genes = 2, gpr_genes = {'a', 'b'} gpr_output_string = 'a and b' @pytest.mark.parametrize( "gpr_input, num_genes, gpr_genes, gpr_output_string", [ ("a & b", 2, {"a", "b"}, "a and b"), ("a and b", 2, {"a", "b"}, "a and b"), pytest.param( "a AND b", 2, {"a", "b"}, "a and b", marks=pytest.mark.filterwarnings ), ("a & b & c", 3, {"a", "b", "c"}, "(a and b) and c"), ("a and b and c", 3, {"a", "b", "c"}, "a and b and c"), ], ) def test_and_gpr(gpr_input, num_genes, gpr_genes, gpr_output_string) -> None: """Test 'and' GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in powerset_ne(gpr_genes): assert not gpr1.eval(ko_genes) assert gpr1.body > gpr1.copy() tests/test_core/test_gpr.py:92: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a and b'), memo = {} func = args = . at 0xe910edc0> state = {'_genes': {'a', 'b'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ------------------------------ Captured log call ------------------------------- WARNING cobra.core.gene:gene.py:354 Uppercase AND/OR found in rule 'a AND b'. WARNING cobra.core.gene:gene.py:357 invalid syntax _____________ test_and_gpr[a & b & c-3-gpr_genes3-(a and b) and c] _____________ gpr_input = 'a & b & c', num_genes = 3, gpr_genes = {'a', 'b', 'c'} gpr_output_string = '(a and b) and c' @pytest.mark.parametrize( "gpr_input, num_genes, gpr_genes, gpr_output_string", [ ("a & b", 2, {"a", "b"}, "a and b"), ("a and b", 2, {"a", "b"}, "a and b"), pytest.param( "a AND b", 2, {"a", "b"}, "a and b", marks=pytest.mark.filterwarnings ), ("a & b & c", 3, {"a", "b", "c"}, "(a and b) and c"), ("a and b and c", 3, {"a", "b", "c"}, "a and b and c"), ], ) def test_and_gpr(gpr_input, num_genes, gpr_genes, gpr_output_string) -> None: """Test 'and' GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in powerset_ne(gpr_genes): assert not gpr1.eval(ko_genes) assert gpr1.body > gpr1.copy() tests/test_core/test_gpr.py:92: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('(a and b) and c'), memo = {} func = args = . at 0xe9a79cd0> state = {'_genes': {'a', 'b', 'c'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________ test_and_gpr[a and b and c-3-gpr_genes4-a and b and c] ____________ gpr_input = 'a and b and c', num_genes = 3, gpr_genes = {'a', 'b', 'c'} gpr_output_string = 'a and b and c' @pytest.mark.parametrize( "gpr_input, num_genes, gpr_genes, gpr_output_string", [ ("a & b", 2, {"a", "b"}, "a and b"), ("a and b", 2, {"a", "b"}, "a and b"), pytest.param( "a AND b", 2, {"a", "b"}, "a and b", marks=pytest.mark.filterwarnings ), ("a & b & c", 3, {"a", "b", "c"}, "(a and b) and c"), ("a and b and c", 3, {"a", "b", "c"}, "a and b and c"), ], ) def test_and_gpr(gpr_input, num_genes, gpr_genes, gpr_output_string) -> None: """Test 'and' GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in powerset_ne(gpr_genes): assert not gpr1.eval(ko_genes) assert gpr1.body > gpr1.copy() tests/test_core/test_gpr.py:92: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a and b and c'), memo = {} func = args = . at 0xe9a8aaf0> state = {'_genes': {'a', 'b', 'c'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________ test_or_gpr[a | b-2-gpr_genes0-a or b] ____________________ gpr_input = 'a | b', num_genes = 2, gpr_genes = {'a', 'b'} gpr_output_string = 'a or b' @pytest.mark.parametrize( "gpr_input, num_genes, gpr_genes, gpr_output_string", [ ("a | b", 2, {"a", "b"}, "a or b"), ("a or b", 2, {"a", "b"}, "a or b"), pytest.param( "a OR b", 2, {"a", "b"}, "a or b", marks=pytest.mark.filterwarnings ), ("a | b | c", 3, {"a", "b", "c"}, "(a or b) or c"), ("a or b or c", 3, {"a", "b", "c"}, "a or b or c"), ], ) def test_or_gpr( gpr_input: str, num_genes: int, gpr_genes: Set, gpr_output_string: str ) -> None: """Test 'or' GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in all_except_one(gpr_genes): assert gpr1.eval(ko_genes) assert not gpr1.eval(gpr_genes) assert gpr1.body > gpr1.copy() tests/test_core/test_gpr.py:135: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a or b'), memo = {} func = args = . at 0xe924d028> state = {'_genes': {'a', 'b'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ test_or_gpr[a or b-2-gpr_genes1-a or b] ____________________ gpr_input = 'a or b', num_genes = 2, gpr_genes = {'a', 'b'} gpr_output_string = 'a or b' @pytest.mark.parametrize( "gpr_input, num_genes, gpr_genes, gpr_output_string", [ ("a | b", 2, {"a", "b"}, "a or b"), ("a or b", 2, {"a", "b"}, "a or b"), pytest.param( "a OR b", 2, {"a", "b"}, "a or b", marks=pytest.mark.filterwarnings ), ("a | b | c", 3, {"a", "b", "c"}, "(a or b) or c"), ("a or b or c", 3, {"a", "b", "c"}, "a or b or c"), ], ) def test_or_gpr( gpr_input: str, num_genes: int, gpr_genes: Set, gpr_output_string: str ) -> None: """Test 'or' GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in all_except_one(gpr_genes): assert gpr1.eval(ko_genes) assert not gpr1.eval(gpr_genes) assert gpr1.body > gpr1.copy() tests/test_core/test_gpr.py:135: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a or b'), memo = {} func = args = . at 0xe9a79028> state = {'_genes': {'a', 'b'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ___________________ test_or_gpr[a OR b-2-gpr_genes2-a or b] ____________________ gpr_input = 'a OR b', num_genes = 2, gpr_genes = {'a', 'b'} gpr_output_string = 'a or b' @pytest.mark.parametrize( "gpr_input, num_genes, gpr_genes, gpr_output_string", [ ("a | b", 2, {"a", "b"}, "a or b"), ("a or b", 2, {"a", "b"}, "a or b"), pytest.param( "a OR b", 2, {"a", "b"}, "a or b", marks=pytest.mark.filterwarnings ), ("a | b | c", 3, {"a", "b", "c"}, "(a or b) or c"), ("a or b or c", 3, {"a", "b", "c"}, "a or b or c"), ], ) def test_or_gpr( gpr_input: str, num_genes: int, gpr_genes: Set, gpr_output_string: str ) -> None: """Test 'or' GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in all_except_one(gpr_genes): assert gpr1.eval(ko_genes) assert not gpr1.eval(gpr_genes) assert gpr1.body > gpr1.copy() tests/test_core/test_gpr.py:135: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a or b'), memo = {} func = args = . at 0xe9253cd0> state = {'_genes': {'a', 'b'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ------------------------------ Captured log call ------------------------------- WARNING cobra.core.gene:gene.py:354 Uppercase AND/OR found in rule 'a OR b'. WARNING cobra.core.gene:gene.py:357 invalid syntax ______________ test_or_gpr[a | b | c-3-gpr_genes3-(a or b) or c] _______________ gpr_input = 'a | b | c', num_genes = 3, gpr_genes = {'a', 'b', 'c'} gpr_output_string = '(a or b) or c' @pytest.mark.parametrize( "gpr_input, num_genes, gpr_genes, gpr_output_string", [ ("a | b", 2, {"a", "b"}, "a or b"), ("a or b", 2, {"a", "b"}, "a or b"), pytest.param( "a OR b", 2, {"a", "b"}, "a or b", marks=pytest.mark.filterwarnings ), ("a | b | c", 3, {"a", "b", "c"}, "(a or b) or c"), ("a or b or c", 3, {"a", "b", "c"}, "a or b or c"), ], ) def test_or_gpr( gpr_input: str, num_genes: int, gpr_genes: Set, gpr_output_string: str ) -> None: """Test 'or' GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in all_except_one(gpr_genes): assert gpr1.eval(ko_genes) assert not gpr1.eval(gpr_genes) assert gpr1.body > gpr1.copy() tests/test_core/test_gpr.py:135: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('(a or b) or c'), memo = {} func = args = . at 0xe9252820> state = {'_genes': {'a', 'b', 'c'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________ test_or_gpr[a or b or c-3-gpr_genes4-a or b or c] _______________ gpr_input = 'a or b or c', num_genes = 3, gpr_genes = {'a', 'b', 'c'} gpr_output_string = 'a or b or c' @pytest.mark.parametrize( "gpr_input, num_genes, gpr_genes, gpr_output_string", [ ("a | b", 2, {"a", "b"}, "a or b"), ("a or b", 2, {"a", "b"}, "a or b"), pytest.param( "a OR b", 2, {"a", "b"}, "a or b", marks=pytest.mark.filterwarnings ), ("a | b | c", 3, {"a", "b", "c"}, "(a or b) or c"), ("a or b or c", 3, {"a", "b", "c"}, "a or b or c"), ], ) def test_or_gpr( gpr_input: str, num_genes: int, gpr_genes: Set, gpr_output_string: str ) -> None: """Test 'or' GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in all_except_one(gpr_genes): assert gpr1.eval(ko_genes) assert not gpr1.eval(gpr_genes) assert gpr1.body > gpr1.copy() tests/test_core/test_gpr.py:135: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a or b or c'), memo = {} func = args = . at 0xe9520820> state = {'_genes': {'a', 'b', 'c'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________ test_complicated_gpr[(a | b) & c] _______________________ gpr_input = '(a | b) & c' @pytest.mark.parametrize( "gpr_input", [ "(a | b) & c", "(a or b) and c", pytest.param("(a OR b) AND c", marks=pytest.mark.filterwarnings), ], ) def test_complicated_gpr(gpr_input: str) -> None: """Test complicated GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == 3 gpr1.update_genes() assert len(gpr1.genes) == 3 assert gpr1.to_string() == "(a or b) and c" assert gpr1.eval() assert gpr1.body assert gpr1.eval() assert gpr1.eval("a") assert gpr1.eval("b") assert not gpr1.eval("c") assert not gpr1.eval(["a", "b"]) assert not gpr1.eval(["a", "b", "c"]) > gpr1.copy() tests/test_core/test_gpr.py:161: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('(a or b) and c'), memo = {} func = args = . at 0xe9a790a0> state = {'_genes': {'a', 'b', 'c'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ test_complicated_gpr[(a or b) and c] _____________________ gpr_input = '(a or b) and c' @pytest.mark.parametrize( "gpr_input", [ "(a | b) & c", "(a or b) and c", pytest.param("(a OR b) AND c", marks=pytest.mark.filterwarnings), ], ) def test_complicated_gpr(gpr_input: str) -> None: """Test complicated GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == 3 gpr1.update_genes() assert len(gpr1.genes) == 3 assert gpr1.to_string() == "(a or b) and c" assert gpr1.eval() assert gpr1.body assert gpr1.eval() assert gpr1.eval("a") assert gpr1.eval("b") assert not gpr1.eval("c") assert not gpr1.eval(["a", "b"]) assert not gpr1.eval(["a", "b", "c"]) > gpr1.copy() tests/test_core/test_gpr.py:161: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('(a or b) and c'), memo = {} func = args = . at 0xe91decd0> state = {'_genes': {'a', 'b', 'c'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________________ test_complicated_gpr[(a OR b) AND c] _____________________ gpr_input = '(a OR b) AND c' @pytest.mark.parametrize( "gpr_input", [ "(a | b) & c", "(a or b) and c", pytest.param("(a OR b) AND c", marks=pytest.mark.filterwarnings), ], ) def test_complicated_gpr(gpr_input: str) -> None: """Test complicated GPR.""" gpr1 = GPR.from_string(gpr_input) assert len(gpr1.genes) == 3 gpr1.update_genes() assert len(gpr1.genes) == 3 assert gpr1.to_string() == "(a or b) and c" assert gpr1.eval() assert gpr1.body assert gpr1.eval() assert gpr1.eval("a") assert gpr1.eval("b") assert not gpr1.eval("c") assert not gpr1.eval(["a", "b"]) assert not gpr1.eval(["a", "b", "c"]) > gpr1.copy() tests/test_core/test_gpr.py:161: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('(a or b) and c'), memo = {} func = args = . at 0xe90f2be0> state = {'_genes': {'a', 'b', 'c'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ------------------------------ Captured log call ------------------------------- WARNING cobra.core.gene:gene.py:354 Uppercase AND/OR found in rule '(a OR b) AND c'. WARNING cobra.core.gene:gene.py:357 invalid syntax. Perhaps you forgot a comma? ____________________ test_gpr_from_ast_or[a-1-gpr_genes0-a] ____________________ string_to_ast = 'a', num_genes = 1, gpr_genes = {'a'}, gpr_output_string = 'a' @pytest.mark.parametrize( "string_to_ast, num_genes, gpr_genes, gpr_output_string", [ ("a", 1, {"a"}, "a"), ("a | b", 2, {"a", "b"}, "a or b"), ("a or b", 2, {"a", "b"}, "a or b"), pytest.param("a OR b", 2, {"a", "b"}, "a or b", marks=pytest.mark.xfail), ], ) def test_gpr_from_ast_or( string_to_ast: str, num_genes: int, gpr_genes: set, gpr_output_string: str ) -> None: """Test GPR from AST 'or'.""" ast_tree = ast_parse(string_to_ast, "", "eval") gpr1 = GPR(ast_tree) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in all_except_one(gpr_genes): assert gpr1.eval(ko_genes) assert not gpr1.eval(gpr_genes) > gpr1.copy() tests/test_core/test_gpr.py:188: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a'), memo = {}, func = args = . at 0xe9a81208> state = {'_genes': {'a'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________ test_gpr_from_ast_or[a | b-2-gpr_genes1-a or b] ________________ string_to_ast = 'a | b', num_genes = 2, gpr_genes = {'a', 'b'} gpr_output_string = 'a or b' @pytest.mark.parametrize( "string_to_ast, num_genes, gpr_genes, gpr_output_string", [ ("a", 1, {"a"}, "a"), ("a | b", 2, {"a", "b"}, "a or b"), ("a or b", 2, {"a", "b"}, "a or b"), pytest.param("a OR b", 2, {"a", "b"}, "a or b", marks=pytest.mark.xfail), ], ) def test_gpr_from_ast_or( string_to_ast: str, num_genes: int, gpr_genes: set, gpr_output_string: str ) -> None: """Test GPR from AST 'or'.""" ast_tree = ast_parse(string_to_ast, "", "eval") gpr1 = GPR(ast_tree) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in all_except_one(gpr_genes): assert gpr1.eval(ko_genes) assert not gpr1.eval(gpr_genes) > gpr1.copy() tests/test_core/test_gpr.py:188: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a or b'), memo = {} func = args = . at 0xe9a79af0> state = {'_genes': {'a', 'b'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _______________ test_gpr_from_ast_or[a or b-2-gpr_genes2-a or b] _______________ string_to_ast = 'a or b', num_genes = 2, gpr_genes = {'a', 'b'} gpr_output_string = 'a or b' @pytest.mark.parametrize( "string_to_ast, num_genes, gpr_genes, gpr_output_string", [ ("a", 1, {"a"}, "a"), ("a | b", 2, {"a", "b"}, "a or b"), ("a or b", 2, {"a", "b"}, "a or b"), pytest.param("a OR b", 2, {"a", "b"}, "a or b", marks=pytest.mark.xfail), ], ) def test_gpr_from_ast_or( string_to_ast: str, num_genes: int, gpr_genes: set, gpr_output_string: str ) -> None: """Test GPR from AST 'or'.""" ast_tree = ast_parse(string_to_ast, "", "eval") gpr1 = GPR(ast_tree) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in all_except_one(gpr_genes): assert gpr1.eval(ko_genes) assert not gpr1.eval(gpr_genes) > gpr1.copy() tests/test_core/test_gpr.py:188: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a or b'), memo = {} func = args = . at 0xe93fb820> state = {'_genes': {'a', 'b'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________ test_gpr_from_ast_and[a & b-2-gpr_genes0-a and b] _______________ string_to_ast = 'a & b', num_genes = 2, gpr_genes = {'a', 'b'} gpr_output_string = 'a and b' @pytest.mark.parametrize( "string_to_ast, num_genes, gpr_genes, gpr_output_string", [ ("a & b", 2, {"a", "b"}, "a and b"), ("a and b", 2, {"a", "b"}, "a and b"), pytest.param("a AND b", 2, {"a", "b"}, "a and b", marks=pytest.mark.xfail), ], ) def test_gpr_from_ast_and( string_to_ast: str, num_genes: int, gpr_genes: set, gpr_output_string: str ) -> None: """Test GPR from AST 'and'.""" ast_tree = ast_parse(string_to_ast, "", "eval") gpr1 = GPR(ast_tree) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in powerset_ne(gpr_genes): assert not gpr1.eval(ko_genes) > gpr1.copy() tests/test_core/test_gpr.py:213: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a and b'), memo = {} func = args = . at 0xe93635c8> state = {'_genes': {'a', 'b'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError _____________ test_gpr_from_ast_and[a and b-2-gpr_genes1-a and b] ______________ string_to_ast = 'a and b', num_genes = 2, gpr_genes = {'a', 'b'} gpr_output_string = 'a and b' @pytest.mark.parametrize( "string_to_ast, num_genes, gpr_genes, gpr_output_string", [ ("a & b", 2, {"a", "b"}, "a and b"), ("a and b", 2, {"a", "b"}, "a and b"), pytest.param("a AND b", 2, {"a", "b"}, "a and b", marks=pytest.mark.xfail), ], ) def test_gpr_from_ast_and( string_to_ast: str, num_genes: int, gpr_genes: set, gpr_output_string: str ) -> None: """Test GPR from AST 'and'.""" ast_tree = ast_parse(string_to_ast, "", "eval") gpr1 = GPR(ast_tree) assert len(gpr1.genes) == num_genes gpr1.update_genes() assert len(gpr1.genes) == num_genes assert gpr1.genes == gpr_genes assert gpr1.to_string() == gpr_output_string assert gpr1.eval() for ko_genes in powerset_ne(gpr_genes): assert not gpr1.eval(ko_genes) > gpr1.copy() tests/test_core/test_gpr.py:213: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('a and b'), memo = {} func = args = . at 0xe93fb2f8> state = {'_genes': {'a', 'b'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ______________________________ test_figure1[glpk] ______________________________ figure1_model = , all_solvers = 'glpk' def test_figure1(figure1_model: Model, all_solvers: List[str]) -> None: """Test FASTCC.""" figure1_model.solver = all_solvers > consistent_model = fastcc(figure1_model) tests/test_flux_analysis/test_fastcc.py:92: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/flux_analysis/fastcc.py:175: in fastcc consistent_model = model.copy() cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe8a79898> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ---------------------------- Captured stdout setup ----------------------------- unknown metabolite 'A' created unknown metabolite 'B' created unknown metabolite 'D' created unknown metabolite 'C' created _____________________________ test_opposing[glpk] ______________________________ opposing_model = , all_solvers = 'glpk' def test_opposing(opposing_model: Model, all_solvers: List[str]) -> None: """Test FASTCC.""" opposing_model.solver = all_solvers > consistent_model = fastcc(opposing_model) tests/test_flux_analysis/test_fastcc.py:100: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/flux_analysis/fastcc.py:175: in fastcc consistent_model = model.copy() cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe8554820> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ---------------------------- Captured stdout setup ----------------------------- unknown metabolite 'A' created unknown metabolite 'C' created unknown metabolite 'D' created ______________________________ test_remove_genes _______________________________ def test_remove_genes() -> None: """Test gene removal.""" m = Model("test") m.add_reactions([Reaction("r" + str(i + 1)) for i in range(8)]) assert len(m.reactions) == 8 rxns = m.reactions rxns.r1.gene_reaction_rule = "(a and b) or (c and a)" rxns.r2.gene_reaction_rule = "(a and b and d and e)" rxns.r3.gene_reaction_rule = "(a and b) or (b and c)" rxns.r4.gene_reaction_rule = "(f and b) or (b and c)" rxns.r5.gene_reaction_rule = "x" rxns.r6.gene_reaction_rule = "y" rxns.r7.gene_reaction_rule = "x or z" rxns.r8.gene_reaction_rule = "" assert "a" in m.genes assert "x" in m.genes > remove_genes(m, ["a"], remove_reactions=False) tests/test_manipulation/test_delete.py:192: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/manipulation/delete.py:250: in remove_genes old_gpr = rxn.gpr.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('(a and b) or (c and a)'), memo = {} func = args = . at 0xe85f6af0> state = {'_genes': {'a', 'b', 'c'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ________________________ test_remove_genes_with_context ________________________ def test_remove_genes_with_context() -> None: """Test gene removal is reversed in context.""" m = Model("test") m.add_reactions([Reaction("r" + str(i + 1)) for i in range(8)]) assert len(m.reactions) == 8 rxns = m.reactions rxns.r1.gene_reaction_rule = "(a and b) or (c and a)" rxns.r2.gene_reaction_rule = "(a and b and d and e)" rxns.r3.gene_reaction_rule = "(a and b) or (b and c)" rxns.r4.gene_reaction_rule = "(f and b) or (b and c)" rxns.r5.gene_reaction_rule = "x" rxns.r6.gene_reaction_rule = "y" rxns.r7.gene_reaction_rule = "x or z" rxns.r8.gene_reaction_rule = "" with m: > remove_genes(m, ["a"], remove_reactions=False) tests/test_manipulation/test_delete.py:232: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/manipulation/delete.py:250: in remove_genes old_gpr = rxn.gpr.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR('(a and b) or (c and a)'), memo = {} func = args = . at 0xe8aa8af0> state = {'_genes': {'a', 'b', 'c'}, 'body': , 'type_ignores': []} listiter = None, dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError ____________________________ test_complicated_model ____________________________ def test_complicated_model() -> None: """Test a complicated model. Difficult model since the online mean calculation is numerically unstable, so many samples weakly violate the equality constraints. """ model = Model("flux_split") reaction1 = Reaction("V1") reaction2 = Reaction("V2") reaction3 = Reaction("V3") reaction1.bounds = (0, 6) reaction2.bounds = (0, 8) reaction3.bounds = (0, 10) A = Metabolite("A") reaction1.add_metabolites({A: -1}) reaction2.add_metabolites({A: -1}) reaction3.add_metabolites({A: 1}) model.add_reactions([reaction1, reaction2, reaction3]) > optgp = OptGPSampler(model, 1, seed=42) tests/test_sampling/test_sampling.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cobra/sampling/optgp.py:115: in __init__ super().__init__(model, thinning, nproj=nproj, seed=seed, **kwargs) cobra/sampling/hr_sampler.py:198: in __init__ self.model = model.copy() cobra/core/model.py:426: in copy new_reaction.__dict__[attr] = copy(value) /usr/lib/python3.13/copy.py:80: in copy return copier(x) cobra/core/gene.py:554: in __copy__ return self.copy() cobra/core/gene.py:550: in copy return deepcopy(self) /usr/lib/python3.13/copy.py:163: in deepcopy y = _reconstruct(x, memo, *rv) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ x = cobra.core.gene.GPR(''), memo = {}, func = args = . at 0xe86d6370> state = {'_genes': set(), 'body': None, 'type_ignores': []}, listiter = None dictiter = None def _reconstruct(x, memo, func, args, state=None, listiter=None, dictiter=None, *, deepcopy=deepcopy): deep = memo is not None if deep and args: args = (deepcopy(arg, memo) for arg in args) > y = func(*args) E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given /usr/lib/python3.13/copy.py:254: TypeError =============================== warnings summary =============================== :488 :488 :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute :488 :488 :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute :488 :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_and_gpr[a AND b-2-gpr_genes2-a and b] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b'. warn( .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_or_gpr[a OR b-2-gpr_genes2-a or b] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[a OR b-symbolic_gpr2] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_from_symbolic[a OR b-symbolic_gpr5] /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b'. warn( .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_complicated_gpr[(a OR b) AND c] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[(a OR b) AND c-symbolic_gpr6] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_and_strs] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_from_symbolic[(a OR b) AND c-symbolic_gpr9] /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule '(a OR b) AND c'. warn( .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_that_needs_two_replacements /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule '(591001.3.peg.1891 AND 591001.3.peg.1892 AND 591001.3.peg.1893)'. warn( .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b AND a'. warn( .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b OR a'. warn( .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_strs] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b or c'. warn( .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_and_strs] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] .pybuild/cpython3_3.13_cobra/build/tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b and c'. warn( .pybuild/cpython3_3.13_cobra/build/tests/test_flux_analysis/test_gapfilling.py: 980 warnings /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/tests/conftest.py:53: DeprecationWarning: BoolOp.__init__ missing 1 required positional argument: 'op'. This will become an error in Python 3.15. return _load(infile) .pybuild/cpython3_3.13_cobra/build/tests/test_flux_analysis/test_gapfilling.py: 4020 warnings /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/tests/conftest.py:53: DeprecationWarning: Name.__init__ missing 1 required positional argument: 'id'. This will become an error in Python 3.15. return _load(infile) .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_json.py: 34 warnings .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py: 34 warnings .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_pickle.py: 34 warnings .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_yaml.py: 34 warnings /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/tests/test_io/conftest.py:17: DeprecationWarning: Name.__init__ missing 1 required positional argument: 'id'. This will become an error in Python 3.15. return load(infile) .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_json.py: 11 warnings .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py: 11 warnings .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_pickle.py: 11 warnings .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_yaml.py: 11 warnings /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/tests/test_io/conftest.py:17: DeprecationWarning: BoolOp.__init__ missing 1 required positional argument: 'op'. This will become an error in Python 3.15. return load(infile) .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_json.py: 1 warning .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py: 3 warnings .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_pickle.py: 1 warning .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_sbml.py: 9 warnings .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_yaml.py: 1 warning /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/util/solver.py:554: UserWarning: Solver status is 'infeasible'. warn(f"Solver status is '{status}'.", UserWarning) .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py::test_load_matlab_model[raven_model-data_directory-raven.mat] .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py::test_save_matlab_model[raven_model-raven.mat] /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py:32: DeprecationWarning: BoolOp.__init__ missing 1 required positional argument: 'op'. This will become an error in Python 3.15. return load(infile) .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py::test_load_matlab_model[raven_model-data_directory-raven.mat] .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py::test_load_matlab_model[raven_model-data_directory-raven.mat] .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py::test_load_matlab_model[raven_model-data_directory-raven.mat] .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py::test_save_matlab_model[raven_model-raven.mat] .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py::test_save_matlab_model[raven_model-raven.mat] .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py::test_save_matlab_model[raven_model-raven.mat] /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/tests/test_io/test_mat.py:32: DeprecationWarning: Name.__init__ missing 1 required positional argument: 'id'. This will become an error in Python 3.15. return load(infile) .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_pickle.py: 34 warnings /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/tests/test_io/test_pickle.py:24: DeprecationWarning: Name.__init__ missing 1 required positional argument: 'id'. This will become an error in Python 3.15. pickle_model = load_function(infile) .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_pickle.py: 11 warnings /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/tests/test_io/test_pickle.py:24: DeprecationWarning: BoolOp.__init__ missing 1 required positional argument: 'op'. This will become an error in Python 3.15. pickle_model = load_function(infile) .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_sbml.py: 136 warnings /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/tests/test_io/test_sbml.py:268: DeprecationWarning: Name.__init__ missing 1 required positional argument: 'id'. This will become an error in Python 3.15. reference_model = load(infile) .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_sbml.py: 44 warnings /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/tests/test_io/test_sbml.py:268: DeprecationWarning: BoolOp.__init__ missing 1 required positional argument: 'op'. This will become an error in Python 3.15. reference_model = load(infile) .pybuild/cpython3_3.13_cobra/build/tests/test_io/test_yaml.py::test_save_yaml_model /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/tests/test_io/test_yaml.py:29: PendingDeprecationWarning: you should no longer specify 'unsafe'. For **dumping only** use yaml=YAML(typ='full') yaml = YAML(typ="unsafe") .pybuild/cpython3_3.13_cobra/build/tests/test_util/test_process_pool.py::test_with_context /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build/cobra/util/process_pool.py:71: PytestMockWarning: Mocks returned by pytest-mock do not need to be used as context managers. The mocker fixture automatically undoes mocking at the end of a test. This warning can be ignored if it was triggered by mocking a context manager. https://pytest-mock.readthedocs.io/en/latest/remarks.html#usage-as-context-manager self._pool.__enter__() -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -------------------------------------------------------------------------------------- benchmark: 2 tests ------------------------------------------------------------------------------------- Name (time in ms) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- test_loopless_benchmark_after 1.5909 (1.0) 1.8403 (1.0) 1.6969 (1.0) 0.0440 (1.0) 1.6968 (1.0) 0.0581 (1.0) 86;1 589.2932 (1.0) 287 1 test_loopless_benchmark_before 7.0060 (4.40) 7.6736 (4.17) 7.2055 (4.25) 0.1345 (3.06) 7.2045 (4.25) 0.1865 (3.21) 11;1 138.7829 (0.24) 44 1 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Legend: Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile. OPS: Operations Per Second, computed as 1 / Mean =========================== short test summary info ============================ FAILED tests/test_core/test_gpr.py::test_gpr - TypeError: GPR.__init__() take... FAILED tests/test_core/test_gpr.py::test_and_gpr[a & b-2-gpr_genes0-a and b] FAILED tests/test_core/test_gpr.py::test_and_gpr[a and b-2-gpr_genes1-a and b] FAILED tests/test_core/test_gpr.py::test_and_gpr[a AND b-2-gpr_genes2-a and b] FAILED tests/test_core/test_gpr.py::test_and_gpr[a & b & c-3-gpr_genes3-(a and b) and c] FAILED tests/test_core/test_gpr.py::test_and_gpr[a and b and c-3-gpr_genes4-a and b and c] FAILED tests/test_core/test_gpr.py::test_or_gpr[a | b-2-gpr_genes0-a or b] - ... FAILED tests/test_core/test_gpr.py::test_or_gpr[a or b-2-gpr_genes1-a or b] FAILED tests/test_core/test_gpr.py::test_or_gpr[a OR b-2-gpr_genes2-a or b] FAILED tests/test_core/test_gpr.py::test_or_gpr[a | b | c-3-gpr_genes3-(a or b) or c] FAILED tests/test_core/test_gpr.py::test_or_gpr[a or b or c-3-gpr_genes4-a or b or c] FAILED tests/test_core/test_gpr.py::test_complicated_gpr[(a | b) & c] - TypeE... FAILED tests/test_core/test_gpr.py::test_complicated_gpr[(a or b) and c] - Ty... FAILED tests/test_core/test_gpr.py::test_complicated_gpr[(a OR b) AND c] - Ty... FAILED tests/test_core/test_gpr.py::test_gpr_from_ast_or[a-1-gpr_genes0-a] - ... FAILED tests/test_core/test_gpr.py::test_gpr_from_ast_or[a | b-2-gpr_genes1-a or b] FAILED tests/test_core/test_gpr.py::test_gpr_from_ast_or[a or b-2-gpr_genes2-a or b] FAILED tests/test_core/test_gpr.py::test_gpr_from_ast_and[a & b-2-gpr_genes0-a and b] FAILED tests/test_core/test_gpr.py::test_gpr_from_ast_and[a and b-2-gpr_genes1-a and b] FAILED tests/test_flux_analysis/test_fastcc.py::test_figure1[glpk] - TypeErro... FAILED tests/test_flux_analysis/test_fastcc.py::test_opposing[glpk] - TypeErr... FAILED tests/test_manipulation/test_delete.py::test_remove_genes - TypeError:... FAILED tests/test_manipulation/test_delete.py::test_remove_genes_with_context FAILED tests/test_sampling/test_sampling.py::test_complicated_model - TypeErr... ERROR tests/test_core/test_configuration.py::test_default_tolerance - TypeErr... ERROR tests/test_core/test_configuration.py::test_tolerance_assignment - Type... ERROR tests/test_core/test_core_reaction.py::test_gpr_modification - TypeErro... ERROR tests/test_core/test_core_reaction.py::test_gpr_modification_with_context ERROR tests/test_core/test_core_reaction.py::test_gene_knock_out - TypeError:... ERROR tests/test_core/test_core_reaction.py::test_str_from_model - TypeError:... ERROR tests/test_core/test_core_reaction.py::test_add_metabolite_from_solved_model[glpk] ERROR tests/test_core/test_core_reaction.py::test_add_metabolite_benchmark[glpk] ERROR tests/test_core/test_core_reaction.py::test_add_metabolite_benchmark[cplex] ERROR tests/test_core/test_core_reaction.py::test_add_metabolite_benchmark[gurobi] ERROR tests/test_core/test_core_reaction.py::test_add_metabolite - TypeError:... ERROR tests/test_core/test_core_reaction.py::test_subtract_metabolite_benchmark[glpk] ERROR tests/test_core/test_core_reaction.py::test_subtract_metabolite_benchmark[cplex] ERROR tests/test_core/test_core_reaction.py::test_subtract_metabolite_benchmark[gurobi] ERROR tests/test_core/test_core_reaction.py::test_subtract_metabolite[glpk] ERROR tests/test_core/test_core_reaction.py::test_subtract_metabolite[cplex] ERROR tests/test_core/test_core_reaction.py::test_subtract_metabolite[gurobi] ERROR tests/test_core/test_core_reaction.py::test_mass_balance - TypeError: G... ERROR tests/test_core/test_core_reaction.py::test_build_from_string - TypeErr... ERROR tests/test_core/test_core_reaction.py::test_bounds_setter - TypeError: ... ERROR tests/test_core/test_core_reaction.py::test_copy - TypeError: GPR.__ini... ERROR tests/test_core/test_core_reaction.py::test_iadd - TypeError: GPR.__ini... ERROR tests/test_core/test_core_reaction.py::test_iadd_with_context - TypeErr... ERROR tests/test_core/test_core_reaction.py::test_add - TypeError: GPR.__init... ERROR tests/test_core/test_core_reaction.py::test_radd - TypeError: GPR.__ini... ERROR tests/test_core/test_core_reaction.py::test_mul - TypeError: GPR.__init... ERROR tests/test_core/test_core_reaction.py::test_sub - TypeError: GPR.__init... ERROR tests/test_core/test_core_reaction.py::test_removal_from_model_retains_bounds ERROR tests/test_core/test_core_reaction.py::test_set_bounds_scenario_1 - Typ... ERROR tests/test_core/test_core_reaction.py::test_set_bounds_scenario_2 - Typ... ERROR tests/test_core/test_core_reaction.py::test_set_bounds_scenario_3 - Typ... ERROR tests/test_core/test_core_reaction.py::test_set_bounds_scenario_4 - Typ... ERROR tests/test_core/test_core_reaction.py::test_set_upper_before_lower_bound_to_0 ERROR tests/test_core/test_core_reaction.py::test_change_bounds - TypeError: ... ERROR tests/test_core/test_core_reaction.py::test_make_irreversible - TypeErr... ERROR tests/test_core/test_core_reaction.py::test_make_reversible - TypeError... ERROR tests/test_core/test_core_reaction.py::test_make_irreversible_irreversible_to_the_other_side ERROR tests/test_core/test_core_reaction.py::test_make_lhs_irreversible_reversible ERROR tests/test_core/test_core_reaction.py::test_model_less_reaction - TypeE... ERROR tests/test_core/test_core_reaction.py::test_knockout - TypeError: GPR._... ERROR tests/test_core/test_core_reaction.py::test_irrev_reaction_set_negative_lb ERROR tests/test_core/test_core_reaction.py::test_twist_irrev_right_to_left_reaction_to_left_to_right ERROR tests/test_core/test_core_reaction.py::test_set_lb_higher_than_ub_sets_ub_to_new_lb ERROR tests/test_core/test_core_reaction.py::test_set_ub_lower_than_lb_sets_lb_to_new_ub ERROR tests/test_core/test_core_reaction.py::test_add_metabolites_combine_true ERROR tests/test_core/test_core_reaction.py::test_reaction_imul - TypeError: ... ERROR tests/test_core/test_core_reaction.py::test_remove_from_model - TypeErr... ERROR tests/test_core/test_core_reaction.py::test_change_id_is_reflected_in_solver ERROR tests/test_core/test_core_reaction.py::test_repr_html_ - TypeError: GPR... ERROR tests/test_core/test_core_reaction.py::test_compartment_changes - TypeE... ERROR tests/test_core/test_core_reaction.py::test_gpr_serialization - TypeErr... ERROR tests/test_core/test_core_reaction.py::test_gpr_serialization_backwards_compatibility ERROR tests/test_core/test_gene.py::test_repr_html_ - TypeError: GPR.__init__... ERROR tests/test_core/test_gpr.py::test_gpr_symbolism_benchmark - TypeError: ... ERROR tests/test_core/test_gpr.py::test_gpr_equality_benchmark - TypeError: G... ERROR tests/test_core/test_gpr.py::test_gpr_from_as_symbolic_equality - TypeE... ERROR tests/test_core/test_group.py::test_group_add_elements - TypeError: GPR... ERROR tests/test_core/test_metabolite.py::test_formula_element_setting - Type... ERROR tests/test_core/test_metabolite.py::test_set_id[glpk] - TypeError: GPR.... ERROR tests/test_core/test_metabolite.py::test_remove_from_model[glpk] - Type... ERROR tests/test_core/test_metabolite.py::test_repr_html_ - TypeError: GPR.__... ERROR tests/test_core/test_model.py::test_add_metabolite - TypeError: GPR.__i... ERROR tests/test_core/test_model.py::test_remove_metabolite_subtractive - Typ... ERROR tests/test_core/test_model.py::test_remove_metabolite_destructive - Typ... ERROR tests/test_core/test_model.py::test_compartments - TypeError: GPR.__ini... ERROR tests/test_core/test_model.py::test_model_remove_reaction - TypeError: ... ERROR tests/test_core/test_model.py::test_reaction_remove - TypeError: GPR.__... ERROR tests/test_core/test_model.py::test_reaction_delete - TypeError: GPR.__... ERROR tests/test_core/test_model.py::test_remove_gene - TypeError: GPR.__init... ERROR tests/test_core/test_model.py::test_group_model_reaction_association - ... ERROR tests/test_core/test_model.py::test_group_members_add_to_model - TypeEr... ERROR tests/test_core/test_model.py::test_group_loss_of_elements - TypeError:... ERROR tests/test_core/test_model.py::test_exchange_reactions - TypeError: GPR... ERROR tests/test_core/test_model.py::test_add_boundary[exchange-exchange-EX_] ERROR tests/test_core/test_model.py::test_add_boundary[demand-demand-DM_] - T... ERROR tests/test_core/test_model.py::test_add_boundary[sink-sink-SK_] - TypeE... ERROR tests/test_core/test_model.py::test_add_boundary_context[exchange-exchange-EX_] ERROR tests/test_core/test_model.py::test_add_boundary_context[demand-demand-DM_] ERROR tests/test_core/test_model.py::test_add_boundary_context[sink-sink-SK_] ERROR tests/test_core/test_model.py::test_add_existing_boundary[exchange-exchange] ERROR tests/test_core/test_model.py::test_add_existing_boundary[demand-demand] ERROR tests/test_core/test_model.py::test_add_existing_boundary[sink-sink] - ... ERROR tests/test_core/test_model.py::test_copy_benchmark[optlang-glpk] - Type... ERROR tests/test_core/test_model.py::test_copy_benchmark_large_model[optlang-glpk] ERROR tests/test_core/test_model.py::test_copy - TypeError: GPR.__init__() ta... ERROR tests/test_core/test_model.py::test_copy_with_groups - TypeError: GPR._... ERROR tests/test_core/test_model.py::test_deepcopy_benchmark - TypeError: GPR... ERROR tests/test_core/test_model.py::test_deepcopy - TypeError: GPR.__init__(... ERROR tests/test_core/test_model.py::test_add_reaction_orphans - TypeError: G... ERROR tests/test_core/test_model.py::test_merge_models - TypeError: GPR.__ini... ERROR tests/test_core/test_model.py::test_change_objective_benchmark[optlang-glpk] ERROR tests/test_core/test_model.py::test_get_objective_direction - TypeError... ERROR tests/test_core/test_model.py::test_set_objective_direction - TypeError... ERROR tests/test_core/test_model.py::test_slim_optimize - TypeError: GPR.__in... ERROR tests/test_core/test_model.py::test_optimize[optlang-glpk] - TypeError:... ERROR tests/test_core/test_model.py::test_change_objective - TypeError: GPR._... ERROR tests/test_core/test_model.py::test_problem_properties - TypeError: GPR... ERROR tests/test_core/test_model.py::test_solution_data_frame - TypeError: GP... ERROR tests/test_core/test_model.py::test_context_manager - TypeError: GPR.__... ERROR tests/test_core/test_model.py::test_objective_coefficient_reflects_changed_objective ERROR tests/test_core/test_model.py::test_change_objective_through_objective_coefficient ERROR tests/test_core/test_model.py::test_transfer_objective - TypeError: GPR... ERROR tests/test_core/test_model.py::test_model_from_other_model - TypeError:... ERROR tests/test_core/test_model.py::test_add_reactions - TypeError: GPR.__in... ERROR tests/test_core/test_model.py::test_add_reactions_single_existing - Typ... ERROR tests/test_core/test_model.py::test_add_reactions_duplicate - TypeError... ERROR tests/test_core/test_model.py::test_all_objects_point_to_all_other_correct_objects ERROR tests/test_core/test_model.py::test_objects_point_to_correct_other_after_copy ERROR tests/test_core/test_model.py::test_remove_reactions - TypeError: GPR._... ERROR tests/test_core/test_model.py::test_objective - TypeError: GPR.__init__... ERROR tests/test_core/test_model.py::test_change_objective_with_context - Typ... ERROR tests/test_core/test_model.py::test_set_reaction_objective - TypeError:... ERROR tests/test_core/test_model.py::test_set_reaction_objective_str - TypeEr... ERROR tests/test_core/test_model.py::test_invalid_objective_raises - TypeErro... ERROR tests/test_core/test_model.py::test_no_change_for_same_solver - TypeErr... ERROR tests/test_core/test_model.py::test_invalid_solver_change_raises - Type... ERROR tests/test_core/test_model.py::test_copy_preserves_existing_solution[glpk] ERROR tests/test_core/test_model.py::test_repr_html_ - TypeError: GPR.__init_... ERROR tests/test_core/test_solution.py::test_solution_contains_only_reaction_specific_values[glpk] ERROR tests/test_flux_analysis/test_deletion.py::test_single_gene_deletion_fba_benchmark[glpk] ERROR tests/test_flux_analysis/test_deletion.py::test_single_gene_deletion_fba[glpk] ERROR tests/test_flux_analysis/test_deletion.py::test_single_gene_deletion_linear_moma_benchmark[glpk] ERROR tests/test_flux_analysis/test_deletion.py::test_single_gene_deletion_linear_moma[glpk] ERROR tests/test_flux_analysis/test_deletion.py::test_single_gene_deletion_room_benchmark[glpk] ERROR tests/test_flux_analysis/test_deletion.py::test_single_gene_deletion_linear_room_benchmark[glpk] ERROR tests/test_flux_analysis/test_deletion.py::test_single_reaction_deletion_benchmark[glpk] ERROR tests/test_flux_analysis/test_deletion.py::test_single_reaction_deletion[glpk] ERROR tests/test_flux_analysis/test_fastcc.py::test_fastcc_benchmark[glpk] - ... ERROR tests/test_flux_analysis/test_fastcc.py::test_fastcc_against_fva_nonblocked_rxns[glpk] ERROR tests/test_flux_analysis/test_geometric.py::test_geometric_fba_benchmark[glpk] ERROR tests/test_flux_analysis/test_moma.py::test_linear_moma_sanity[glpk] - ... ERROR tests/test_flux_analysis/test_parsimonious.py::test_pfba_benchmark[glpk] ERROR tests/test_flux_analysis/test_parsimonious.py::test_pfba[glpk] - TypeEr... ERROR tests/test_flux_analysis/test_reaction.py::test_assess[glpk] - TypeErro... ERROR tests/test_flux_analysis/test_room.py::test_room_sanity[glpk-True-0.03-0.001] ERROR tests/test_flux_analysis/test_room.py::test_room_sanity[glpk-False-0.03-0.001] ERROR tests/test_flux_analysis/test_room.py::test_room_sanity[glpk-True-0.1-0.01] ERROR tests/test_flux_analysis/test_room.py::test_room_sanity[glpk-False-0.1-0.01] ERROR tests/test_flux_analysis/test_variability.py::test_flux_variability_benchmark[glpk] ERROR tests/test_flux_analysis/test_variability.py::test_pfba_flux_variability[glpk] ERROR tests/test_flux_analysis/test_variability.py::test_flux_variability[glpk] ERROR tests/test_flux_analysis/test_variability.py::test_parallel_flux_variability[glpk] ERROR tests/test_flux_analysis/test_variability.py::test_flux_variability_loopless_benchmark[glpk] ERROR tests/test_flux_analysis/test_variability.py::test_flux_variability_loopless[glpk] ERROR tests/test_flux_analysis/test_variability.py::test_find_blocked_reactions[glpk] ERROR tests/test_flux_analysis/test_deletion.py::test_double_gene_deletion_benchmark ERROR tests/test_flux_analysis/test_deletion.py::test_double_gene_deletion - ... ERROR tests/test_flux_analysis/test_deletion.py::test_double_gene_knockout_bug ERROR tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion_benchmark ERROR tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion ERROR tests/test_flux_analysis/test_gapfilling.py::test_gapfilling - TypeErro... ERROR tests/test_flux_analysis/test_helpers.py::test_normalize_cutoff - TypeE... ERROR tests/test_flux_analysis/test_helpers.py::test_normalize_cutoff_with_specified_cutoff_above_default ERROR tests/test_flux_analysis/test_helpers.py::test_normalize_cutoff_with_specified_cutoff_below_default ERROR tests/test_flux_analysis/test_loopless.py::test_loopless_solution_fluxes ERROR tests/test_flux_analysis/test_phenotype_phase_plane.py::test_envelope_one ERROR tests/test_flux_analysis/test_phenotype_phase_plane.py::test_envelope_multi_reaction_objective ERROR tests/test_flux_analysis/test_phenotype_phase_plane.py::test_multi_variable_envelope[variables0-30] ERROR tests/test_flux_analysis/test_phenotype_phase_plane.py::test_multi_variable_envelope[variables1-20] ERROR tests/test_flux_analysis/test_phenotype_phase_plane.py::test_multi_variable_envelope[variables2-10] ERROR tests/test_flux_analysis/test_phenotype_phase_plane.py::test_envelope_two ERROR tests/test_flux_analysis/test_variability.py::test_loopless_pfba_fva - ... ERROR tests/test_flux_analysis/test_variability.py::test_fva_data_frame - Typ... ERROR tests/test_flux_analysis/test_variability.py::test_fva_infeasible - Typ... ERROR tests/test_flux_analysis/test_variability.py::test_fva_minimization - T... ERROR tests/test_flux_analysis/test_variability.py::test_find_blocked_reactions_solver_none ERROR tests/test_flux_analysis/test_variability.py::test_essential_genes - Ty... ERROR tests/test_flux_analysis/test_variability.py::test_essential_reactions ERROR tests/test_io/test_io_order.py::test_io_order[metabolites-minimized_shuffle-read_sbml_model-write_sbml_model-.xml] ERROR tests/test_io/test_io_order.py::test_io_order[metabolites-minimized_shuffle-load_json_model-save_json_model-.json] ERROR tests/test_io/test_io_order.py::test_io_order[metabolites-minimized_shuffle-load_yaml_model-save_yaml_model-.yml] ERROR tests/test_io/test_io_order.py::test_io_order[metabolites-minimized_reverse-read_sbml_model-write_sbml_model-.xml] ERROR tests/test_io/test_io_order.py::test_io_order[metabolites-minimized_reverse-load_json_model-save_json_model-.json] ERROR tests/test_io/test_io_order.py::test_io_order[metabolites-minimized_reverse-load_yaml_model-save_yaml_model-.yml] ERROR tests/test_io/test_io_order.py::test_io_order[reactions-minimized_reverse-read_sbml_model-write_sbml_model-.xml] ERROR tests/test_io/test_io_order.py::test_io_order[reactions-minimized_reverse-load_json_model-save_json_model-.json] ERROR tests/test_io/test_io_order.py::test_io_order[reactions-minimized_reverse-load_yaml_model-save_yaml_model-.yml] ERROR tests/test_io/test_io_order.py::test_io_order[reactions-minimized_shuffle-read_sbml_model-write_sbml_model-.xml] ERROR tests/test_io/test_io_order.py::test_io_order[reactions-minimized_shuffle-load_json_model-save_json_model-.json] ERROR tests/test_io/test_io_order.py::test_io_order[reactions-minimized_shuffle-load_yaml_model-save_yaml_model-.yml] ERROR tests/test_io/test_io_order.py::test_io_order[reactions-minimized_sorted-read_sbml_model-write_sbml_model-.xml] ERROR tests/test_io/test_io_order.py::test_io_order[reactions-minimized_sorted-load_json_model-save_json_model-.json] ERROR tests/test_io/test_io_order.py::test_io_order[reactions-minimized_sorted-load_yaml_model-save_yaml_model-.yml] ERROR tests/test_io/test_io_order.py::test_io_order[metabolites-minimized_sorted-read_sbml_model-write_sbml_model-.xml] ERROR tests/test_io/test_io_order.py::test_io_order[metabolites-minimized_sorted-load_json_model-save_json_model-.json] ERROR tests/test_io/test_io_order.py::test_io_order[metabolites-minimized_sorted-load_yaml_model-save_yaml_model-.yml] ERROR tests/test_io/test_io_order.py::test_io_order[genes-minimized_sorted-read_sbml_model-write_sbml_model-.xml] ERROR tests/test_io/test_io_order.py::test_io_order[genes-minimized_sorted-load_json_model-save_json_model-.json] ERROR tests/test_io/test_io_order.py::test_io_order[genes-minimized_sorted-load_yaml_model-save_yaml_model-.yml] ERROR tests/test_io/test_io_order.py::test_io_order[genes-minimized_reverse-read_sbml_model-write_sbml_model-.xml] ERROR tests/test_io/test_io_order.py::test_io_order[genes-minimized_reverse-load_json_model-save_json_model-.json] ERROR tests/test_io/test_io_order.py::test_io_order[genes-minimized_reverse-load_yaml_model-save_yaml_model-.yml] ERROR tests/test_io/test_io_order.py::test_io_order[genes-minimized_shuffle-read_sbml_model-write_sbml_model-.xml] ERROR tests/test_io/test_io_order.py::test_io_order[genes-minimized_shuffle-load_json_model-save_json_model-.json] ERROR tests/test_io/test_io_order.py::test_io_order[genes-minimized_shuffle-load_yaml_model-save_yaml_model-.yml] ERROR tests/test_io/test_mat.py::test_large_bounds - TypeError: GPR.__init__(... ERROR tests/test_io/test_sbml.py::test_gprs - TypeError: GPR.__init__() takes... ERROR tests/test_io/test_web/test_load.py::test_local_load - TypeError: GPR._... ERROR tests/test_manipulation/test_annotate.py::test_sbo_annotation - TypeErr... ERROR tests/test_manipulation/test_delete.py::test_prune_unused_metabolites_output_type ERROR tests/test_manipulation/test_delete.py::test_prune_unused_metabolites_sanity ERROR tests/test_manipulation/test_delete.py::test_prune_unused_reactions_output_type ERROR tests/test_manipulation/test_delete.py::test_prune_unused_rxns_functionality ERROR tests/test_manipulation/test_delete.py::test_gene_knockout - TypeError:... ERROR tests/test_manipulation/test_modify.py::test_escape_ids - TypeError: GP... ERROR tests/test_manipulation/test_modify.py::test_rename_genes - TypeError: ... ERROR tests/test_manipulation/test_modify.py::test_rename_genes_with_context ERROR tests/test_manipulation/test_validate.py::test_validate_mass_balance - ... ERROR tests/test_manipulation/test_validate.py::test_validate_formula_compartment ERROR tests/test_medium/test_boundary_types.py::test_find_external_compartment_single ERROR tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi ERROR tests/test_medium/test_boundary_types.py::test_find_external_popular_reconstructions[C_e] ERROR tests/test_medium/test_boundary_types.py::test_find_external_popular_reconstructions[e0] ERROR tests/test_medium/test_boundary_types.py::test_find_boundary_types_exchange ERROR tests/test_medium/test_boundary_types.py::test_find_boundary_types_demand ERROR tests/test_medium/test_boundary_types.py::test_find_boundary_types_sink ERROR tests/test_medium/test_boundary_types.py::test_is_boundary_type - TypeE... ERROR tests/test_medium/test_boundary_types.py::test_bad_exchange - TypeError... ERROR tests/test_medium/test_minimal_medium.py::test_minimal_medium_linear - ... ERROR tests/test_medium/test_minimal_medium.py::test_minimal_medium_linear_benchmark ERROR tests/test_medium/test_minimal_medium.py::test_minimal_medium_mip - Typ... ERROR tests/test_medium/test_minimal_medium.py::test_minimal_medium_mip_benchmark ERROR tests/test_medium/test_minimal_medium.py::test_minimal_medium_alternative_mip ERROR tests/test_medium/test_minimal_medium.py::test_minimal_medium_exports ERROR tests/test_medium/test_minimal_medium.py::test_minimal_medium_open_exchanges ERROR tests/test_medium/test_minimal_medium.py::test_model_medium - TypeError... ERROR tests/test_medium/test_minimal_medium.py::test_medium_does_not_affect_reactant_exports ERROR tests/test_medium/test_minimal_medium.py::test_medium_does_not_affect_product_exports ERROR tests/test_sampling/test_achr.py::test_achr_init_benchmark - TypeError:... ERROR tests/test_sampling/test_achr.py::test_achr_sample_benchmark - TypeErro... ERROR tests/test_sampling/test_achr.py::test_validate_wrong_sample - TypeErro... ERROR tests/test_sampling/test_achr.py::test_sampling - TypeError: GPR.__init... ERROR tests/test_sampling/test_achr.py::test_batch_sampling - TypeError: GPR.... ERROR tests/test_sampling/test_achr.py::test_variables_samples - TypeError: G... ERROR tests/test_sampling/test_optgp.py::test_optgp_init_benchmark - TypeErro... ERROR tests/test_sampling/test_optgp.py::test_optgp_sample_benchmark - TypeEr... ERROR tests/test_sampling/test_optgp.py::test_sampling - TypeError: GPR.__ini... ERROR tests/test_sampling/test_optgp.py::test_batch_sampling - TypeError: GPR... ERROR tests/test_sampling/test_optgp.py::test_variables_samples - TypeError: ... ERROR tests/test_sampling/test_optgp.py::test_reproject - TypeError: GPR.__in... ERROR tests/test_sampling/test_sampling.py::test_single_achr - TypeError: GPR... ERROR tests/test_sampling/test_sampling.py::test_single_optgp - TypeError: GP... ERROR tests/test_sampling/test_sampling.py::test_multi_optgp - TypeError: GPR... ERROR tests/test_sampling/test_sampling.py::test_wrong_method - TypeError: GP... ERROR tests/test_sampling/test_sampling.py::test_fixed_seed - TypeError: GPR.... ERROR tests/test_sampling/test_sampling.py::test_equality_constraint - TypeEr... ERROR tests/test_sampling/test_sampling.py::test_inequality_constraint - Type... ERROR tests/test_sampling/test_sampling.py::test_inhomogeneous_sanity - TypeE... ERROR tests/test_sampling/test_sampling.py::test_single_point_space - TypeErr... ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_interface[optlang-glpk] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_frame[optlang-glpk] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_string[optlang-glpk-kwargs0] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_string[optlang-glpk-kwargs1] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_string[optlang-glpk-kwargs2] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_string[optlang-glpk-kwargs3] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_string[optlang-glpk-kwargs4] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_html[optlang-glpk-kwargs0] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_html[optlang-glpk-kwargs1] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_html[optlang-glpk-kwargs2] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_to_html[optlang-glpk-kwargs3] ERROR tests/test_summary/test_metabolite_summary.py::test_q8_producing_summary[optlang-glpk] ERROR tests/test_summary/test_metabolite_summary.py::test_q8_consuming_summary[optlang-glpk] ERROR tests/test_summary/test_metabolite_summary.py::test_fdp_production_with_fva[optlang-glpk] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_flux_in_context[optlang-glpk-q8_c] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_flux_in_context[optlang-glpk-fdp_c] ERROR tests/test_summary/test_metabolite_summary.py::test_metabolite_summary_flux_in_context[optlang-glpk-atp_c] ERROR tests/test_summary/test_model_summary.py::test_model_summary_interface[optlang-glpk] ERROR tests/test_summary/test_model_summary.py::test_model_summary_to_frame[optlang-glpk] ERROR tests/test_summary/test_model_summary.py::test_model_summary_to_string[optlang-glpk-kwargs0] ERROR tests/test_summary/test_model_summary.py::test_model_summary_to_string[optlang-glpk-kwargs1] ERROR tests/test_summary/test_model_summary.py::test_model_summary_to_string[optlang-glpk-kwargs2] ERROR tests/test_summary/test_model_summary.py::test_model_summary_to_string[optlang-glpk-kwargs3] ERROR tests/test_summary/test_model_summary.py::test_model_summary_to_string[optlang-glpk-kwargs4] ERROR tests/test_summary/test_model_summary.py::test_model_summary_to_html[optlang-glpk-kwargs0] ERROR tests/test_summary/test_model_summary.py::test_model_summary_to_html[optlang-glpk-kwargs1] ERROR tests/test_summary/test_model_summary.py::test_model_summary_to_html[optlang-glpk-kwargs2] ERROR tests/test_summary/test_model_summary.py::test_model_summary_to_html[optlang-glpk-kwargs3] ERROR tests/test_summary/test_model_summary.py::test_model_summary_to_frame_previous_solution[optlang-glpk] ERROR tests/test_summary/test_model_summary.py::test_model_summary_flux[optlang-glpk] ERROR tests/test_summary/test_model_summary.py::test_model_summary_fva[optlang-glpk] ERROR tests/test_summary/test_model_summary.py::test_model_summary_flux_in_context[optlang-glpk] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_interface[optlang-glpk] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_to_frame[optlang-glpk] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_to_string[optlang-glpk-kwargs0] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_to_string[optlang-glpk-kwargs1] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_to_string[optlang-glpk-kwargs2] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_to_string[optlang-glpk-kwargs3] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_to_string[optlang-glpk-kwargs4] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_to_html[optlang-glpk-kwargs0] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_to_html[optlang-glpk-kwargs1] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_to_html[optlang-glpk-kwargs2] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_to_html[optlang-glpk-kwargs3] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_flux[ACALD-0.0] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_flux[FUM-5.06] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_flux[PFK-7.48] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_flux_fva[ACALD--1.27-0.0] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_flux_fva[FUM-0.79-7.38] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_flux_fva[PFK-2.58-16.38] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_flux_in_context[ACALD] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_flux_in_context[FUM] ERROR tests/test_summary/test_reaction_summary.py::test_reaction_summary_flux_in_context[PFK] ERROR tests/test_util/test_array.py::test_dense_matrix - TypeError: GPR.__ini... ERROR tests/test_util/test_array.py::test_sparse_matrix - TypeError: GPR.__in... ERROR tests/test_util/test_context.py::test_get_context - TypeError: GPR.__in... ERROR tests/test_util/test_solver.py::test_choose_solver - TypeError: GPR.__i... ERROR tests/test_util/test_solver.py::test_linear_reaction_coefficients - Typ... ERROR tests/test_util/test_solver.py::test_fail_non_linear_reaction_coefficients ERROR tests/test_util/test_solver.py::test_add_remove - TypeError: GPR.__init... ERROR tests/test_util/test_solver.py::test_add_remove_in_context - TypeError:... ERROR tests/test_util/test_solver.py::test_absolute_expression - TypeError: G... ERROR tests/test_util/test_solver.py::test_fix_objective_as_constraint[optlang-glpk] ERROR tests/test_util/test_solver.py::test_fix_objective_as_constraint_minimize[optlang-glpk] ERROR tests/test_util/test_solver.py::test_add_lp_feasibility[optlang-glpk] ERROR tests/test_util/test_solver.py::test_add_lexicographic_constraints[optlang-glpk] ERROR tests/test_util/test_solver.py::test_time_limit - TypeError: GPR.__init... = 24 failed, 173 passed, 30 skipped, 11 xfailed, 5478 warnings, 315 errors in 31.66s = E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/python-cobra-0.29.1/.pybuild/cpython3_3.13_cobra/build; python3.13 -m pytest tests dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13 make: *** [debian/rules:10: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/118571 and its subdirectories