cmd: autopkgtest --apt-upgrade --output-dir=artifact-dir --summary=artifact-dir/summary --no-built-binaries --needs-internet=run --copy=/etc/resolv.conf:/etc/resolv.conf /tmp/debusine-fetch-exec-upload-irbad5aq/python-cobra-data_0.29.1-1_all.deb /tmp/debusine-fetch-exec-upload-irbad5aq/python3-cobra_0.29.1-1_amd64.deb /tmp/debusine-fetch-exec-upload-irbad5aq/python3-rich_13.9.4-0.1_all.deb /tmp/debusine-fetch-exec-upload-irbad5aq/python-cobra_0.29.1-1.dsc -- unshare --arch amd64 --release sid --tarball /var/lib/debusine/worker/system-images/1099747/system.tar.xz
output (contains stdout and stderr):
autopkgtest [13:56:13]: starting date and time: 2024-12-18 13:56:13+0000
autopkgtest [13:56:13]: version 5.38~bpo12+1
autopkgtest [13:56:13]: host debusine-worker-amd64-hades-06; command line: /usr/bin/autopkgtest --apt-upgrade --output-dir=artifact-dir --summary=artifact-dir/summary --no-built-binaries --needs-internet=run --copy=/etc/resolv.conf:/etc/resolv.conf /tmp/debusine-fetch-exec-upload-irbad5aq/python-cobra-data_0.29.1-1_all.deb /tmp/debusine-fetch-exec-upload-irbad5aq/python3-cobra_0.29.1-1_amd64.deb /tmp/debusine-fetch-exec-upload-irbad5aq/python3-rich_13.9.4-0.1_all.deb /tmp/debusine-fetch-exec-upload-irbad5aq/python-cobra_0.29.1-1.dsc -- unshare --arch amd64 --release sid --tarball /var/lib/debusine/worker/system-images/1099747/system.tar.xz
autopkgtest [13:56:17]: testbed dpkg architecture: amd64
autopkgtest [13:56:17]: testbed apt version: 2.9.17
autopkgtest [13:56:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup
Get:1 http://deb.debian.org/debian sid InRelease [202 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB]
Get:3 http://deb.debian.org/debian sid/main Translation-en [7350 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 Components [4974 kB]
Fetched 22.6 MB in 2s (9531 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
gcc-14-base gettext gettext-base libatomic1 libgcc-s1 libgomp1 libstdc++6
7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 2779 kB of archives.
After this operation, 1024 B of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-11 [9284 B]
Get:2 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-11 [48.0 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-11 [713 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-11 [137 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-11 [72.7 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 gettext-base amd64 0.22.5-3 [200 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 gettext amd64 0.22.5-3 [1600 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 2779 kB in 0s (38.5 MB/s)
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(Reading database ... 17030 files and directories currently installed.)
Preparing to unpack .../libatomic1_14.2.0-11_amd64.deb ...
Unpacking libatomic1:amd64 (14.2.0-11) over (14.2.0-8) ...
Preparing to unpack .../gcc-14-base_14.2.0-11_amd64.deb ...
Unpacking gcc-14-base:amd64 (14.2.0-11) over (14.2.0-8) ...
Setting up gcc-14-base:amd64 (14.2.0-11) ...
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(Reading database ... 17030 files and directories currently installed.)
Preparing to unpack .../libstdc++6_14.2.0-11_amd64.deb ...
Unpacking libstdc++6:amd64 (14.2.0-11) over (14.2.0-8) ...
Setting up libstdc++6:amd64 (14.2.0-11) ...
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Preparing to unpack .../libgomp1_14.2.0-11_amd64.deb ...
Unpacking libgomp1:amd64 (14.2.0-11) over (14.2.0-8) ...
Preparing to unpack .../libgcc-s1_14.2.0-11_amd64.deb ...
Unpacking libgcc-s1:amd64 (14.2.0-11) over (14.2.0-8) ...
Setting up libgcc-s1:amd64 (14.2.0-11) ...
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(Reading database ... 17030 files and directories currently installed.)
Preparing to unpack .../gettext-base_0.22.5-3_amd64.deb ...
Unpacking gettext-base (0.22.5-3) over (0.22.5-2) ...
Preparing to unpack .../gettext_0.22.5-3_amd64.deb ...
Unpacking gettext (0.22.5-3) over (0.22.5-2) ...
Setting up gettext-base (0.22.5-3) ...
Setting up libgomp1:amd64 (14.2.0-11) ...
Setting up libatomic1:amd64 (14.2.0-11) ...
Setting up gettext (0.22.5-3) ...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for libc-bin (2.40-4) ...
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
autopkgtest [13:56:24]: testbed running kernel: Linux 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22)
autopkgtest [13:56:24]: @@@@@@@@@@@@@@@@@@@@ source /tmp/debusine-fetch-exec-upload-irbad5aq/python-cobra_0.29.1-1.dsc
gpgv: Signature made Sun Sep 22 13:24:18 2024 UTC
gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A
gpgv: issuer "tchet@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for /tmp/autopkgtest.tIrtam/python-cobra_0.29.1-1.dsc: no acceptable signature found
dpkg-source: info: extracting python-cobra in src
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
autopkgtest [13:56:24]: testing package python-cobra version 0.29.1-1
autopkgtest [13:56:24]: build not needed
autopkgtest [13:56:24]: test run-unit-test: preparing testbed
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
apt-utils
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 328 kB of archives.
After this operation, 1097 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 apt-utils amd64 2.9.17 [328 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 328 kB in 0s (8077 kB/s)
Selecting previously unselected package apt-utils.
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(Reading database ... 17030 files and directories currently installed.)
Preparing to unpack .../apt-utils_2.9.17_amd64.deb ...
Unpacking apt-utils (2.9.17) ...
Setting up apt-utils (2.9.17) ...
Processing triggers for man-db (2.13.0-1) ...
Ign:1 file:/tmp/autopkgtest.tIrtam/binaries InRelease
Get:2 file:/tmp/autopkgtest.tIrtam/binaries Release [816 B]
Get:2 file:/tmp/autopkgtest.tIrtam/binaries Release [816 B]
Ign:3 file:/tmp/autopkgtest.tIrtam/binaries Release.gpg
Get:4 file:/tmp/autopkgtest.tIrtam/binaries Packages [5089 B]
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Starting pkgProblemResolver with broken count: 0
Starting 2 pkgProblemResolver with broken count: 0
Done
The following NEW packages will be installed:
ed libamd3 libblas3 libcolamd3 libexpat1 libgfortran5 libglpk40 liblapack3
liblbfgsb0 libltdl7 libnsl2 libpython3-stdlib libpython3.12-minimal
libpython3.12-stdlib libpython3.12t64 libsuitesparseconfig7 libtirpc-common
libtirpc3t64 media-types python-cobra-data python3 python3-annotated-types
python3-anyio python3-attr python3-autocommand python3-certifi python3-click
python3-cobra python3-colorama python3-cpuinfo python3-dateutil
python3-decorator python3-depinfo python3-diskcache python3-dnspython
python3-email-validator python3-h11 python3-httpcore python3-httpx
python3-idna python3-importlib-resources python3-inflect python3-iniconfig
python3-jaraco.context python3-jaraco.functools python3-jsonschema
python3-jsonschema-specifications python3-markdown-it python3-mdurl
python3-minimal python3-more-itertools python3-mpmath python3-numpy
python3-optlang python3-packaging python3-pandas python3-pandas-lib
python3-pkg-resources python3-platformdirs python3-pluggy python3-pydantic
python3-pydantic-core python3-pygments python3-pytest
python3-pytest-benchmark python3-pytest-mock python3-referencing
python3-rich python3-rpds-py python3-ruamel.yaml python3-ruamel.yaml.clib
python3-sbml5 python3-scipy python3-sniffio python3-swiglpk python3-sympy
python3-tabulate python3-typeguard python3-typing-extensions python3-tz
python3.12 python3.12-minimal quilt
0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded.
Need to get 67.7 MB/70.4 MB of archives.
After this operation, 393 MB of additional disk space will be used.
Get:1 file:/tmp/autopkgtest.tIrtam/binaries python-cobra-data 0.29.1-1 [1437 kB]
Get:2 file:/tmp/autopkgtest.tIrtam/binaries python3-rich 13.9.4-0.1 [203 kB]
Get:3 file:/tmp/autopkgtest.tIrtam/binaries python3-cobra 0.29.1-1 [1119 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.8-3 [817 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.8-3 [2162 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:10 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB]
Get:11 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB]
Get:12 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.8-3 [1969 kB]
Get:13 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.8-3 [677 kB]
Get:14 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B]
Get:15 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.12.7-1 [27.8 kB]
Get:16 http://deb.debian.org/debian sid/main amd64 ed amd64 1.20.2-2 [60.8 kB]
Get:17 http://deb.debian.org/debian sid/main amd64 libsuitesparseconfig7 amd64 1:7.8.3+dfsg-2 [23.8 kB]
Get:18 http://deb.debian.org/debian sid/main amd64 libamd3 amd64 1:7.8.3+dfsg-2 [40.7 kB]
Get:19 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-4 [152 kB]
Get:20 http://deb.debian.org/debian sid/main amd64 libcolamd3 amd64 1:7.8.3+dfsg-2 [32.5 kB]
Get:21 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-11 [836 kB]
Get:22 http://deb.debian.org/debian sid/main amd64 libltdl7 amd64 2.4.7-8 [393 kB]
Get:23 http://deb.debian.org/debian sid/main amd64 libglpk40 amd64 5.0-1+b2 [401 kB]
Get:24 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB]
Get:25 http://deb.debian.org/debian sid/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB]
Get:26 http://deb.debian.org/debian sid/main amd64 libpython3.12t64 amd64 3.12.8-3 [2154 kB]
Get:27 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:28 http://deb.debian.org/debian sid/main amd64 python3-annotated-types all 0.7.0-1 [18.8 kB]
Get:29 http://deb.debian.org/debian sid/main amd64 python3-idna all 3.8-2 [41.6 kB]
Get:30 http://deb.debian.org/debian sid/main amd64 python3-sniffio all 1.3.1-1 [7120 B]
Get:31 http://deb.debian.org/debian sid/main amd64 python3-anyio all 4.6.2-4 [60.0 kB]
Get:32 http://deb.debian.org/debian sid/main amd64 python3-attr all 24.2.0-1 [68.4 kB]
Get:33 http://deb.debian.org/debian sid/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:34 http://deb.debian.org/debian sid/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B]
Get:35 http://deb.debian.org/debian sid/main amd64 python3-colorama all 0.4.6-4 [36.2 kB]
Get:36 http://deb.debian.org/debian sid/main amd64 python3-click all 8.1.7-2 [94.3 kB]
Get:37 http://deb.debian.org/debian sid/main amd64 python3-depinfo amd64 2.2.0-3 [11.6 kB]
Get:38 http://deb.debian.org/debian sid/main amd64 python3-diskcache all 5.6.3-1 [34.4 kB]
Get:39 http://deb.debian.org/debian sid/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:40 http://deb.debian.org/debian sid/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get:41 http://deb.debian.org/debian sid/main amd64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:42 http://deb.debian.org/debian sid/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:43 http://deb.debian.org/debian sid/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:44 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB]
Get:45 http://deb.debian.org/debian sid/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB]
Get:46 http://deb.debian.org/debian sid/main amd64 python3-mdurl all 0.1.2-1 [9444 B]
Get:47 http://deb.debian.org/debian sid/main amd64 python3-markdown-it all 3.0.0-2 [62.5 kB]
Get:48 http://deb.debian.org/debian sid/main amd64 python3-h11 all 0.14.0-1 [50.1 kB]
Get:49 http://deb.debian.org/debian sid/main amd64 python3-httpcore all 1.0.7-1 [44.7 kB]
Get:50 http://deb.debian.org/debian sid/main amd64 python3-httpx all 0.27.2-1 [77.6 kB]
Get:51 http://deb.debian.org/debian sid/main amd64 python3-importlib-resources all 6.4.5-1 [23.1 kB]
Get:52 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB]
Get:53 http://deb.debian.org/debian sid/main amd64 python3-swiglpk amd64 5.0.10-2+b1 [65.4 kB]
Get:54 http://deb.debian.org/debian sid/main amd64 python3-mpmath all 1.3.0-1 [419 kB]
Get:55 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.13.3-1 [4147 kB]
Get:56 http://deb.debian.org/debian sid/main amd64 python3-optlang all 1.8.2-3 [5376 kB]
Get:57 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get:58 http://deb.debian.org/debian sid/main amd64 python3-tz all 2024.2-1 [31.0 kB]
Get:59 http://deb.debian.org/debian sid/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-5+b1 [7307 kB]
Get:60 http://deb.debian.org/debian sid/main amd64 python3-pandas all 2.2.3+dfsg-5 [3096 kB]
Get:61 http://deb.debian.org/debian sid/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB]
Get:62 http://deb.debian.org/debian sid/main amd64 python3-pydantic-core amd64 2.27.1-1 [1737 kB]
Get:63 http://deb.debian.org/debian sid/main amd64 python3-dnspython all 2.7.0-1 [164 kB]
Get:64 http://deb.debian.org/debian sid/main amd64 python3-email-validator all 2.2.0-1 [31.6 kB]
Get:65 http://deb.debian.org/debian sid/main amd64 python3-pydantic amd64 2.10.3-1 [365 kB]
Get:66 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml.clib amd64 0.2.8+ds-2+b1 [179 kB]
Get:67 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml all 0.18.6+ds-3 [145 kB]
Get:68 http://deb.debian.org/debian sid/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB]
Get:69 http://deb.debian.org/debian sid/main amd64 python3-sbml5 amd64 5.20.2+dfsg-8+b1 [3428 kB]
Get:70 http://deb.debian.org/debian sid/main amd64 python3-cpuinfo all 9.0.0+git20221119-2 [23.4 kB]
Get:71 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:72 http://deb.debian.org/debian sid/main amd64 python3-iniconfig all 1.1.1-2 [6396 B]
Get:73 http://deb.debian.org/debian sid/main amd64 python3-rpds-py amd64 0.21.0-2 [287 kB]
Get:74 http://deb.debian.org/debian sid/main amd64 python3-referencing all 0.35.1-2 [23.5 kB]
Get:75 http://deb.debian.org/debian sid/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B]
Get:76 http://deb.debian.org/debian sid/main amd64 python3-jsonschema all 4.19.2-5 [71.4 kB]
Get:77 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get:78 http://deb.debian.org/debian sid/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB]
Get:79 http://deb.debian.org/debian sid/main amd64 python3-pytest all 8.3.4-1 [250 kB]
Get:80 http://deb.debian.org/debian sid/main amd64 python3-pytest-benchmark all 5.1.0-1 [44.4 kB]
Get:81 http://deb.debian.org/debian sid/main amd64 python3-pytest-mock all 3.14.0-2 [18.3 kB]
Get:82 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.14.1-3 [20.5 MB]
Get:83 http://deb.debian.org/debian sid/main amd64 quilt all 0.68-1 [437 kB]
Fetched 67.7 MB in 1s (60.2 MB/s)
Selecting previously unselected package libpython3.12-minimal:amd64.
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(Reading database ... 17112 files and directories currently installed.)
Preparing to unpack .../libpython3.12-minimal_3.12.8-3_amd64.deb ...
Unpacking libpython3.12-minimal:amd64 (3.12.8-3) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.6.4-1) ...
Selecting previously unselected package python3.12-minimal.
Preparing to unpack .../python3.12-minimal_3.12.8-3_amd64.deb ...
Unpacking python3.12-minimal (3.12.8-3) ...
Setting up libpython3.12-minimal:amd64 (3.12.8-3) ...
Setting up libexpat1:amd64 (2.6.4-1) ...
Setting up python3.12-minimal (3.12.8-3) ...
Selecting previously unselected package python3-minimal.
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/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')
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autopkgtest [13:57:02]: test run-unit-test: [-----------------------
File series fully applied, ends at patch debian/patches/remove-appdirs.patch
Running Tests
Since python3-sbml5 can only deal with one Python3 version we restrict the test to default Python3
============================= test session starts ==============================
platform linux -- Python 3.12.8, pytest-8.3.4, 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: /tmp/autopkgtest.tIrtam/autopkgtest_tmp
plugins: mock-3.14.0, anyio-4.6.2, benchmark-5.1.0, typeguard-4.4.1
collected 553 items
tests/test_core/test_configuration.py ...... [ 1%]
tests/test_core/test_core_reaction.py ..........ss...................... [ 7%]
...................x....... [ 12%]
tests/test_core/test_dictlist.py ...................... [ 16%]
tests/test_core/test_formula.py ..... [ 16%]
tests/test_core/test_gene.py . [ 17%]
tests/test_core/test_gpr.py .....................x..x................... [ 25%]
.......................... [ 29%]
tests/test_core/test_group.py .. [ 30%]
tests/test_core/test_metabolite.py ...ss.ss. [ 31%]
tests/test_core/test_model.py .......................................... [ 39%]
...........s..s.ss. [ 42%]
tests/test_core/test_solution.py .ss [ 43%]
tests/test_flux_analysis/test_deletion.py ....s..... [ 45%]
tests/test_flux_analysis/test_fastcc.py .... [ 45%]
tests/test_flux_analysis/test_geometric.py .. [ 46%]
tests/test_flux_analysis/test_moma.py . [ 46%]
tests/test_flux_analysis/test_parsimonious.py .. [ 46%]
tests/test_flux_analysis/test_reaction.py . [ 47%]
tests/test_flux_analysis/test_room.py .... [ 47%]
tests/test_flux_analysis/test_variability.py ....... [ 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 ...... [ 50%]
tests/test_flux_analysis/test_gapfilling.py . [ 50%]
tests/test_flux_analysis/test_helpers.py ... [ 51%]
tests/test_flux_analysis/test_loopless.py ..... [ 52%]
tests/test_flux_analysis/test_phenotype_phase_plane.py ...... [ 53%]
tests/test_flux_analysis/test_variability.py ....... [ 54%]
tests/test_io/test_annotation.py .. [ 55%]
tests/test_io/test_annotation_format.py .. [ 55%]
tests/test_io/test_io_order.py ........................... [ 60%]
tests/test_io/test_json.py .... [ 61%]
tests/test_io/test_mat.py ............... [ 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............. [ 71%]
tests/test_io/test_web/test_load.py ..ssss. [ 73%]
tests/test_io/test_yaml.py .x [ 73%]
tests/test_manipulation/test_annotate.py . [ 73%]
tests/test_manipulation/test_delete.py ....... [ 74%]
tests/test_manipulation/test_modify.py ... [ 75%]
tests/test_manipulation/test_validate.py .. [ 75%]
tests/test_medium/test_boundary_types.py ........... [ 77%]
tests/test_medium/test_minimal_medium.py .......... [ 79%]
tests/test_sampling/test_achr.py ...... [ 80%]
tests/test_sampling/test_optgp.py ...... [ 81%]
tests/test_sampling/test_sampling.py .......... [ 83%]
tests/test_summary/test_metabolite_summary.py ................. [ 86%]
tests/test_summary/test_model_summary.py ............... [ 89%]
tests/test_summary/test_reaction_summary.py .................... [ 92%]
tests/test_util/test_array.py .. [ 93%]
tests/test_util/test_context.py ... [ 93%]
tests/test_util/test_process_pool.py ............... [ 96%]
tests/test_util/test_solver.py ..............s [ 99%]
tests/test_util/test_util.py ...X [100%]
=============================== warnings summary ===============================
tests/test_core/test_gpr.py::test_and_gpr[a AND b-2-gpr_genes2-a and b]
tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3]
/usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b'.
warn(
tests/test_core/test_gpr.py::test_or_gpr[a OR b-2-gpr_genes2-a or b]
tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[a OR b-symbolic_gpr2]
tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6]
tests/test_core/test_gpr.py::test_gpr_from_symbolic[a OR b-symbolic_gpr5]
/usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b'.
warn(
tests/test_core/test_gpr.py::test_complicated_gpr[(a OR b) AND c]
tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[(a OR b) AND c-symbolic_gpr6]
tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_and_strs]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9]
tests/test_core/test_gpr.py::test_gpr_from_symbolic[(a OR b) AND c-symbolic_gpr9]
/usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule '(a OR b) AND c'.
warn(
tests/test_core/test_gpr.py::test_gpr_that_needs_two_replacements
/usr/lib/python3/dist-packages/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(
tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3]
/usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b AND a'.
warn(
tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6]
/usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b OR a'.
warn(
tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_strs]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8]
/usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b or c'.
warn(
tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_and_strs]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7]
tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9]
/usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b and c'.
warn(
tests/test_core/test_model.py::test_reaction_delete
tests/test_core/test_model.py::test_reaction_delete
/usr/lib/python3/dist-packages/cobra/core/reaction.py:879: DeprecationWarning: delete is deprecated. Use reaction.remove_from_model instead
warn(
tests/test_core/test_model.py::test_group_loss_of_elements
tests/test_flux_analysis/test_gapfilling.py::test_gapfilling
/usr/lib/python3/dist-packages/cobra/core/group.py:147: UserWarning: need to pass in a list
warn("need to pass in a list")
tests/test_core/test_model.py::test_change_objective
tests/test_core/test_model.py::test_change_objective
tests/test_core/test_model.py::test_change_objective
/usr/lib/python3/dist-packages/cobra/core/reaction.py:761: DeprecationWarning: Please use reaction.flux instead.
warn("Please use reaction.flux instead.", DeprecationWarning)
tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion
tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion
/tmp/autopkgtest.tIrtam/autopkgtest_tmp/tests/test_flux_analysis/test_deletion.py:437: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
assert math.isnan(sol.growth)
tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion
tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion
/tmp/autopkgtest.tIrtam/autopkgtest_tmp/tests/test_flux_analysis/test_deletion.py:438: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead
assert math.isnan(sol_one.growth)
tests/test_io/test_json.py: 1 warning
tests/test_io/test_mat.py: 5 warnings
tests/test_io/test_pickle.py: 1 warning
tests/test_io/test_sbml.py: 9 warnings
tests/test_io/test_yaml.py: 1 warning
/usr/lib/python3/dist-packages/cobra/util/solver.py:554: UserWarning: Solver status is 'infeasible'.
warn(f"Solver status is '{status}'.", UserWarning)
tests/test_io/test_yaml.py::test_save_yaml_model
/tmp/autopkgtest.tIrtam/autopkgtest_tmp/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")
tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi
tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi
tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi
/usr/lib/python3/dist-packages/cobra/medium/boundary_types.py:74: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
compartment = most[matches[most]][0]
tests/test_util/test_process_pool.py::test_with_context
/usr/lib/python3/dist-packages/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: 31 tests ---------------------------------------------------------------------------------------------------------------------
Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_subtract_metabolite_benchmark[gurobi] 1.8310 (1.0) 62.6601 (3.39) 1.9792 (1.0) 0.6831 (1.84) 1.9500 (1.0) 0.0510 (1.02) 92;373 505,266.1023 (1.0) 9954 1
test_subtract_metabolite_benchmark[cplex] 1.8398 (1.00) 18.5100 (1.0) 2.0002 (1.01) 0.3715 (1.0) 1.9511 (1.00) 0.0589 (1.18) 287;447 499,938.4919 (0.99) 9910 1
test_subtract_metabolite_benchmark[glpk] 1.8501 (1.01) 23.1301 (1.25) 1.9965 (1.01) 0.4520 (1.22) 1.9602 (1.01) 0.0501 (1.0) 132;426 500,876.3110 (0.99) 10641 1
test_achr_sample_benchmark 82.4700 (45.04) 5,979.2080 (323.03) 89.6706 (45.31) 120.3922 (324.08) 85.3701 (43.78) 2.1333 (42.62) 1;311 11,151.9210 (0.02) 2401 1
test_change_objective_benchmark[optlang-glpk] 111.9401 (61.14) 461.4589 (24.93) 119.1059 (60.18) 12.7059 (34.20) 116.5899 (59.79) 2.6300 (52.54) 252;708 8,395.8896 (0.02) 6711 1
test_optgp_sample_benchmark 127.8399 (69.82) 200.3410 (10.82) 133.6178 (67.51) 5.9779 (16.09) 131.7998 (67.59) 2.9500 (58.93) 285;324 7,484.0323 (0.01) 2654 1
test_loopless_benchmark_after 543.1410 (296.64) 699.4698 (37.79) 560.3927 (283.15) 16.2304 (43.69) 555.1699 (284.71) 17.2902 (345.40) 41;14 1,784.4628 (0.00) 294 1
test_loopless_benchmark_before 3,002.8292 (>1000.0) 7,386.6181 (399.06) 3,107.1382 (>1000.0) 294.8316 (793.65) 3,085.3981 (>1000.0) 40.4799 (808.65) 1;7 321.8396 (0.00) 216 1
test_minimal_medium_mip_benchmark 3,505.9890 (>1000.0) 3,632.9289 (196.27) 3,547.9834 (>1000.0) 20.1231 (54.17) 3,547.1080 (>1000.0) 24.6148 (491.72) 44;4 281.8502 (0.00) 155 1
test_minimal_medium_linear_benchmark 3,559.9291 (>1000.0) 3,762.3581 (203.26) 3,622.9614 (>1000.0) 29.6569 (79.83) 3,617.1840 (>1000.0) 29.7299 (593.90) 30;7 276.0173 (0.00) 158 1
test_copy_benchmark[optlang-glpk] 7,605.0870 (>1000.0) 206,360.6849 (>1000.0) 11,032.0585 (>1000.0) 23,320.0219 (>1000.0) 7,963.1070 (>1000.0) 540.1295 (>1000.0) 2;2 90.6449 (0.00) 123 1
test_gpr_equality_benchmark 10,667.6461 (>1000.0) 11,131.5360 (601.38) 10,824.4721 (>1000.0) 90.9207 (244.75) 10,812.8559 (>1000.0) 97.1848 (>1000.0) 23;4 92.3833 (0.00) 76 1
test_deepcopy_benchmark 12,536.2349 (>1000.0) 367,000.8660 (>1000.0) 18,801.7116 (>1000.0) 41,368.6174 (>1000.0) 13,323.7445 (>1000.0) 551.4401 (>1000.0) 1;4 53.1866 (0.00) 74 1
test_single_reaction_deletion_benchmark[glpk] 14,945.7941 (>1000.0) 15,159.2940 (818.98) 15,030.7002 (>1000.0) 46.1026 (124.10) 15,038.1450 (>1000.0) 67.6368 (>1000.0) 21;0 66.5305 (0.00) 63 1
test_fastcc_benchmark[glpk] 31,242.9790 (>1000.0) 164,221.7310 (>1000.0) 36,800.3540 (>1000.0) 24,519.7178 (>1000.0) 31,787.7391 (>1000.0) 1,530.2108 (>1000.0) 1;1 27.1737 (0.00) 29 1
test_add_metabolite_benchmark[cplex] 32,170.1989 (>1000.0) 32,491.0788 (>1000.0) 32,323.0359 (>1000.0) 79.9368 (215.18) 32,326.2931 (>1000.0) 118.4202 (>1000.0) 11;0 30.9377 (0.00) 30 1
test_add_metabolite_benchmark[gurobi] 32,237.1989 (>1000.0) 33,209.7579 (>1000.0) 32,768.2475 (>1000.0) 225.9865 (608.33) 32,797.4780 (>1000.0) 309.4049 (>1000.0) 10;0 30.5173 (0.00) 32 1
test_add_metabolite_benchmark[glpk] 32,512.6180 (>1000.0) 32,968.3879 (>1000.0) 32,708.7041 (>1000.0) 112.1028 (301.77) 32,706.8176 (>1000.0) 127.0646 (>1000.0) 10;2 30.5729 (0.00) 32 1
test_optgp_init_benchmark 48,706.3620 (>1000.0) 57,468.7500 (>1000.0) 50,293.5418 (>1000.0) 2,052.5855 (>1000.0) 49,963.5020 (>1000.0) 1,326.7276 (>1000.0) 2;2 19.8833 (0.00) 21 1
test_achr_init_benchmark 49,090.7722 (>1000.0) 51,938.3310 (>1000.0) 49,846.9900 (>1000.0) 717.6407 (>1000.0) 49,744.7520 (>1000.0) 1,058.8492 (>1000.0) 2;1 20.0614 (0.00) 20 1
test_single_gene_deletion_fba_benchmark[glpk] 56,478.3590 (>1000.0) 109,359.7000 (>1000.0) 78,069.8850 (>1000.0) 15,117.9115 (>1000.0) 72,989.0040 (>1000.0) 24,599.5916 (>1000.0) 5;0 12.8090 (0.00) 16 1
test_gpr_symbolism_benchmark 74,311.8229 (>1000.0) 75,781.0529 (>1000.0) 75,050.4504 (>1000.0) 406.8705 (>1000.0) 75,085.8230 (>1000.0) 291.2598 (>1000.0) 4;3 13.3244 (0.00) 13 1
test_single_gene_deletion_linear_moma_benchmark[glpk] 101,116.0631 (>1000.0) 103,328.0028 (>1000.0) 102,513.0547 (>1000.0) 666.8197 (>1000.0) 102,460.1921 (>1000.0) 809.5365 (>1000.0) 3;0 9.7549 (0.00) 9 1
test_double_gene_deletion_benchmark 126,534.7940 (>1000.0) 137,844.3900 (>1000.0) 129,090.5090 (>1000.0) 4,925.9518 (>1000.0) 126,639.4740 (>1000.0) 3,816.6183 (>1000.0) 1;1 7.7465 (0.00) 5 1
test_pfba_benchmark[glpk] 138,192.6690 (>1000.0) 304,975.8591 (>1000.0) 171,843.9092 (>1000.0) 74,423.7111 (>1000.0) 138,696.9788 (>1000.0) 42,203.2767 (>1000.0) 1;1 5.8192 (0.00) 5 1
test_single_gene_deletion_linear_room_benchmark[glpk] 147,474.4361 (>1000.0) 153,076.6550 (>1000.0) 149,699.4636 (>1000.0) 2,369.8425 (>1000.0) 149,035.9961 (>1000.0) 3,899.0441 (>1000.0) 1;0 6.6801 (0.00) 5 1
test_flux_variability_loopless_benchmark[glpk] 150,360.9451 (>1000.0) 201,748.9059 (>1000.0) 184,377.0192 (>1000.0) 19,351.9999 (>1000.0) 187,380.5316 (>1000.0) 21,464.1131 (>1000.0) 1;0 5.4237 (0.00) 6 1
test_copy_benchmark_large_model[optlang-glpk] 171,433.5179 (>1000.0) 425,358.7550 (>1000.0) 253,693.3610 (>1000.0) 125,411.9709 (>1000.0) 173,641.2320 (>1000.0) 232,762.7749 (>1000.0) 2;0 3.9418 (0.00) 6 1
test_double_reaction_deletion_benchmark 193,620.3989 (>1000.0) 212,100.5231 (>1000.0) 200,804.8050 (>1000.0) 7,145.3131 (>1000.0) 201,103.8170 (>1000.0) 8,754.9971 (>1000.0) 2;0 4.9800 (0.00) 5 1
test_geometric_fba_benchmark[glpk] 219,091.7400 (>1000.0) 376,204.0331 (>1000.0) 252,358.1464 (>1000.0) 69,251.3939 (>1000.0) 222,057.4701 (>1000.0) 41,309.0950 (>1000.0) 1;1 3.9626 (0.00) 5 1
test_flux_variability_benchmark[glpk] 227,014.6471 (>1000.0) 229,594.9871 (>1000.0) 228,260.1208 (>1000.0) 1,146.8339 (>1000.0) 227,677.7269 (>1000.0) 1,929.8116 (>1000.0) 2;0 4.3810 (0.00) 5 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
= 515 passed, 27 skipped, 10 xfailed, 1 xpassed, 76 warnings in 73.95s (0:01:13) =
Removing patch debian/patches/remove-appdirs.patch
Restoring src/cobra/core/configuration.py
Restoring setup.cfg
Removing patch debian/patches/no_future_dependency.patch
Restoring setup.cfg
Removing patch debian/patches/32-bit-test.patch
Restoring tests/test_io/test_mat.py
Removing patch debian/patches/ignore_tests.patch
Restoring tests/test_io/test_web/test_load.py
Removing patch debian/patches/xfail_test_show_versions.patch
Restoring tests/test_util/test_util.py
Removing patch debian/patches/mathjax.patch
Restoring documentation_builder/conf.py
No patches applied
PASS
autopkgtest [13:58:19]: test run-unit-test: -----------------------]
autopkgtest [13:58:19]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -
run-unit-test PASS
autopkgtest [13:58:19]: @@@@@@@@@@@@@@@@@@@@ summary
run-unit-test PASS
aborted: False
returncode: 0
Files in working directory:
artifact-dir
artifact-dir/binaries
artifact-dir/binaries/python-cobra-data.deb
artifact-dir/binaries/python3-cobra.deb
artifact-dir/binaries/python3-rich.deb
artifact-dir/log
artifact-dir/run-unit-test-packages
artifact-dir/run-unit-test-stderr
artifact-dir/run-unit-test-stdout
artifact-dir/summary
artifact-dir/testbed-packages
artifact-dir/testinfo.json
artifact-dir/testpkg-version
--------------------