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-9h8puwia/python-cobra-data_0.29.1-1_all.deb /tmp/debusine-fetch-exec-upload-9h8puwia/python3-cobra_0.29.1-1_arm64.deb /tmp/debusine-fetch-exec-upload-9h8puwia/python3-rich_13.9.4-0.1_all.deb /tmp/debusine-fetch-exec-upload-9h8puwia/python-cobra_0.29.1-1.dsc -- unshare --arch arm64 --release sid --tarball /var/lib/debusine/worker/system-images/1099773/system.tar.xz
output (contains stdout and stderr):
autopkgtest [13:52:21]: starting date and time: 2024-12-18 13:52:21+0000
autopkgtest [13:52:21]: version 5.38~bpo12+1
autopkgtest [13:52:21]: host debusine-worker-arm64-demeter-09; 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-9h8puwia/python-cobra-data_0.29.1-1_all.deb /tmp/debusine-fetch-exec-upload-9h8puwia/python3-cobra_0.29.1-1_arm64.deb /tmp/debusine-fetch-exec-upload-9h8puwia/python3-rich_13.9.4-0.1_all.deb /tmp/debusine-fetch-exec-upload-9h8puwia/python-cobra_0.29.1-1.dsc -- unshare --arch arm64 --release sid --tarball /var/lib/debusine/worker/system-images/1099773/system.tar.xz
autopkgtest [13:52:27]: testbed dpkg architecture: arm64
autopkgtest [13:52:27]: testbed apt version: 2.9.17
autopkgtest [13:52:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup
Get:1 http://deb.debian.org/debian sid InRelease [202 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 Packages [9977 kB]
Get:3 http://deb.debian.org/debian sid/main Translation-en [7350 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 Components [4840 kB]
Fetched 22.4 MB in 3s (6400 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 2603 kB of archives.
After this operation, 65.5 kB disk space will be freed.
Get:1 http://deb.debian.org/debian sid/main arm64 libatomic1 arm64 14.2.0-11 [10.1 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 gcc-14-base arm64 14.2.0-11 [48.0 kB]
Get:3 http://deb.debian.org/debian sid/main arm64 libstdc++6 arm64 14.2.0-11 [638 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libgomp1 arm64 14.2.0-11 [124 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 libgcc-s1 arm64 14.2.0-11 [54.1 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 gettext-base arm64 0.22.5-3 [198 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 gettext arm64 0.22.5-3 [1532 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 2603 kB in 0s (19.0 MB/s)
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(Reading database ... 17276 files and directories currently installed.)
Preparing to unpack .../libatomic1_14.2.0-11_arm64.deb ...
Unpacking libatomic1:arm64 (14.2.0-11) over (14.2.0-9) ...
Preparing to unpack .../gcc-14-base_14.2.0-11_arm64.deb ...
Unpacking gcc-14-base:arm64 (14.2.0-11) over (14.2.0-9) ...
Setting up gcc-14-base:arm64 (14.2.0-11) ...
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(Reading database ... 17276 files and directories currently installed.)
Preparing to unpack .../libstdc++6_14.2.0-11_arm64.deb ...
Unpacking libstdc++6:arm64 (14.2.0-11) over (14.2.0-9) ...
Setting up libstdc++6:arm64 (14.2.0-11) ...
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(Reading database ... 17276 files and directories currently installed.)
Preparing to unpack .../libgomp1_14.2.0-11_arm64.deb ...
Unpacking libgomp1:arm64 (14.2.0-11) over (14.2.0-9) ...
Preparing to unpack .../libgcc-s1_14.2.0-11_arm64.deb ...
Unpacking libgcc-s1:arm64 (14.2.0-11) over (14.2.0-9) ...
Setting up libgcc-s1:arm64 (14.2.0-11) ...
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(Reading database ... 17276 files and directories currently installed.)
Preparing to unpack .../gettext-base_0.22.5-3_arm64.deb ...
Unpacking gettext-base (0.22.5-3) over (0.22.5-2) ...
Preparing to unpack .../gettext_0.22.5-3_arm64.deb ...
Unpacking gettext (0.22.5-3) over (0.22.5-2) ...
Setting up gettext-base (0.22.5-3) ...
Setting up libgomp1:arm64 (14.2.0-11) ...
Setting up libatomic1:arm64 (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 [13:52:37]: testbed running kernel: Linux 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22)
autopkgtest [13:52:37]: @@@@@@@@@@@@@@@@@@@@ source /tmp/debusine-fetch-exec-upload-9h8puwia/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.Io69TF/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 [13:52:38]: testing package python-cobra version 0.29.1-1
autopkgtest [13:52:38]: build not needed
autopkgtest [13:52:38]: 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 308 kB of archives.
After this operation, 1170 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main arm64 apt-utils arm64 2.9.17 [308 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 308 kB in 0s (7122 kB/s)
Selecting previously unselected package apt-utils.
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(Reading database ... 17276 files and directories currently installed.)
Preparing to unpack .../apt-utils_2.9.17_arm64.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.Io69TF/binaries InRelease
Get:2 file:/tmp/autopkgtest.Io69TF/binaries Release [816 B]
Get:2 file:/tmp/autopkgtest.Io69TF/binaries Release [816 B]
Ign:3 file:/tmp/autopkgtest.Io69TF/binaries Release.gpg
Get:4 file:/tmp/autopkgtest.Io69TF/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 61.1 MB/63.8 MB of archives.
After this operation, 367 MB of additional disk space will be used.
Get:1 file:/tmp/autopkgtest.Io69TF/binaries python-cobra-data 0.29.1-1 [1437 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 libpython3.12-minimal arm64 3.12.8-3 [810 kB]
Get:3 file:/tmp/autopkgtest.Io69TF/binaries python3-rich 13.9.4-0.1 [203 kB]
Get:4 file:/tmp/autopkgtest.Io69TF/binaries python3-cobra 0.29.1-1 [1119 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 python3.12-minimal arm64 3.12.8-3 [1941 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 media-types all 10.1.0 [26.9 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:10 http://deb.debian.org/debian sid/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB]
Get:11 http://deb.debian.org/debian sid/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 libpython3.12-stdlib arm64 3.12.8-3 [1906 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 python3.12 arm64 3.12.8-3 [677 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B]
Get:15 http://deb.debian.org/debian sid/main arm64 python3 arm64 3.12.7-1 [27.8 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 ed arm64 1.20.2-2+b1 [59.8 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libsuitesparseconfig7 arm64 1:7.8.3+dfsg-2 [23.7 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libamd3 arm64 1:7.8.3+dfsg-2 [38.1 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 libcolamd3 arm64 1:7.8.3+dfsg-2 [31.5 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libgfortran5 arm64 14.2.0-11 [361 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libltdl7 arm64 2.4.7-8 [392 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libglpk40 arm64 5.0-1+b2 [346 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 libpython3.12t64 arm64 3.12.8-3 [1983 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 python3-annotated-types all 0.7.0-1 [18.8 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 python3-idna all 3.8-2 [41.6 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 python3-sniffio all 1.3.1-1 [7120 B]
Get:31 http://deb.debian.org/debian sid/main arm64 python3-anyio all 4.6.2-4 [60.0 kB]
Get:32 http://deb.debian.org/debian sid/main arm64 python3-attr all 24.2.0-1 [68.4 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B]
Get:35 http://deb.debian.org/debian sid/main arm64 python3-colorama all 0.4.6-4 [36.2 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 python3-click all 8.1.7-2 [94.3 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 python3-depinfo arm64 2.2.0-3 [11.6 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 python3-diskcache all 5.6.3-1 [34.4 kB]
Get:39 http://deb.debian.org/debian sid/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:40 http://deb.debian.org/debian sid/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get:41 http://deb.debian.org/debian sid/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:42 http://deb.debian.org/debian sid/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:43 http://deb.debian.org/debian sid/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 python3-mdurl all 0.1.2-1 [9444 B]
Get:47 http://deb.debian.org/debian sid/main arm64 python3-markdown-it all 3.0.0-2 [62.5 kB]
Get:48 http://deb.debian.org/debian sid/main arm64 python3-h11 all 0.14.0-1 [50.1 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 python3-httpcore all 1.0.7-1 [44.7 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 python3-httpx all 0.27.2-1 [77.6 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 python3-importlib-resources all 6.4.5-1 [23.1 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB]
Get:53 http://deb.debian.org/debian sid/main arm64 python3-swiglpk arm64 5.0.10-2+b2 [75.5 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 python3-mpmath all 1.3.0-1 [419 kB]
Get:55 http://deb.debian.org/debian sid/main arm64 python3-sympy all 1.13.3-1 [4147 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 python3-optlang all 1.8.2-3 [5376 kB]
Get:57 http://deb.debian.org/debian sid/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get:58 http://deb.debian.org/debian sid/main arm64 python3-tz all 2024.2-1 [31.0 kB]
Get:59 http://deb.debian.org/debian sid/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5+b1 [6028 kB]
Get:60 http://deb.debian.org/debian sid/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB]
Get:61 http://deb.debian.org/debian sid/main arm64 python3-platformdirs all 4.3.6-1 [16.6 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 python3-pydantic-core arm64 2.27.1-1 [1501 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 python3-dnspython all 2.7.0-1 [164 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 python3-email-validator all 2.2.0-1 [31.6 kB]
Get:65 http://deb.debian.org/debian sid/main arm64 python3-pydantic arm64 2.10.3-1 [365 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 python3-ruamel.yaml.clib arm64 0.2.8+ds-2+b1 [144 kB]
Get:67 http://deb.debian.org/debian sid/main arm64 python3-ruamel.yaml all 0.18.6+ds-3 [145 kB]
Get:68 http://deb.debian.org/debian sid/main arm64 python3-tabulate all 0.9.0-1 [45.9 kB]
Get:69 http://deb.debian.org/debian sid/main arm64 python3-sbml5 arm64 5.20.2+dfsg-8+b1 [3110 kB]
Get:70 http://deb.debian.org/debian sid/main arm64 python3-cpuinfo all 9.0.0+git20221119-2 [23.4 kB]
Get:71 http://deb.debian.org/debian sid/main arm64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 python3-iniconfig all 1.1.1-2 [6396 B]
Get:73 http://deb.debian.org/debian sid/main arm64 python3-rpds-py arm64 0.21.0-2 [259 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 python3-referencing all 0.35.1-2 [23.5 kB]
Get:75 http://deb.debian.org/debian sid/main arm64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B]
Get:76 http://deb.debian.org/debian sid/main arm64 python3-jsonschema all 4.19.2-5 [71.4 kB]
Get:77 http://deb.debian.org/debian sid/main arm64 python3-packaging all 24.2-1 [55.3 kB]
Get:78 http://deb.debian.org/debian sid/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB]
Get:79 http://deb.debian.org/debian sid/main arm64 python3-pytest all 8.3.4-1 [250 kB]
Get:80 http://deb.debian.org/debian sid/main arm64 python3-pytest-benchmark all 5.1.0-1 [44.4 kB]
Get:81 http://deb.debian.org/debian sid/main arm64 python3-pytest-mock all 3.14.0-2 [18.3 kB]
Get:82 http://deb.debian.org/debian sid/main arm64 python3-scipy arm64 1.14.1-3 [18.5 MB]
Get:83 http://deb.debian.org/debian sid/main arm64 quilt all 0.68-1 [437 kB]
Fetched 61.1 MB in 1s (70.4 MB/s)
Selecting previously unselected package libpython3.12-minimal:arm64.
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Preparing to unpack .../libpython3.12-minimal_3.12.8-3_arm64.deb ...
Unpacking libpython3.12-minimal:arm64 (3.12.8-3) ...
Selecting previously unselected package libexpat1:arm64.
Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ...
Unpacking libexpat1:arm64 (2.6.4-1) ...
Selecting previously unselected package python3.12-minimal.
Preparing to unpack .../python3.12-minimal_3.12.8-3_arm64.deb ...
Unpacking python3.12-minimal (3.12.8-3) ...
Setting up libpython3.12-minimal:arm64 (3.12.8-3) ...
Setting up libexpat1:arm64 (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 [13:53:30]: 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.Io69TF/autopkgtest_tmp
plugins: anyio-4.6.2, typeguard-4.4.1, benchmark-5.1.0, mock-3.14.0
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.Io69TF/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.Io69TF/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.Io69TF/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[cplex] 3.1600 (1.0) 25.7599 (1.25) 3.2892 (1.00) 0.5036 (1.0) 3.2401 (1.0) 0.0400 (1.0) 33;297 304,022.0955 (1.00) 6338 1
test_subtract_metabolite_benchmark[glpk] 3.1600 (1.0) 20.6800 (1.0) 3.2974 (1.00) 0.5047 (1.00) 3.2799 (1.01) 0.0400 (1.0) 29;346 303,268.1701 (1.00) 6260 1
test_subtract_metabolite_benchmark[gurobi] 3.1600 (1.0) 31.7600 (1.54) 3.2832 (1.0) 0.5505 (1.09) 3.2401 (1.0) 0.0400 (1.0) 51;296 304,576.9028 (1.0) 6538 1
test_achr_sample_benchmark 173.3999 (54.87) 283.1600 (13.69) 183.2954 (55.83) 11.5532 (22.94) 178.6000 (55.12) 6.7202 (167.81) 159;167 5,455.6740 (0.02) 1238 1
test_change_objective_benchmark[optlang-glpk] 194.2399 (61.47) 708.8801 (34.28) 210.1642 (64.01) 19.4091 (38.54) 203.1999 (62.71) 12.7399 (318.12) 363;313 4,758.1853 (0.02) 4004 1
test_optgp_sample_benchmark 266.8800 (84.46) 844.3999 (40.83) 280.4366 (85.41) 19.7046 (39.13) 274.4999 (84.72) 13.1400 (328.12) 179;142 3,565.8683 (0.01) 1684 1
test_loopless_benchmark_after 1,038.4801 (328.64) 1,205.5601 (58.30) 1,081.9783 (329.55) 24.2736 (48.20) 1,081.7600 (333.87) 35.8801 (895.95) 127;3 924.2330 (0.00) 374 1
test_loopless_benchmark_before 4,895.7600 (>1000.0) 5,100.0800 (246.62) 4,964.4967 (>1000.0) 39.7923 (79.02) 4,960.1200 (>1000.0) 55.3201 (>1000.0) 32;1 201.4303 (0.00) 98 1
test_minimal_medium_mip_benchmark 6,245.0801 (>1000.0) 6,669.4799 (322.51) 6,388.1349 (>1000.0) 72.7337 (144.43) 6,378.2000 (>1000.0) 89.8403 (>1000.0) 27;2 156.5402 (0.00) 94 1
test_minimal_medium_linear_benchmark 6,349.7999 (>1000.0) 6,664.6801 (322.28) 6,458.1260 (>1000.0) 49.9756 (99.24) 6,450.7601 (>1000.0) 54.7201 (>1000.0) 21;4 154.8437 (0.00) 94 1
test_copy_benchmark[optlang-glpk] 12,001.8399 (>1000.0) 268,323.2799 (>1000.0) 18,640.3164 (>1000.0) 38,523.0156 (>1000.0) 12,644.8401 (>1000.0) 1,268.6801 (>1000.0) 1;1 53.6472 (0.00) 44 1
test_gpr_equality_benchmark 16,785.2801 (>1000.0) 17,433.7600 (843.02) 16,950.5437 (>1000.0) 122.1163 (242.50) 16,925.0001 (>1000.0) 124.0199 (>1000.0) 9;2 58.9952 (0.00) 49 1
test_deepcopy_benchmark 19,897.5601 (>1000.0) 409,069.5998 (>1000.0) 32,212.4674 (>1000.0) 62,888.7925 (>1000.0) 21,362.4199 (>1000.0) 651.8399 (>1000.0) 1;12 31.0439 (0.00) 38 1
test_single_reaction_deletion_benchmark[glpk] 22,282.2400 (>1000.0) 23,035.7600 (>1000.0) 22,395.9395 (>1000.0) 114.8578 (228.08) 22,384.6799 (>1000.0) 98.9700 (>1000.0) 2;1 44.6510 (0.00) 43 1
test_fastcc_benchmark[glpk] 49,697.7998 (>1000.0) 248,091.6800 (>1000.0) 61,822.4260 (>1000.0) 43,880.0281 (>1000.0) 51,808.2600 (>1000.0) 3,031.5600 (>1000.0) 1;1 16.1754 (0.00) 20 1
test_add_metabolite_benchmark[glpk] 56,082.1600 (>1000.0) 56,654.4801 (>1000.0) 56,249.8653 (>1000.0) 147.3875 (292.68) 56,203.0000 (>1000.0) 202.2099 (>1000.0) 4;1 17.7778 (0.00) 19 1
test_add_metabolite_benchmark[gurobi] 56,257.6801 (>1000.0) 56,865.7601 (>1000.0) 56,479.0021 (>1000.0) 164.9165 (327.49) 56,462.8001 (>1000.0) 195.0201 (>1000.0) 6;1 17.7057 (0.00) 19 1
test_add_metabolite_benchmark[cplex] 56,662.7202 (>1000.0) 59,228.8000 (>1000.0) 57,037.9431 (>1000.0) 584.9791 (>1000.0) 56,873.4398 (>1000.0) 202.6598 (>1000.0) 2;3 17.5322 (0.00) 19 1
test_achr_init_benchmark 80,507.3602 (>1000.0) 83,233.2000 (>1000.0) 81,696.1001 (>1000.0) 1,051.6788 (>1000.0) 81,400.7600 (>1000.0) 1,813.4400 (>1000.0) 5;0 12.2405 (0.00) 12 1
test_optgp_init_benchmark 80,935.0798 (>1000.0) 83,821.8799 (>1000.0) 82,301.5262 (>1000.0) 911.0763 (>1000.0) 82,281.1602 (>1000.0) 1,326.6800 (>1000.0) 5;0 12.1504 (0.00) 13 1
test_single_gene_deletion_fba_benchmark[glpk] 81,781.9200 (>1000.0) 98,202.3599 (>1000.0) 86,630.7520 (>1000.0) 3,795.1447 (>1000.0) 86,134.0000 (>1000.0) 3,080.6100 (>1000.0) 2;1 11.5432 (0.00) 15 1
test_gpr_symbolism_benchmark 121,466.5999 (>1000.0) 123,913.9598 (>1000.0) 122,864.1000 (>1000.0) 880.3064 (>1000.0) 123,225.7800 (>1000.0) 1,386.1802 (>1000.0) 3;0 8.1391 (0.00) 8 1
test_single_gene_deletion_linear_moma_benchmark[glpk] 164,429.1598 (>1000.0) 167,485.3598 (>1000.0) 166,135.0159 (>1000.0) 1,123.2802 (>1000.0) 166,412.0799 (>1000.0) 1,276.9299 (>1000.0) 2;0 6.0192 (0.00) 5 1
test_double_gene_deletion_benchmark 226,775.8800 (>1000.0) 228,951.6800 (>1000.0) 227,408.2240 (>1000.0) 957.5431 (>1000.0) 226,786.7199 (>1000.0) 1,261.1600 (>1000.0) 1;0 4.3974 (0.00) 5 1
test_flux_variability_loopless_benchmark[glpk] 229,023.1599 (>1000.0) 259,728.8799 (>1000.0) 248,064.8400 (>1000.0) 11,487.1237 (>1000.0) 250,631.2800 (>1000.0) 11,197.4700 (>1000.0) 2;0 4.0312 (0.00) 5 1
test_single_gene_deletion_linear_room_benchmark[glpk] 239,700.6000 (>1000.0) 488,679.2800 (>1000.0) 290,633.7840 (>1000.0) 110,715.0476 (>1000.0) 241,562.2801 (>1000.0) 63,340.1800 (>1000.0) 1;1 3.4408 (0.00) 5 1
test_pfba_benchmark[glpk] 247,004.5600 (>1000.0) 257,755.2800 (>1000.0) 251,735.5041 (>1000.0) 4,160.2795 (>1000.0) 251,032.0402 (>1000.0) 6,032.7100 (>1000.0) 2;0 3.9724 (0.00) 5 1
test_copy_benchmark_large_model[optlang-glpk] 286,549.7598 (>1000.0) 833,483.5600 (>1000.0) 545,746.9520 (>1000.0) 241,024.4813 (>1000.0) 641,568.7201 (>1000.0) 408,148.4900 (>1000.0) 3;0 1.8324 (0.00) 5 1
test_double_reaction_deletion_benchmark 300,461.4001 (>1000.0) 336,718.3602 (>1000.0) 321,014.4881 (>1000.0) 13,205.0087 (>1000.0) 323,066.0402 (>1000.0) 13,846.1200 (>1000.0) 2;0 3.1151 (0.00) 5 1
test_geometric_fba_benchmark[glpk] 367,910.2000 (>1000.0) 373,799.1599 (>1000.0) 370,183.3200 (>1000.0) 2,235.8117 (>1000.0) 370,165.2798 (>1000.0) 2,465.1499 (>1000.0) 2;0 2.7014 (0.00) 5 1
test_flux_variability_benchmark[glpk] 423,445.6799 (>1000.0) 424,074.0798 (>1000.0) 423,790.4880 (>1000.0) 262.4505 (521.17) 423,865.1600 (>1000.0) 438.8000 (>1000.0) 2;0 2.3597 (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 106.78s (0:01:46) =
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 [13:55:21]: test run-unit-test: -----------------------]
autopkgtest [13:55:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -
run-unit-test PASS
autopkgtest [13:55:21]: @@@@@@@@@@@@@@@@@@@@ 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
--------------------