2024-02-19T13:41:19,137 Created temporary directory: /tmp/pip-build-tracker-4f681gj_ 2024-02-19T13:41:19,138 Initialized build tracking at /tmp/pip-build-tracker-4f681gj_ 2024-02-19T13:41:19,138 Created build tracker: /tmp/pip-build-tracker-4f681gj_ 2024-02-19T13:41:19,139 Entered build tracker: /tmp/pip-build-tracker-4f681gj_ 2024-02-19T13:41:19,140 Created temporary directory: /tmp/pip-wheel-w1i4rxce 2024-02-19T13:41:19,143 Created temporary directory: /tmp/pip-ephem-wheel-cache-18a1vbqn 2024-02-19T13:41:19,165 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-02-19T13:41:19,168 2 location(s) to search for versions of reframed: 2024-02-19T13:41:19,168 * https://pypi.org/simple/reframed/ 2024-02-19T13:41:19,168 * https://www.piwheels.org/simple/reframed/ 2024-02-19T13:41:19,169 Fetching project page and analyzing links: https://pypi.org/simple/reframed/ 2024-02-19T13:41:19,170 Getting page https://pypi.org/simple/reframed/ 2024-02-19T13:41:19,172 Found index url https://pypi.org/simple/ 2024-02-19T13:41:19,387 Fetched page https://pypi.org/simple/reframed/ as application/vnd.pypi.simple.v1+json 2024-02-19T13:41:19,391 Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/4c/95/ca11b1ab535308d1ce05189fd6fd6b9fd97e0475ba6eddef49f213398279/reframed-0.1.0-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,392 Found link https://files.pythonhosted.org/packages/96/16/bf504bb5562c0cb5f8a52b99f1d003d62b95fe989884cff2704d861662a9/reframed-0.1.0.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.6), version: 0.1.0 2024-02-19T13:41:19,392 Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/38/31/8e6b377135857f650a09b8483b24f2bda3f7af6711a092f0c315ab6eb060/reframed-1.0.0-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,393 Found link https://files.pythonhosted.org/packages/44/55/6da6d6bebea285a694c10021b001d66e6468fe564c583a6adb9532b07a7c/reframed-1.0.0.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.6), version: 1.0.0 2024-02-19T13:41:19,394 Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/33/52/027e95cbca8f8220e036edd5be338e7d386359cbd34e54f9cf5d485b7b0b/reframed-1.1.0-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,395 Found link https://files.pythonhosted.org/packages/8e/06/4c5a0ff4029981ef46345b46c0adfb5ccb2d7439d646e83cdc8b33d9d355/reframed-1.1.0.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.6), version: 1.1.0 2024-02-19T13:41:19,396 Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/bb/2e/a1d728d7321f4059f884abb2bdca8fc5ecab82fcab6de59dbe92eb8aaec8/reframed-1.2.0-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,397 Found link https://files.pythonhosted.org/packages/cb/e4/ad6b474f3e45dc17e1c1f8ddedc0ef50f54ef9844401612a8014af663733/reframed-1.2.0.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.6), version: 1.2.0 2024-02-19T13:41:19,397 Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/d6/1f/933814fb871c5a897eac44d174bf5c487e4e8317323713eff52a337fcd39/reframed-1.2.1-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,398 Found link https://files.pythonhosted.org/packages/fb/c4/b486830cb03628806d682df1438239b9a978a46abd00b4290844a5de8815/reframed-1.2.1.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.6), version: 1.2.1 2024-02-19T13:41:19,399 Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/00/24/7be3f3cfb1b5b8a30846e43635df4123ee8b838c4c87d07efc7b6f090f32/reframed-1.3.0-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,400 Found link https://files.pythonhosted.org/packages/8d/c5/eac5c9a85133f37d1fae31888d9bc84474ee57ab35eeb13793ee6e92351a/reframed-1.3.0.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.6), version: 1.3.0 2024-02-19T13:41:19,400 Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/b4/47/ac9f9d0e63814afe9fc70c0a6c91055356976bc6dbf7f50905807d291e4c/reframed-1.4.0-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,401 Found link https://files.pythonhosted.org/packages/80/b6/a21d3ea303d3eb74cc6b8fb1dfcfb1ceba70b847137112ae19f9a8833d81/reframed-1.4.0.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.6), version: 1.4.0 2024-02-19T13:41:19,402 Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/cf/6a/a10e5a5ab5a192e41901b4472314dc6453c2ddde27bb5ccbd7f8a267ecf9/reframed-1.5.0-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,403 Found link https://files.pythonhosted.org/packages/fe/fb/98d4497abcb4c9637977e0c79c5bf722eeda37ce9815166b6b2ae2cbad3a/reframed-1.5.0.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.6), version: 1.5.0 2024-02-19T13:41:19,403 Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/f7/8b/37d07ab953e288bbe9ebed2d90895a579aaf78ec157cbac5035a38cd07d4/reframed-1.5.1-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,404 Found link https://files.pythonhosted.org/packages/7b/af/384a1024605225b233c8da7dd2fa05f07b209b6dab2defdcc26dc819aa09/reframed-1.5.1.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.6), version: 1.5.1 2024-02-19T13:41:19,405 Fetching project page and analyzing links: https://www.piwheels.org/simple/reframed/ 2024-02-19T13:41:19,406 Getting page https://www.piwheels.org/simple/reframed/ 2024-02-19T13:41:19,407 Found index url https://www.piwheels.org/simple/ 2024-02-19T13:41:19,567 Fetched page https://www.piwheels.org/simple/reframed/ as text/html 2024-02-19T13:41:19,570 Skipping link: No binaries permitted for reframed: https://www.piwheels.org/simple/reframed/reframed-1.5.0-py3-none-any.whl#sha256=fb599b43bd5101cd2f6669892af2463bab8d5e3bc9897ca062c077ff4fabb794 (from https://www.piwheels.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,571 Skipping link: No binaries permitted for reframed: https://www.piwheels.org/simple/reframed/reframed-1.4.0-py3-none-any.whl#sha256=a09b2e2318b1e1ba19d6349547e39ad38ab27511d71014cbfbf69a9f34703e76 (from https://www.piwheels.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,572 Skipping link: No binaries permitted for reframed: https://www.piwheels.org/simple/reframed/reframed-1.3.0-py3-none-any.whl#sha256=98e139990db40e866cf444f5c450cfb51f17d5a44b55d6a3ba4aee7450b604e8 (from https://www.piwheels.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,572 Skipping link: No binaries permitted for reframed: https://www.piwheels.org/simple/reframed/reframed-1.2.1-py3-none-any.whl#sha256=3ceb92c8a30883d2baf45f4d40ed2cd3a8bfc8ce258802dd020fa0b3b7c59ce6 (from https://www.piwheels.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,573 Skipping link: No binaries permitted for reframed: https://www.piwheels.org/simple/reframed/reframed-1.2.0-py3-none-any.whl#sha256=ab487507a7d904499f878fbee75e976f85d5549bbf27dcb4a0f5887d190b273a (from https://www.piwheels.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,573 Skipping link: No binaries permitted for reframed: https://www.piwheels.org/simple/reframed/reframed-1.1.0-py3-none-any.whl#sha256=3b96243ab342939256c3dd8790b9fbea4a4fc30c0ff5d08d1aa42dae2592b5e7 (from https://www.piwheels.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,573 Skipping link: No binaries permitted for reframed: https://www.piwheels.org/simple/reframed/reframed-1.0.0-py3-none-any.whl#sha256=3a4cc946c0dfad3d01ffd7911585af761e56ae42505a5876f174face5e6ac194 (from https://www.piwheels.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,574 Skipping link: No binaries permitted for reframed: https://www.piwheels.org/simple/reframed/reframed-0.1.0-py3-none-any.whl#sha256=bc75129a078901da2215f918b135f9f36f3ee006f8a5d0f363cd42abcf3299c9 (from https://www.piwheels.org/simple/reframed/) (requires-python:>=3.6) 2024-02-19T13:41:19,575 Skipping link: not a file: https://www.piwheels.org/simple/reframed/ 2024-02-19T13:41:19,575 Skipping link: not a file: https://pypi.org/simple/reframed/ 2024-02-19T13:41:19,595 Given no hashes to check 1 links for project 'reframed': discarding no candidates 2024-02-19T13:41:19,613 Collecting reframed==1.5.1 2024-02-19T13:41:19,615 Created temporary directory: /tmp/pip-unpack-q1h6fmrf 2024-02-19T13:41:20,064 Downloading reframed-1.5.1.tar.gz (613 kB) 2024-02-19T13:41:20,345 Added reframed==1.5.1 from https://files.pythonhosted.org/packages/7b/af/384a1024605225b233c8da7dd2fa05f07b209b6dab2defdcc26dc819aa09/reframed-1.5.1.tar.gz to build tracker '/tmp/pip-build-tracker-4f681gj_' 2024-02-19T13:41:20,347 Running setup.py (path:/tmp/pip-wheel-w1i4rxce/reframed_5912bcd476f54386b8ee5fc99fa0700f/setup.py) egg_info for package reframed 2024-02-19T13:41:20,348 Created temporary directory: /tmp/pip-pip-egg-info-rexhrdg4 2024-02-19T13:41:20,348 Preparing metadata (setup.py): started 2024-02-19T13:41:20,349 Running command python setup.py egg_info 2024-02-19T13:41:21,366 running egg_info 2024-02-19T13:41:21,367 creating /tmp/pip-pip-egg-info-rexhrdg4/reframed.egg-info 2024-02-19T13:41:21,391 writing /tmp/pip-pip-egg-info-rexhrdg4/reframed.egg-info/PKG-INFO 2024-02-19T13:41:21,395 writing dependency_links to /tmp/pip-pip-egg-info-rexhrdg4/reframed.egg-info/dependency_links.txt 2024-02-19T13:41:21,397 writing requirements to /tmp/pip-pip-egg-info-rexhrdg4/reframed.egg-info/requires.txt 2024-02-19T13:41:21,398 writing top-level names to /tmp/pip-pip-egg-info-rexhrdg4/reframed.egg-info/top_level.txt 2024-02-19T13:41:21,399 writing manifest file '/tmp/pip-pip-egg-info-rexhrdg4/reframed.egg-info/SOURCES.txt' 2024-02-19T13:41:21,483 reading manifest file '/tmp/pip-pip-egg-info-rexhrdg4/reframed.egg-info/SOURCES.txt' 2024-02-19T13:41:21,484 reading manifest template 'MANIFEST.in' 2024-02-19T13:41:21,485 warning: no files found matching 'CONTRIBUTING.rst' 2024-02-19T13:41:21,486 warning: no files found matching 'HISTORY.rst' 2024-02-19T13:41:21,490 warning: no previously-included files matching '__pycache__' found under directory '*' 2024-02-19T13:41:21,491 warning: no previously-included files matching '*.py[co]' found under directory '*' 2024-02-19T13:41:21,524 warning: no files found matching '*.jpg' under directory 'docs' 2024-02-19T13:41:21,542 warning: no files found matching '*.gif' under directory 'docs' 2024-02-19T13:41:21,542 adding license file 'LICENSE' 2024-02-19T13:41:21,546 writing manifest file '/tmp/pip-pip-egg-info-rexhrdg4/reframed.egg-info/SOURCES.txt' 2024-02-19T13:41:21,653 Preparing metadata (setup.py): finished with status 'done' 2024-02-19T13:41:21,657 Source in /tmp/pip-wheel-w1i4rxce/reframed_5912bcd476f54386b8ee5fc99fa0700f has version 1.5.1, which satisfies requirement reframed==1.5.1 from https://files.pythonhosted.org/packages/7b/af/384a1024605225b233c8da7dd2fa05f07b209b6dab2defdcc26dc819aa09/reframed-1.5.1.tar.gz 2024-02-19T13:41:21,658 Removed reframed==1.5.1 from https://files.pythonhosted.org/packages/7b/af/384a1024605225b233c8da7dd2fa05f07b209b6dab2defdcc26dc819aa09/reframed-1.5.1.tar.gz from build tracker '/tmp/pip-build-tracker-4f681gj_' 2024-02-19T13:41:21,664 Created temporary directory: /tmp/pip-unpack-_jvq_wq8 2024-02-19T13:41:21,665 Created temporary directory: /tmp/pip-unpack-yfr74r_t 2024-02-19T13:41:21,672 Building wheels for collected packages: reframed 2024-02-19T13:41:21,676 Created temporary directory: /tmp/pip-wheel-wl_07sgd 2024-02-19T13:41:21,677 Building wheel for reframed (setup.py): started 2024-02-19T13:41:21,678 Destination directory: /tmp/pip-wheel-wl_07sgd 2024-02-19T13:41:21,678 Running command python setup.py bdist_wheel 2024-02-19T13:41:22,668 running bdist_wheel 2024-02-19T13:41:22,763 running build 2024-02-19T13:41:22,763 running build_py 2024-02-19T13:41:22,790 creating build 2024-02-19T13:41:22,791 creating build/lib 2024-02-19T13:41:22,792 creating build/lib/tests 2024-02-19T13:41:22,793 copying tests/test_reframed.py -> build/lib/tests 2024-02-19T13:41:22,795 copying tests/scip_carveme.py -> build/lib/tests 2024-02-19T13:41:22,797 copying tests/__init__.py -> build/lib/tests 2024-02-19T13:41:22,800 creating build/lib/reframed 2024-02-19T13:41:22,800 copying reframed/__init__.py -> build/lib/reframed 2024-02-19T13:41:22,803 creating build/lib/reframed/core 2024-02-19T13:41:22,804 copying reframed/core/environment.py -> build/lib/reframed/core 2024-02-19T13:41:22,806 copying reframed/core/elements.py -> build/lib/reframed/core 2024-02-19T13:41:22,808 copying reframed/core/parser.py -> build/lib/reframed/core 2024-02-19T13:41:22,810 copying reframed/core/model.py -> build/lib/reframed/core 2024-02-19T13:41:22,813 copying reframed/core/transformation.py -> build/lib/reframed/core 2024-02-19T13:41:22,815 copying reframed/core/cbmodel.py -> build/lib/reframed/core 2024-02-19T13:41:22,817 copying reframed/core/__init__.py -> build/lib/reframed/core 2024-02-19T13:41:22,819 creating build/lib/reframed/solvers 2024-02-19T13:41:22,820 copying reframed/solvers/optlang_solver.py -> build/lib/reframed/solvers 2024-02-19T13:41:22,823 copying reframed/solvers/solver.py -> build/lib/reframed/solvers 2024-02-19T13:41:22,825 copying reframed/solvers/scip_solver.py -> build/lib/reframed/solvers 2024-02-19T13:41:22,827 copying reframed/solvers/cplex_solver.py -> build/lib/reframed/solvers 2024-02-19T13:41:22,829 copying reframed/solvers/gurobi_solver.py -> build/lib/reframed/solvers 2024-02-19T13:41:22,832 copying reframed/solvers/solution.py -> build/lib/reframed/solvers 2024-02-19T13:41:22,834 copying reframed/solvers/pulp_solver.py -> build/lib/reframed/solvers 2024-02-19T13:41:22,836 copying reframed/solvers/__init__.py -> build/lib/reframed/solvers 2024-02-19T13:41:22,838 creating build/lib/reframed/external 2024-02-19T13:41:22,839 copying reframed/external/escher.py -> build/lib/reframed/external 2024-02-19T13:41:22,841 copying reframed/external/__init__.py -> build/lib/reframed/external 2024-02-19T13:41:22,842 copying reframed/external/cobrapy.py -> build/lib/reframed/external 2024-02-19T13:41:22,844 creating build/lib/reframed/io 2024-02-19T13:41:22,845 copying reframed/io/sbml.py -> build/lib/reframed/io 2024-02-19T13:41:22,848 copying reframed/io/cache.py -> build/lib/reframed/io 2024-02-19T13:41:22,850 copying reframed/io/__init__.py -> build/lib/reframed/io 2024-02-19T13:41:22,852 creating build/lib/reframed/alpha 2024-02-19T13:41:22,853 copying reframed/alpha/fluxutils.py -> build/lib/reframed/alpha 2024-02-19T13:41:22,854 copying reframed/alpha/sampling.py -> build/lib/reframed/alpha 2024-02-19T13:41:22,856 copying reframed/alpha/plotting.py -> build/lib/reframed/alpha 2024-02-19T13:41:22,858 copying reframed/alpha/gapMake.py -> build/lib/reframed/alpha 2024-02-19T13:41:22,859 copying reframed/alpha/geneswitch.py -> build/lib/reframed/alpha 2024-02-19T13:41:22,861 copying reframed/alpha/__init__.py -> build/lib/reframed/alpha 2024-02-19T13:41:22,864 creating build/lib/reframed/cobra 2024-02-19T13:41:22,864 copying reframed/cobra/thermodynamics.py -> build/lib/reframed/cobra 2024-02-19T13:41:22,867 copying reframed/cobra/medium.py -> build/lib/reframed/cobra 2024-02-19T13:41:22,869 copying reframed/cobra/simulation.py -> build/lib/reframed/cobra 2024-02-19T13:41:22,872 copying reframed/cobra/plotting.py -> build/lib/reframed/cobra 2024-02-19T13:41:22,873 copying reframed/cobra/transcriptomics.py -> build/lib/reframed/cobra 2024-02-19T13:41:22,876 copying reframed/cobra/ensemble.py -> build/lib/reframed/cobra 2024-02-19T13:41:22,878 copying reframed/cobra/knockout.py -> build/lib/reframed/cobra 2024-02-19T13:41:22,881 copying reframed/cobra/auxotrophy.py -> build/lib/reframed/cobra 2024-02-19T13:41:22,882 copying reframed/cobra/__init__.py -> build/lib/reframed/cobra 2024-02-19T13:41:22,883 copying reframed/cobra/variability.py -> build/lib/reframed/cobra 2024-02-19T13:41:22,886 creating build/lib/reframed/community 2024-02-19T13:41:22,886 copying reframed/community/simulation.py -> build/lib/reframed/community 2024-02-19T13:41:22,888 copying reframed/community/SteadyCom.py -> build/lib/reframed/community 2024-02-19T13:41:22,890 copying reframed/community/solution.py -> build/lib/reframed/community 2024-02-19T13:41:22,893 copying reframed/community/model.py -> build/lib/reframed/community 2024-02-19T13:41:22,895 copying reframed/community/simulation_old.py -> build/lib/reframed/community 2024-02-19T13:41:22,897 copying reframed/community/__init__.py -> build/lib/reframed/community 2024-02-19T13:41:22,898 running egg_info 2024-02-19T13:41:22,954 writing reframed.egg-info/PKG-INFO 2024-02-19T13:41:22,957 writing dependency_links to reframed.egg-info/dependency_links.txt 2024-02-19T13:41:22,959 writing requirements to reframed.egg-info/requires.txt 2024-02-19T13:41:22,960 writing top-level names to reframed.egg-info/top_level.txt 2024-02-19T13:41:22,993 reading manifest file 'reframed.egg-info/SOURCES.txt' 2024-02-19T13:41:22,997 reading manifest template 'MANIFEST.in' 2024-02-19T13:41:22,997 warning: no files found matching 'CONTRIBUTING.rst' 2024-02-19T13:41:22,998 warning: no files found matching 'HISTORY.rst' 2024-02-19T13:41:23,002 warning: no previously-included files matching '__pycache__' found under directory '*' 2024-02-19T13:41:23,003 warning: no previously-included files matching '*.py[co]' found under directory '*' 2024-02-19T13:41:23,034 warning: no files found matching '*.jpg' under directory 'docs' 2024-02-19T13:41:23,051 warning: no files found matching '*.gif' under directory 'docs' 2024-02-19T13:41:23,052 adding license file 'LICENSE' 2024-02-19T13:41:23,056 writing manifest file 'reframed.egg-info/SOURCES.txt' 2024-02-19T13:41:23,059 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'tests.data' is absent from the `packages` configuration. 2024-02-19T13:41:23,060 !! 2024-02-19T13:41:23,061 ******************************************************************************** 2024-02-19T13:41:23,061 ############################ 2024-02-19T13:41:23,062 # Package would be ignored # 2024-02-19T13:41:23,062 ############################ 2024-02-19T13:41:23,063 Python recognizes 'tests.data' as an importable package[^1], 2024-02-19T13:41:23,063 but it is absent from setuptools' `packages` configuration. 2024-02-19T13:41:23,064 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-19T13:41:23,065 package, please make sure that 'tests.data' is explicitly added 2024-02-19T13:41:23,065 to the `packages` configuration field. 2024-02-19T13:41:23,066 Alternatively, you can also rely on setuptools' discovery methods 2024-02-19T13:41:23,067 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-19T13:41:23,067 instead of `find_packages(...)`/`find:`). 2024-02-19T13:41:23,068 You can read more about "package discovery" on setuptools documentation page: 2024-02-19T13:41:23,069 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-19T13:41:23,070 If you don't want 'tests.data' to be distributed and are 2024-02-19T13:41:23,071 already explicitly excluding 'tests.data' via 2024-02-19T13:41:23,072 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-19T13:41:23,072 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-19T13:41:23,073 combination with a more fine grained `package-data` configuration. 2024-02-19T13:41:23,075 You can read more about "package data files" on setuptools documentation page: 2024-02-19T13:41:23,076 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-19T13:41:23,078 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-19T13:41:23,078 even if it does not contain any `.py` files. 2024-02-19T13:41:23,079 On the other hand, currently there is no concept of package data 2024-02-19T13:41:23,079 directory, all directories are treated like packages. 2024-02-19T13:41:23,080 ******************************************************************************** 2024-02-19T13:41:23,081 !! 2024-02-19T13:41:23,081 check.warn(importable) 2024-02-19T13:41:23,082 creating build/lib/tests/data 2024-02-19T13:41:23,083 copying tests/data/e_coli_core.xml.gz -> build/lib/tests/data 2024-02-19T13:41:23,083 copying tests/data/iML1515.xml.gz -> build/lib/tests/data 2024-02-19T13:41:23,083 copying tests/data/model_cobra.xml.gz -> build/lib/tests/data 2024-02-19T13:41:23,086 copying tests/data/model_fbc2.xml.gz -> build/lib/tests/data 2024-02-19T13:41:23,116 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-02-19T13:41:23,116 !! 2024-02-19T13:41:23,117 ******************************************************************************** 2024-02-19T13:41:23,118 Please avoid running ``setup.py`` directly. 2024-02-19T13:41:23,118 Instead, use pypa/build, pypa/installer or other 2024-02-19T13:41:23,118 standards-based tools. 2024-02-19T13:41:23,120 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-02-19T13:41:23,120 ******************************************************************************** 2024-02-19T13:41:23,121 !! 2024-02-19T13:41:23,122 self.initialize_options() 2024-02-19T13:41:23,142 installing to build/bdist.linux-armv7l/wheel 2024-02-19T13:41:23,142 running install 2024-02-19T13:41:23,167 running install_lib 2024-02-19T13:41:23,192 creating build/bdist.linux-armv7l 2024-02-19T13:41:23,192 creating build/bdist.linux-armv7l/wheel 2024-02-19T13:41:23,193 creating build/bdist.linux-armv7l/wheel/tests 2024-02-19T13:41:23,195 creating build/bdist.linux-armv7l/wheel/tests/data 2024-02-19T13:41:23,196 copying build/lib/tests/data/e_coli_core.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data 2024-02-19T13:41:23,199 copying build/lib/tests/data/iML1515.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data 2024-02-19T13:41:23,213 copying build/lib/tests/data/model_fbc2.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data 2024-02-19T13:41:23,215 copying build/lib/tests/data/model_cobra.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data 2024-02-19T13:41:23,217 copying build/lib/tests/test_reframed.py -> build/bdist.linux-armv7l/wheel/tests 2024-02-19T13:41:23,220 copying build/lib/tests/scip_carveme.py -> build/bdist.linux-armv7l/wheel/tests 2024-02-19T13:41:23,221 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests 2024-02-19T13:41:23,224 creating build/bdist.linux-armv7l/wheel/reframed 2024-02-19T13:41:23,225 creating build/bdist.linux-armv7l/wheel/reframed/core 2024-02-19T13:41:23,226 copying build/lib/reframed/core/environment.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-02-19T13:41:23,228 copying build/lib/reframed/core/elements.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-02-19T13:41:23,231 copying build/lib/reframed/core/parser.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-02-19T13:41:23,233 copying build/lib/reframed/core/model.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-02-19T13:41:23,235 copying build/lib/reframed/core/transformation.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-02-19T13:41:23,238 copying build/lib/reframed/core/cbmodel.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-02-19T13:41:23,240 copying build/lib/reframed/core/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-02-19T13:41:23,242 creating build/bdist.linux-armv7l/wheel/reframed/solvers 2024-02-19T13:41:23,243 copying build/lib/reframed/solvers/optlang_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-02-19T13:41:23,245 copying build/lib/reframed/solvers/solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-02-19T13:41:23,248 copying build/lib/reframed/solvers/scip_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-02-19T13:41:23,250 copying build/lib/reframed/solvers/cplex_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-02-19T13:41:23,252 copying build/lib/reframed/solvers/gurobi_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-02-19T13:41:23,255 copying build/lib/reframed/solvers/solution.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-02-19T13:41:23,256 copying build/lib/reframed/solvers/pulp_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-02-19T13:41:23,259 copying build/lib/reframed/solvers/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-02-19T13:41:23,261 creating build/bdist.linux-armv7l/wheel/reframed/external 2024-02-19T13:41:23,261 copying build/lib/reframed/external/escher.py -> build/bdist.linux-armv7l/wheel/reframed/external 2024-02-19T13:41:23,263 copying build/lib/reframed/external/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/external 2024-02-19T13:41:23,265 copying build/lib/reframed/external/cobrapy.py -> build/bdist.linux-armv7l/wheel/reframed/external 2024-02-19T13:41:23,267 creating build/bdist.linux-armv7l/wheel/reframed/io 2024-02-19T13:41:23,268 copying build/lib/reframed/io/sbml.py -> build/bdist.linux-armv7l/wheel/reframed/io 2024-02-19T13:41:23,271 copying build/lib/reframed/io/cache.py -> build/bdist.linux-armv7l/wheel/reframed/io 2024-02-19T13:41:23,273 copying build/lib/reframed/io/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/io 2024-02-19T13:41:23,274 creating build/bdist.linux-armv7l/wheel/reframed/alpha 2024-02-19T13:41:23,275 copying build/lib/reframed/alpha/fluxutils.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2024-02-19T13:41:23,277 copying build/lib/reframed/alpha/sampling.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2024-02-19T13:41:23,279 copying build/lib/reframed/alpha/plotting.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2024-02-19T13:41:23,281 copying build/lib/reframed/alpha/gapMake.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2024-02-19T13:41:23,283 copying build/lib/reframed/alpha/geneswitch.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2024-02-19T13:41:23,285 copying build/lib/reframed/alpha/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2024-02-19T13:41:23,287 creating build/bdist.linux-armv7l/wheel/reframed/cobra 2024-02-19T13:41:23,288 copying build/lib/reframed/cobra/thermodynamics.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-02-19T13:41:23,290 copying build/lib/reframed/cobra/medium.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-02-19T13:41:23,293 copying build/lib/reframed/cobra/simulation.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-02-19T13:41:23,295 copying build/lib/reframed/cobra/plotting.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-02-19T13:41:23,297 copying build/lib/reframed/cobra/transcriptomics.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-02-19T13:41:23,299 copying build/lib/reframed/cobra/ensemble.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-02-19T13:41:23,301 copying build/lib/reframed/cobra/knockout.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-02-19T13:41:23,304 copying build/lib/reframed/cobra/auxotrophy.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-02-19T13:41:23,305 copying build/lib/reframed/cobra/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-02-19T13:41:23,307 copying build/lib/reframed/cobra/variability.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-02-19T13:41:23,309 copying build/lib/reframed/__init__.py -> build/bdist.linux-armv7l/wheel/reframed 2024-02-19T13:41:23,311 creating build/bdist.linux-armv7l/wheel/reframed/community 2024-02-19T13:41:23,312 copying build/lib/reframed/community/simulation.py -> build/bdist.linux-armv7l/wheel/reframed/community 2024-02-19T13:41:23,314 copying build/lib/reframed/community/SteadyCom.py -> build/bdist.linux-armv7l/wheel/reframed/community 2024-02-19T13:41:23,316 copying build/lib/reframed/community/solution.py -> build/bdist.linux-armv7l/wheel/reframed/community 2024-02-19T13:41:23,319 copying build/lib/reframed/community/model.py -> build/bdist.linux-armv7l/wheel/reframed/community 2024-02-19T13:41:23,321 copying build/lib/reframed/community/simulation_old.py -> build/bdist.linux-armv7l/wheel/reframed/community 2024-02-19T13:41:23,323 copying build/lib/reframed/community/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/community 2024-02-19T13:41:23,324 running install_egg_info 2024-02-19T13:41:23,354 Copying reframed.egg-info to build/bdist.linux-armv7l/wheel/reframed-1.5.1-py3.11.egg-info 2024-02-19T13:41:23,367 running install_scripts 2024-02-19T13:41:23,381 creating build/bdist.linux-armv7l/wheel/reframed-1.5.1.dist-info/WHEEL 2024-02-19T13:41:23,384 creating '/tmp/pip-wheel-wl_07sgd/reframed-1.5.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-02-19T13:41:23,386 adding 'reframed/__init__.py' 2024-02-19T13:41:23,388 adding 'reframed/alpha/__init__.py' 2024-02-19T13:41:23,389 adding 'reframed/alpha/fluxutils.py' 2024-02-19T13:41:23,391 adding 'reframed/alpha/gapMake.py' 2024-02-19T13:41:23,392 adding 'reframed/alpha/geneswitch.py' 2024-02-19T13:41:23,394 adding 'reframed/alpha/plotting.py' 2024-02-19T13:41:23,395 adding 'reframed/alpha/sampling.py' 2024-02-19T13:41:23,397 adding 'reframed/cobra/__init__.py' 2024-02-19T13:41:23,398 adding 'reframed/cobra/auxotrophy.py' 2024-02-19T13:41:23,399 adding 'reframed/cobra/ensemble.py' 2024-02-19T13:41:23,401 adding 'reframed/cobra/knockout.py' 2024-02-19T13:41:23,403 adding 'reframed/cobra/medium.py' 2024-02-19T13:41:23,404 adding 'reframed/cobra/plotting.py' 2024-02-19T13:41:23,406 adding 'reframed/cobra/simulation.py' 2024-02-19T13:41:23,408 adding 'reframed/cobra/thermodynamics.py' 2024-02-19T13:41:23,410 adding 'reframed/cobra/transcriptomics.py' 2024-02-19T13:41:23,412 adding 'reframed/cobra/variability.py' 2024-02-19T13:41:23,414 adding 'reframed/community/SteadyCom.py' 2024-02-19T13:41:23,415 adding 'reframed/community/__init__.py' 2024-02-19T13:41:23,416 adding 'reframed/community/model.py' 2024-02-19T13:41:23,418 adding 'reframed/community/simulation.py' 2024-02-19T13:41:23,420 adding 'reframed/community/simulation_old.py' 2024-02-19T13:41:23,422 adding 'reframed/community/solution.py' 2024-02-19T13:41:23,423 adding 'reframed/core/__init__.py' 2024-02-19T13:41:23,426 adding 'reframed/core/cbmodel.py' 2024-02-19T13:41:23,427 adding 'reframed/core/elements.py' 2024-02-19T13:41:23,429 adding 'reframed/core/environment.py' 2024-02-19T13:41:23,431 adding 'reframed/core/model.py' 2024-02-19T13:41:23,432 adding 'reframed/core/parser.py' 2024-02-19T13:41:23,435 adding 'reframed/core/transformation.py' 2024-02-19T13:41:23,436 adding 'reframed/external/__init__.py' 2024-02-19T13:41:23,438 adding 'reframed/external/cobrapy.py' 2024-02-19T13:41:23,439 adding 'reframed/external/escher.py' 2024-02-19T13:41:23,441 adding 'reframed/io/__init__.py' 2024-02-19T13:41:23,442 adding 'reframed/io/cache.py' 2024-02-19T13:41:23,446 adding 'reframed/io/sbml.py' 2024-02-19T13:41:23,448 adding 'reframed/solvers/__init__.py' 2024-02-19T13:41:23,450 adding 'reframed/solvers/cplex_solver.py' 2024-02-19T13:41:23,452 adding 'reframed/solvers/gurobi_solver.py' 2024-02-19T13:41:23,454 adding 'reframed/solvers/optlang_solver.py' 2024-02-19T13:41:23,457 adding 'reframed/solvers/pulp_solver.py' 2024-02-19T13:41:23,458 adding 'reframed/solvers/scip_solver.py' 2024-02-19T13:41:23,460 adding 'reframed/solvers/solution.py' 2024-02-19T13:41:23,462 adding 'reframed/solvers/solver.py' 2024-02-19T13:41:23,464 adding 'tests/__init__.py' 2024-02-19T13:41:23,465 adding 'tests/scip_carveme.py' 2024-02-19T13:41:23,466 adding 'tests/test_reframed.py' 2024-02-19T13:41:23,472 adding 'tests/data/e_coli_core.xml.gz' 2024-02-19T13:41:23,528 adding 'tests/data/iML1515.xml.gz' 2024-02-19T13:41:23,533 adding 'tests/data/model_cobra.xml.gz' 2024-02-19T13:41:23,535 adding 'tests/data/model_fbc2.xml.gz' 2024-02-19T13:41:23,536 adding 'reframed-1.5.1.dist-info/LICENSE' 2024-02-19T13:41:23,537 adding 'reframed-1.5.1.dist-info/METADATA' 2024-02-19T13:41:23,538 adding 'reframed-1.5.1.dist-info/WHEEL' 2024-02-19T13:41:23,539 adding 'reframed-1.5.1.dist-info/top_level.txt' 2024-02-19T13:41:23,540 adding 'reframed-1.5.1.dist-info/RECORD' 2024-02-19T13:41:23,548 removing build/bdist.linux-armv7l/wheel 2024-02-19T13:41:23,675 Building wheel for reframed (setup.py): finished with status 'done' 2024-02-19T13:41:23,684 Created wheel for reframed: filename=reframed-1.5.1-py3-none-any.whl size=602576 sha256=9e8f423e5894428673015b41efa13bd49bad65a5bbbf917b3f933a45a8c5b4e8 2024-02-19T13:41:23,685 Stored in directory: /tmp/pip-ephem-wheel-cache-18a1vbqn/wheels/01/05/a9/e9550e25c8df313116b1c1fb654be15a081b38c9b086371c0a 2024-02-19T13:41:23,697 Successfully built reframed 2024-02-19T13:41:23,716 Removed build tracker: '/tmp/pip-build-tracker-4f681gj_'