2024-06-04T12:59:40,674 Created temporary directory: /tmp/pip-build-tracker-kpntd212 2024-06-04T12:59:40,675 Initialized build tracking at /tmp/pip-build-tracker-kpntd212 2024-06-04T12:59:40,676 Created build tracker: /tmp/pip-build-tracker-kpntd212 2024-06-04T12:59:40,676 Entered build tracker: /tmp/pip-build-tracker-kpntd212 2024-06-04T12:59:40,677 Created temporary directory: /tmp/pip-wheel-l2dymuec 2024-06-04T12:59:40,680 Created temporary directory: /tmp/pip-ephem-wheel-cache-f8kgk2kt 2024-06-04T12:59:40,703 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-06-04T12:59:40,706 2 location(s) to search for versions of reframed: 2024-06-04T12:59:40,706 * https://pypi.org/simple/reframed/ 2024-06-04T12:59:40,706 * https://www.piwheels.org/simple/reframed/ 2024-06-04T12:59:40,707 Fetching project page and analyzing links: https://pypi.org/simple/reframed/ 2024-06-04T12:59:40,708 Getting page https://pypi.org/simple/reframed/ 2024-06-04T12:59:40,709 Found index url https://pypi.org/simple/ 2024-06-04T12:59:40,923 Fetched page https://pypi.org/simple/reframed/ as application/vnd.pypi.simple.v1+json 2024-06-04T12:59:40,927 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) 2024-06-04T12:59:40,928 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 2024-06-04T12:59:40,929 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) 2024-06-04T12:59:40,930 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 2024-06-04T12:59:40,930 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) 2024-06-04T12:59:40,931 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 2024-06-04T12:59:40,932 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) 2024-06-04T12:59:40,933 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 2024-06-04T12:59:40,933 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) 2024-06-04T12:59:40,934 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 2024-06-04T12:59:40,935 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) 2024-06-04T12:59:40,936 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 2024-06-04T12:59:40,937 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) 2024-06-04T12:59:40,938 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 2024-06-04T12:59:40,938 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) 2024-06-04T12:59:40,939 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 2024-06-04T12:59:40,940 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) 2024-06-04T12:59:40,941 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 2024-06-04T12:59:40,941 Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/93/fc/958c7dd8044d1706fd28a4ad80412210f70ab08e626c7044b451c95df95f/reframed-1.5.2-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.8) 2024-06-04T12:59:40,942 Found link https://files.pythonhosted.org/packages/7a/58/3090f6b0bcad09e9624ae8625de8a3715486378a4224f6e5ad2eb3e95564/reframed-1.5.2.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.8), version: 1.5.2 2024-06-04T12:59:40,943 Fetching project page and analyzing links: https://www.piwheels.org/simple/reframed/ 2024-06-04T12:59:40,944 Getting page https://www.piwheels.org/simple/reframed/ 2024-06-04T12:59:40,945 Found index url https://www.piwheels.org/simple/ 2024-06-04T12:59:41,172 Fetched page https://www.piwheels.org/simple/reframed/ as text/html 2024-06-04T12:59:41,176 Skipping link: No binaries permitted for reframed: https://www.piwheels.org/simple/reframed/reframed-1.5.1-py3-none-any.whl#sha256=9e8f423e5894428673015b41efa13bd49bad65a5bbbf917b3f933a45a8c5b4e8 (from https://www.piwheels.org/simple/reframed/) (requires-python:>=3.6) 2024-06-04T12:59:41,177 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) 2024-06-04T12:59:41,177 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) 2024-06-04T12:59:41,178 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) 2024-06-04T12:59:41,178 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) 2024-06-04T12:59:41,179 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) 2024-06-04T12:59:41,180 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) 2024-06-04T12:59:41,180 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) 2024-06-04T12:59:41,181 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) 2024-06-04T12:59:41,181 Skipping link: not a file: https://www.piwheels.org/simple/reframed/ 2024-06-04T12:59:41,182 Skipping link: not a file: https://pypi.org/simple/reframed/ 2024-06-04T12:59:41,203 Given no hashes to check 1 links for project 'reframed': discarding no candidates 2024-06-04T12:59:41,222 Collecting reframed==1.5.2 2024-06-04T12:59:41,224 Created temporary directory: /tmp/pip-unpack-2k92oa6m 2024-06-04T12:59:41,442 Downloading reframed-1.5.2.tar.gz (611 kB) 2024-06-04T12:59:41,731 Added reframed==1.5.2 from https://files.pythonhosted.org/packages/7a/58/3090f6b0bcad09e9624ae8625de8a3715486378a4224f6e5ad2eb3e95564/reframed-1.5.2.tar.gz to build tracker '/tmp/pip-build-tracker-kpntd212' 2024-06-04T12:59:41,734 Running setup.py (path:/tmp/pip-wheel-l2dymuec/reframed_7dfebf8a402d4ef6823d8f6a6d6f8f82/setup.py) egg_info for package reframed 2024-06-04T12:59:41,735 Created temporary directory: /tmp/pip-pip-egg-info-xt1dvmrk 2024-06-04T12:59:41,735 Preparing metadata (setup.py): started 2024-06-04T12:59:41,737 Running command python setup.py egg_info 2024-06-04T12:59:42,642 running egg_info 2024-06-04T12:59:42,644 creating /tmp/pip-pip-egg-info-xt1dvmrk/reframed.egg-info 2024-06-04T12:59:42,669 writing /tmp/pip-pip-egg-info-xt1dvmrk/reframed.egg-info/PKG-INFO 2024-06-04T12:59:42,673 writing dependency_links to /tmp/pip-pip-egg-info-xt1dvmrk/reframed.egg-info/dependency_links.txt 2024-06-04T12:59:42,675 writing requirements to /tmp/pip-pip-egg-info-xt1dvmrk/reframed.egg-info/requires.txt 2024-06-04T12:59:42,676 writing top-level names to /tmp/pip-pip-egg-info-xt1dvmrk/reframed.egg-info/top_level.txt 2024-06-04T12:59:42,678 writing manifest file '/tmp/pip-pip-egg-info-xt1dvmrk/reframed.egg-info/SOURCES.txt' 2024-06-04T12:59:42,768 reading manifest file '/tmp/pip-pip-egg-info-xt1dvmrk/reframed.egg-info/SOURCES.txt' 2024-06-04T12:59:42,769 reading manifest template 'MANIFEST.in' 2024-06-04T12:59:42,770 warning: no files found matching 'CONTRIBUTING.rst' 2024-06-04T12:59:42,771 warning: no files found matching 'HISTORY.rst' 2024-06-04T12:59:42,776 warning: no previously-included files matching '__pycache__' found under directory '*' 2024-06-04T12:59:42,776 warning: no previously-included files matching '*.py[co]' found under directory '*' 2024-06-04T12:59:42,811 warning: no files found matching '*.jpg' under directory 'docs' 2024-06-04T12:59:42,828 warning: no files found matching '*.gif' under directory 'docs' 2024-06-04T12:59:42,829 adding license file 'LICENSE' 2024-06-04T12:59:42,832 writing manifest file '/tmp/pip-pip-egg-info-xt1dvmrk/reframed.egg-info/SOURCES.txt' 2024-06-04T12:59:42,939 Preparing metadata (setup.py): finished with status 'done' 2024-06-04T12:59:42,943 Source in /tmp/pip-wheel-l2dymuec/reframed_7dfebf8a402d4ef6823d8f6a6d6f8f82 has version 1.5.2, which satisfies requirement reframed==1.5.2 from https://files.pythonhosted.org/packages/7a/58/3090f6b0bcad09e9624ae8625de8a3715486378a4224f6e5ad2eb3e95564/reframed-1.5.2.tar.gz 2024-06-04T12:59:42,944 Removed reframed==1.5.2 from https://files.pythonhosted.org/packages/7a/58/3090f6b0bcad09e9624ae8625de8a3715486378a4224f6e5ad2eb3e95564/reframed-1.5.2.tar.gz from build tracker '/tmp/pip-build-tracker-kpntd212' 2024-06-04T12:59:42,950 Created temporary directory: /tmp/pip-unpack-ippofmz0 2024-06-04T12:59:42,951 Created temporary directory: /tmp/pip-unpack-p6zwk_6e 2024-06-04T12:59:42,958 Building wheels for collected packages: reframed 2024-06-04T12:59:42,962 Created temporary directory: /tmp/pip-wheel-_ucbwfm3 2024-06-04T12:59:42,963 Building wheel for reframed (setup.py): started 2024-06-04T12:59:42,964 Destination directory: /tmp/pip-wheel-_ucbwfm3 2024-06-04T12:59:42,964 Running command python setup.py bdist_wheel 2024-06-04T12:59:43,872 running bdist_wheel 2024-06-04T12:59:44,011 running build 2024-06-04T12:59:44,012 running build_py 2024-06-04T12:59:44,042 creating build 2024-06-04T12:59:44,043 creating build/lib 2024-06-04T12:59:44,044 creating build/lib/tests 2024-06-04T12:59:44,045 copying tests/scip_carveme.py -> build/lib/tests 2024-06-04T12:59:44,047 copying tests/test_reframed.py -> build/lib/tests 2024-06-04T12:59:44,050 copying tests/__init__.py -> build/lib/tests 2024-06-04T12:59:44,052 creating build/lib/reframed 2024-06-04T12:59:44,053 copying reframed/__init__.py -> build/lib/reframed 2024-06-04T12:59:44,055 creating build/lib/reframed/solvers 2024-06-04T12:59:44,056 copying reframed/solvers/scip_solver.py -> build/lib/reframed/solvers 2024-06-04T12:59:44,059 copying reframed/solvers/gurobi_solver.py -> build/lib/reframed/solvers 2024-06-04T12:59:44,061 copying reframed/solvers/solution.py -> build/lib/reframed/solvers 2024-06-04T12:59:44,063 copying reframed/solvers/solver.py -> build/lib/reframed/solvers 2024-06-04T12:59:44,066 copying reframed/solvers/__init__.py -> build/lib/reframed/solvers 2024-06-04T12:59:44,068 copying reframed/solvers/optlang_solver.py -> build/lib/reframed/solvers 2024-06-04T12:59:44,070 copying reframed/solvers/cplex_solver.py -> build/lib/reframed/solvers 2024-06-04T12:59:44,073 copying reframed/solvers/pulp_solver.py -> build/lib/reframed/solvers 2024-06-04T12:59:44,076 creating build/lib/reframed/cobra 2024-06-04T12:59:44,077 copying reframed/cobra/auxotrophy.py -> build/lib/reframed/cobra 2024-06-04T12:59:44,079 copying reframed/cobra/transcriptomics.py -> build/lib/reframed/cobra 2024-06-04T12:59:44,081 copying reframed/cobra/plotting.py -> build/lib/reframed/cobra 2024-06-04T12:59:44,083 copying reframed/cobra/knockout.py -> build/lib/reframed/cobra 2024-06-04T12:59:44,085 copying reframed/cobra/ensemble.py -> build/lib/reframed/cobra 2024-06-04T12:59:44,087 copying reframed/cobra/simulation.py -> build/lib/reframed/cobra 2024-06-04T12:59:44,090 copying reframed/cobra/__init__.py -> build/lib/reframed/cobra 2024-06-04T12:59:44,091 copying reframed/cobra/thermodynamics.py -> build/lib/reframed/cobra 2024-06-04T12:59:44,094 copying reframed/cobra/variability.py -> build/lib/reframed/cobra 2024-06-04T12:59:44,096 copying reframed/cobra/medium.py -> build/lib/reframed/cobra 2024-06-04T12:59:44,099 creating build/lib/reframed/io 2024-06-04T12:59:44,100 copying reframed/io/cache.py -> build/lib/reframed/io 2024-06-04T12:59:44,102 copying reframed/io/sbml.py -> build/lib/reframed/io 2024-06-04T12:59:44,104 copying reframed/io/__init__.py -> build/lib/reframed/io 2024-06-04T12:59:44,106 creating build/lib/reframed/community 2024-06-04T12:59:44,107 copying reframed/community/SteadyCom.py -> build/lib/reframed/community 2024-06-04T12:59:44,110 copying reframed/community/solution.py -> build/lib/reframed/community 2024-06-04T12:59:44,112 copying reframed/community/model.py -> build/lib/reframed/community 2024-06-04T12:59:44,114 copying reframed/community/__init__.py -> build/lib/reframed/community 2024-06-04T12:59:44,117 creating build/lib/reframed/core 2024-06-04T12:59:44,118 copying reframed/core/environment.py -> build/lib/reframed/core 2024-06-04T12:59:44,120 copying reframed/core/parser.py -> build/lib/reframed/core 2024-06-04T12:59:44,122 copying reframed/core/elements.py -> build/lib/reframed/core 2024-06-04T12:59:44,124 copying reframed/core/model.py -> build/lib/reframed/core 2024-06-04T12:59:44,128 copying reframed/core/__init__.py -> build/lib/reframed/core 2024-06-04T12:59:44,129 copying reframed/core/transformation.py -> build/lib/reframed/core 2024-06-04T12:59:44,132 copying reframed/core/cbmodel.py -> build/lib/reframed/core 2024-06-04T12:59:44,135 creating build/lib/reframed/external 2024-06-04T12:59:44,136 copying reframed/external/cobrapy.py -> build/lib/reframed/external 2024-06-04T12:59:44,138 copying reframed/external/__init__.py -> build/lib/reframed/external 2024-06-04T12:59:44,140 copying reframed/external/escher.py -> build/lib/reframed/external 2024-06-04T12:59:44,142 creating build/lib/reframed/alpha 2024-06-04T12:59:44,143 copying reframed/alpha/gapMake.py -> build/lib/reframed/alpha 2024-06-04T12:59:44,145 copying reframed/alpha/plotting.py -> build/lib/reframed/alpha 2024-06-04T12:59:44,147 copying reframed/alpha/geneswitch.py -> build/lib/reframed/alpha 2024-06-04T12:59:44,149 copying reframed/alpha/__init__.py -> build/lib/reframed/alpha 2024-06-04T12:59:44,150 copying reframed/alpha/fluxutils.py -> build/lib/reframed/alpha 2024-06-04T12:59:44,152 copying reframed/alpha/sampling.py -> build/lib/reframed/alpha 2024-06-04T12:59:44,154 running egg_info 2024-06-04T12:59:44,182 writing reframed.egg-info/PKG-INFO 2024-06-04T12:59:44,186 writing dependency_links to reframed.egg-info/dependency_links.txt 2024-06-04T12:59:44,187 writing requirements to reframed.egg-info/requires.txt 2024-06-04T12:59:44,189 writing top-level names to reframed.egg-info/top_level.txt 2024-06-04T12:59:44,225 reading manifest file 'reframed.egg-info/SOURCES.txt' 2024-06-04T12:59:44,228 reading manifest template 'MANIFEST.in' 2024-06-04T12:59:44,229 warning: no files found matching 'CONTRIBUTING.rst' 2024-06-04T12:59:44,229 warning: no files found matching 'HISTORY.rst' 2024-06-04T12:59:44,234 warning: no previously-included files matching '__pycache__' found under directory '*' 2024-06-04T12:59:44,235 warning: no previously-included files matching '*.py[co]' found under directory '*' 2024-06-04T12:59:44,267 warning: no files found matching '*.jpg' under directory 'docs' 2024-06-04T12:59:44,284 warning: no files found matching '*.gif' under directory 'docs' 2024-06-04T12:59:44,285 adding license file 'LICENSE' 2024-06-04T12:59:44,289 writing manifest file 'reframed.egg-info/SOURCES.txt' 2024-06-04T12:59:44,292 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'tests.data' is absent from the `packages` configuration. 2024-06-04T12:59:44,293 !! 2024-06-04T12:59:44,294 ******************************************************************************** 2024-06-04T12:59:44,295 ############################ 2024-06-04T12:59:44,295 # Package would be ignored # 2024-06-04T12:59:44,296 ############################ 2024-06-04T12:59:44,296 Python recognizes 'tests.data' as an importable package[^1], 2024-06-04T12:59:44,297 but it is absent from setuptools' `packages` configuration. 2024-06-04T12:59:44,298 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-04T12:59:44,298 package, please make sure that 'tests.data' is explicitly added 2024-06-04T12:59:44,299 to the `packages` configuration field. 2024-06-04T12:59:44,300 Alternatively, you can also rely on setuptools' discovery methods 2024-06-04T12:59:44,301 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-04T12:59:44,302 instead of `find_packages(...)`/`find:`). 2024-06-04T12:59:44,303 You can read more about "package discovery" on setuptools documentation page: 2024-06-04T12:59:44,304 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-04T12:59:44,305 If you don't want 'tests.data' to be distributed and are 2024-06-04T12:59:44,305 already explicitly excluding 'tests.data' via 2024-06-04T12:59:44,306 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-04T12:59:44,306 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-04T12:59:44,307 combination with a more fine grained `package-data` configuration. 2024-06-04T12:59:44,311 You can read more about "package data files" on setuptools documentation page: 2024-06-04T12:59:44,319 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-04T12:59:44,322 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-04T12:59:44,322 even if it does not contain any `.py` files. 2024-06-04T12:59:44,323 On the other hand, currently there is no concept of package data 2024-06-04T12:59:44,323 directory, all directories are treated like packages. 2024-06-04T12:59:44,324 ******************************************************************************** 2024-06-04T12:59:44,325 !! 2024-06-04T12:59:44,325 check.warn(importable) 2024-06-04T12:59:44,326 creating build/lib/tests/data 2024-06-04T12:59:44,327 copying tests/data/e_coli_core.xml.gz -> build/lib/tests/data 2024-06-04T12:59:44,327 copying tests/data/iML1515.xml.gz -> build/lib/tests/data 2024-06-04T12:59:44,328 copying tests/data/model_cobra.xml.gz -> build/lib/tests/data 2024-06-04T12:59:44,329 copying tests/data/model_fbc2.xml.gz -> build/lib/tests/data 2024-06-04T12:59:44,360 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-06-04T12:59:44,361 !! 2024-06-04T12:59:44,362 ******************************************************************************** 2024-06-04T12:59:44,362 Please avoid running ``setup.py`` directly. 2024-06-04T12:59:44,363 Instead, use pypa/build, pypa/installer or other 2024-06-04T12:59:44,364 standards-based tools. 2024-06-04T12:59:44,365 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-06-04T12:59:44,366 ******************************************************************************** 2024-06-04T12:59:44,367 !! 2024-06-04T12:59:44,367 self.initialize_options() 2024-06-04T12:59:44,391 installing to build/bdist.linux-armv7l/wheel 2024-06-04T12:59:44,391 running install 2024-06-04T12:59:44,416 running install_lib 2024-06-04T12:59:44,442 creating build/bdist.linux-armv7l 2024-06-04T12:59:44,443 creating build/bdist.linux-armv7l/wheel 2024-06-04T12:59:44,445 creating build/bdist.linux-armv7l/wheel/tests 2024-06-04T12:59:44,447 creating build/bdist.linux-armv7l/wheel/tests/data 2024-06-04T12:59:44,448 copying build/lib/tests/data/model_cobra.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data 2024-06-04T12:59:44,451 copying build/lib/tests/data/model_fbc2.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data 2024-06-04T12:59:44,453 copying build/lib/tests/data/e_coli_core.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data 2024-06-04T12:59:44,457 copying build/lib/tests/data/iML1515.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data 2024-06-04T12:59:44,474 copying build/lib/tests/scip_carveme.py -> build/bdist.linux-armv7l/wheel/tests 2024-06-04T12:59:44,475 copying build/lib/tests/test_reframed.py -> build/bdist.linux-armv7l/wheel/tests 2024-06-04T12:59:44,478 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests 2024-06-04T12:59:44,480 creating build/bdist.linux-armv7l/wheel/reframed 2024-06-04T12:59:44,481 creating build/bdist.linux-armv7l/wheel/reframed/solvers 2024-06-04T12:59:44,482 copying build/lib/reframed/solvers/scip_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-06-04T12:59:44,485 copying build/lib/reframed/solvers/gurobi_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-06-04T12:59:44,488 copying build/lib/reframed/solvers/solution.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-06-04T12:59:44,490 copying build/lib/reframed/solvers/solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-06-04T12:59:44,493 copying build/lib/reframed/solvers/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-06-04T12:59:44,494 copying build/lib/reframed/solvers/optlang_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-06-04T12:59:44,497 copying build/lib/reframed/solvers/cplex_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-06-04T12:59:44,499 copying build/lib/reframed/solvers/pulp_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2024-06-04T12:59:44,502 creating build/bdist.linux-armv7l/wheel/reframed/cobra 2024-06-04T12:59:44,503 copying build/lib/reframed/cobra/auxotrophy.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-06-04T12:59:44,505 copying build/lib/reframed/cobra/transcriptomics.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-06-04T12:59:44,507 copying build/lib/reframed/cobra/plotting.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-06-04T12:59:44,509 copying build/lib/reframed/cobra/knockout.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-06-04T12:59:44,511 copying build/lib/reframed/cobra/ensemble.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-06-04T12:59:44,513 copying build/lib/reframed/cobra/simulation.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-06-04T12:59:44,516 copying build/lib/reframed/cobra/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-06-04T12:59:44,518 copying build/lib/reframed/cobra/thermodynamics.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-06-04T12:59:44,520 copying build/lib/reframed/cobra/variability.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-06-04T12:59:44,522 copying build/lib/reframed/cobra/medium.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2024-06-04T12:59:44,525 creating build/bdist.linux-armv7l/wheel/reframed/io 2024-06-04T12:59:44,526 copying build/lib/reframed/io/cache.py -> build/bdist.linux-armv7l/wheel/reframed/io 2024-06-04T12:59:44,528 copying build/lib/reframed/io/sbml.py -> build/bdist.linux-armv7l/wheel/reframed/io 2024-06-04T12:59:44,531 copying build/lib/reframed/io/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/io 2024-06-04T12:59:44,532 creating build/bdist.linux-armv7l/wheel/reframed/community 2024-06-04T12:59:44,533 copying build/lib/reframed/community/SteadyCom.py -> build/bdist.linux-armv7l/wheel/reframed/community 2024-06-04T12:59:44,535 copying build/lib/reframed/community/solution.py -> build/bdist.linux-armv7l/wheel/reframed/community 2024-06-04T12:59:44,537 copying build/lib/reframed/community/model.py -> build/bdist.linux-armv7l/wheel/reframed/community 2024-06-04T12:59:44,540 copying build/lib/reframed/community/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/community 2024-06-04T12:59:44,542 creating build/bdist.linux-armv7l/wheel/reframed/core 2024-06-04T12:59:44,543 copying build/lib/reframed/core/environment.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-06-04T12:59:44,545 copying build/lib/reframed/core/parser.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-06-04T12:59:44,547 copying build/lib/reframed/core/elements.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-06-04T12:59:44,549 copying build/lib/reframed/core/model.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-06-04T12:59:44,551 copying build/lib/reframed/core/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-06-04T12:59:44,553 copying build/lib/reframed/core/transformation.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-06-04T12:59:44,555 copying build/lib/reframed/core/cbmodel.py -> build/bdist.linux-armv7l/wheel/reframed/core 2024-06-04T12:59:44,558 copying build/lib/reframed/__init__.py -> build/bdist.linux-armv7l/wheel/reframed 2024-06-04T12:59:44,560 creating build/bdist.linux-armv7l/wheel/reframed/external 2024-06-04T12:59:44,561 copying build/lib/reframed/external/cobrapy.py -> build/bdist.linux-armv7l/wheel/reframed/external 2024-06-04T12:59:44,563 copying build/lib/reframed/external/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/external 2024-06-04T12:59:44,564 copying build/lib/reframed/external/escher.py -> build/bdist.linux-armv7l/wheel/reframed/external 2024-06-04T12:59:44,567 creating build/bdist.linux-armv7l/wheel/reframed/alpha 2024-06-04T12:59:44,567 copying build/lib/reframed/alpha/gapMake.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2024-06-04T12:59:44,569 copying build/lib/reframed/alpha/plotting.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2024-06-04T12:59:44,571 copying build/lib/reframed/alpha/geneswitch.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2024-06-04T12:59:44,573 copying build/lib/reframed/alpha/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2024-06-04T12:59:44,574 copying build/lib/reframed/alpha/fluxutils.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2024-06-04T12:59:44,576 copying build/lib/reframed/alpha/sampling.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2024-06-04T12:59:44,578 running install_egg_info 2024-06-04T12:59:44,611 Copying reframed.egg-info to build/bdist.linux-armv7l/wheel/reframed-1.5.2-py3.11.egg-info 2024-06-04T12:59:44,623 running install_scripts 2024-06-04T12:59:44,637 creating build/bdist.linux-armv7l/wheel/reframed-1.5.2.dist-info/WHEEL 2024-06-04T12:59:44,640 creating '/tmp/pip-wheel-_ucbwfm3/reframed-1.5.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-06-04T12:59:44,642 adding 'reframed/__init__.py' 2024-06-04T12:59:44,644 adding 'reframed/alpha/__init__.py' 2024-06-04T12:59:44,645 adding 'reframed/alpha/fluxutils.py' 2024-06-04T12:59:44,646 adding 'reframed/alpha/gapMake.py' 2024-06-04T12:59:44,648 adding 'reframed/alpha/geneswitch.py' 2024-06-04T12:59:44,649 adding 'reframed/alpha/plotting.py' 2024-06-04T12:59:44,651 adding 'reframed/alpha/sampling.py' 2024-06-04T12:59:44,653 adding 'reframed/cobra/__init__.py' 2024-06-04T12:59:44,654 adding 'reframed/cobra/auxotrophy.py' 2024-06-04T12:59:44,656 adding 'reframed/cobra/ensemble.py' 2024-06-04T12:59:44,658 adding 'reframed/cobra/knockout.py' 2024-06-04T12:59:44,659 adding 'reframed/cobra/medium.py' 2024-06-04T12:59:44,661 adding 'reframed/cobra/plotting.py' 2024-06-04T12:59:44,663 adding 'reframed/cobra/simulation.py' 2024-06-04T12:59:44,665 adding 'reframed/cobra/thermodynamics.py' 2024-06-04T12:59:44,668 adding 'reframed/cobra/transcriptomics.py' 2024-06-04T12:59:44,669 adding 'reframed/cobra/variability.py' 2024-06-04T12:59:44,671 adding 'reframed/community/SteadyCom.py' 2024-06-04T12:59:44,672 adding 'reframed/community/__init__.py' 2024-06-04T12:59:44,674 adding 'reframed/community/model.py' 2024-06-04T12:59:44,676 adding 'reframed/community/solution.py' 2024-06-04T12:59:44,678 adding 'reframed/core/__init__.py' 2024-06-04T12:59:44,680 adding 'reframed/core/cbmodel.py' 2024-06-04T12:59:44,681 adding 'reframed/core/elements.py' 2024-06-04T12:59:44,683 adding 'reframed/core/environment.py' 2024-06-04T12:59:44,686 adding 'reframed/core/model.py' 2024-06-04T12:59:44,688 adding 'reframed/core/parser.py' 2024-06-04T12:59:44,690 adding 'reframed/core/transformation.py' 2024-06-04T12:59:44,692 adding 'reframed/external/__init__.py' 2024-06-04T12:59:44,693 adding 'reframed/external/cobrapy.py' 2024-06-04T12:59:44,694 adding 'reframed/external/escher.py' 2024-06-04T12:59:44,696 adding 'reframed/io/__init__.py' 2024-06-04T12:59:44,697 adding 'reframed/io/cache.py' 2024-06-04T12:59:44,701 adding 'reframed/io/sbml.py' 2024-06-04T12:59:44,703 adding 'reframed/solvers/__init__.py' 2024-06-04T12:59:44,706 adding 'reframed/solvers/cplex_solver.py' 2024-06-04T12:59:44,708 adding 'reframed/solvers/gurobi_solver.py' 2024-06-04T12:59:44,710 adding 'reframed/solvers/optlang_solver.py' 2024-06-04T12:59:44,712 adding 'reframed/solvers/pulp_solver.py' 2024-06-04T12:59:44,713 adding 'reframed/solvers/scip_solver.py' 2024-06-04T12:59:44,715 adding 'reframed/solvers/solution.py' 2024-06-04T12:59:44,717 adding 'reframed/solvers/solver.py' 2024-06-04T12:59:44,719 adding 'tests/__init__.py' 2024-06-04T12:59:44,720 adding 'tests/scip_carveme.py' 2024-06-04T12:59:44,722 adding 'tests/test_reframed.py' 2024-06-04T12:59:44,727 adding 'tests/data/e_coli_core.xml.gz' 2024-06-04T12:59:44,799 adding 'tests/data/iML1515.xml.gz' 2024-06-04T12:59:44,805 adding 'tests/data/model_cobra.xml.gz' 2024-06-04T12:59:44,807 adding 'tests/data/model_fbc2.xml.gz' 2024-06-04T12:59:44,808 adding 'reframed-1.5.2.dist-info/LICENSE' 2024-06-04T12:59:44,810 adding 'reframed-1.5.2.dist-info/METADATA' 2024-06-04T12:59:44,811 adding 'reframed-1.5.2.dist-info/WHEEL' 2024-06-04T12:59:44,812 adding 'reframed-1.5.2.dist-info/top_level.txt' 2024-06-04T12:59:44,814 adding 'reframed-1.5.2.dist-info/RECORD' 2024-06-04T12:59:44,828 removing build/bdist.linux-armv7l/wheel 2024-06-04T12:59:44,957 Building wheel for reframed (setup.py): finished with status 'done' 2024-06-04T12:59:44,966 Created wheel for reframed: filename=reframed-1.5.2-py3-none-any.whl size=597655 sha256=425d17e45e05d154ee66072553e180094da6b943149b6fa332649e44cc635079 2024-06-04T12:59:44,967 Stored in directory: /tmp/pip-ephem-wheel-cache-f8kgk2kt/wheels/13/20/4c/d137f1306c8dca467bdc76a9dd2dd2883c6e31c7d4afae6e32 2024-06-04T12:59:44,978 Successfully built reframed 2024-06-04T12:59:45,001 Removed build tracker: '/tmp/pip-build-tracker-kpntd212'