2024-07-31T15:34:28,880 Created temporary directory: /tmp/pip-build-tracker-1hmr5z5a
2024-07-31T15:34:28,881 Initialized build tracking at /tmp/pip-build-tracker-1hmr5z5a
2024-07-31T15:34:28,882 Created build tracker: /tmp/pip-build-tracker-1hmr5z5a
2024-07-31T15:34:28,882 Entered build tracker: /tmp/pip-build-tracker-1hmr5z5a
2024-07-31T15:34:28,883 Created temporary directory: /tmp/pip-wheel-o81z5fzj
2024-07-31T15:34:28,887 Created temporary directory: /tmp/pip-ephem-wheel-cache-12badexo
2024-07-31T15:34:28,914 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-07-31T15:34:28,917 2 location(s) to search for versions of reframed:
2024-07-31T15:34:28,917 * https://pypi.org/simple/reframed/
2024-07-31T15:34:28,917 * https://www.piwheels.org/simple/reframed/
2024-07-31T15:34:28,918 Fetching project page and analyzing links: https://pypi.org/simple/reframed/
2024-07-31T15:34:28,919 Getting page https://pypi.org/simple/reframed/
2024-07-31T15:34:28,920 Found index url https://pypi.org/simple/
2024-07-31T15:34:29,019 Fetched page https://pypi.org/simple/reframed/ as application/vnd.pypi.simple.v1+json
2024-07-31T15:34:29,025   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)
2024-07-31T15:34:29,026   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
2024-07-31T15:34:29,026   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)
2024-07-31T15:34:29,027   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
2024-07-31T15:34:29,028   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)
2024-07-31T15:34:29,029   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
2024-07-31T15:34:29,029   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)
2024-07-31T15:34:29,030   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
2024-07-31T15:34:29,031   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)
2024-07-31T15:34:29,032   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
2024-07-31T15:34:29,033   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)
2024-07-31T15:34:29,034   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
2024-07-31T15:34:29,034   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)
2024-07-31T15:34:29,036   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
2024-07-31T15:34:29,036   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)
2024-07-31T15:34:29,037   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
2024-07-31T15:34:29,038   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)
2024-07-31T15:34:29,038   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
2024-07-31T15:34:29,039   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)
2024-07-31T15:34:29,040   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
2024-07-31T15:34:29,040   Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/ad/00/b3ea754c513b3e7f89baa7d21f4ee99e8b27eb4370d75a23bf279bbbfba0/reframed-1.5.3-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.8)
2024-07-31T15:34:29,041   Found link https://files.pythonhosted.org/packages/2e/48/9e9b7daee9ebc7699935ac3f77fa88e06e714bafb9a516f2064115fbc50b/reframed-1.5.3.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.8), version: 1.5.3
2024-07-31T15:34:29,042 Fetching project page and analyzing links: https://www.piwheels.org/simple/reframed/
2024-07-31T15:34:29,043 Getting page https://www.piwheels.org/simple/reframed/
2024-07-31T15:34:29,044 Found index url https://www.piwheels.org/simple/
2024-07-31T15:34:29,086 Fetched page https://www.piwheels.org/simple/reframed/ as text/html
2024-07-31T15:34:29,090   Skipping link: No binaries permitted for reframed: https://www.piwheels.org/simple/reframed/reframed-1.5.2-py3-none-any.whl#sha256=425d17e45e05d154ee66072553e180094da6b943149b6fa332649e44cc635079 (from https://www.piwheels.org/simple/reframed/) (requires-python:>=3.8)
2024-07-31T15:34:29,091   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)
2024-07-31T15:34:29,091   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)
2024-07-31T15:34:29,092   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)
2024-07-31T15:34:29,092   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)
2024-07-31T15:34:29,093   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)
2024-07-31T15:34:29,094   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)
2024-07-31T15:34:29,094   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)
2024-07-31T15:34:29,095   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)
2024-07-31T15:34:29,095   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)
2024-07-31T15:34:29,096 Skipping link: not a file: https://www.piwheels.org/simple/reframed/
2024-07-31T15:34:29,096 Skipping link: not a file: https://pypi.org/simple/reframed/
2024-07-31T15:34:29,118 Given no hashes to check 1 links for project 'reframed': discarding no candidates
2024-07-31T15:34:29,138 Collecting reframed==1.5.3
2024-07-31T15:34:29,140   Created temporary directory: /tmp/pip-unpack-6rpcflf4
2024-07-31T15:34:29,238   Downloading reframed-1.5.3.tar.gz (607 kB)
2024-07-31T15:34:29,461   Added reframed==1.5.3 from https://files.pythonhosted.org/packages/2e/48/9e9b7daee9ebc7699935ac3f77fa88e06e714bafb9a516f2064115fbc50b/reframed-1.5.3.tar.gz to build tracker '/tmp/pip-build-tracker-1hmr5z5a'
2024-07-31T15:34:29,462   Running setup.py (path:/tmp/pip-wheel-o81z5fzj/reframed_90b7bc3070ea4a21a90d0a00d4890fe3/setup.py) egg_info for package reframed
2024-07-31T15:34:29,463   Created temporary directory: /tmp/pip-pip-egg-info-ral08uit
2024-07-31T15:34:29,464   Preparing metadata (setup.py): started
2024-07-31T15:34:29,465   Running command python setup.py egg_info
2024-07-31T15:34:30,593   running egg_info
2024-07-31T15:34:30,594   creating /tmp/pip-pip-egg-info-ral08uit/reframed.egg-info
2024-07-31T15:34:30,621   writing /tmp/pip-pip-egg-info-ral08uit/reframed.egg-info/PKG-INFO
2024-07-31T15:34:30,625   writing dependency_links to /tmp/pip-pip-egg-info-ral08uit/reframed.egg-info/dependency_links.txt
2024-07-31T15:34:30,627   writing requirements to /tmp/pip-pip-egg-info-ral08uit/reframed.egg-info/requires.txt
2024-07-31T15:34:30,628   writing top-level names to /tmp/pip-pip-egg-info-ral08uit/reframed.egg-info/top_level.txt
2024-07-31T15:34:30,630   writing manifest file '/tmp/pip-pip-egg-info-ral08uit/reframed.egg-info/SOURCES.txt'
2024-07-31T15:34:30,722   reading manifest file '/tmp/pip-pip-egg-info-ral08uit/reframed.egg-info/SOURCES.txt'
2024-07-31T15:34:30,724   reading manifest template 'MANIFEST.in'
2024-07-31T15:34:30,725   warning: no files found matching 'CONTRIBUTING.rst'
2024-07-31T15:34:30,725   warning: no files found matching 'HISTORY.rst'
2024-07-31T15:34:30,730   warning: no previously-included files matching '__pycache__' found under directory '*'
2024-07-31T15:34:30,730   warning: no previously-included files matching '*.py[co]' found under directory '*'
2024-07-31T15:34:30,763   warning: no files found matching '*.jpg' under directory 'docs'
2024-07-31T15:34:30,779   warning: no files found matching '*.gif' under directory 'docs'
2024-07-31T15:34:30,779   adding license file 'LICENSE'
2024-07-31T15:34:30,782   writing manifest file '/tmp/pip-pip-egg-info-ral08uit/reframed.egg-info/SOURCES.txt'
2024-07-31T15:34:30,896   Preparing metadata (setup.py): finished with status 'done'
2024-07-31T15:34:30,900   Source in /tmp/pip-wheel-o81z5fzj/reframed_90b7bc3070ea4a21a90d0a00d4890fe3 has version 1.5.3, which satisfies requirement reframed==1.5.3 from https://files.pythonhosted.org/packages/2e/48/9e9b7daee9ebc7699935ac3f77fa88e06e714bafb9a516f2064115fbc50b/reframed-1.5.3.tar.gz
2024-07-31T15:34:30,901   Removed reframed==1.5.3 from https://files.pythonhosted.org/packages/2e/48/9e9b7daee9ebc7699935ac3f77fa88e06e714bafb9a516f2064115fbc50b/reframed-1.5.3.tar.gz from build tracker '/tmp/pip-build-tracker-1hmr5z5a'
2024-07-31T15:34:30,907 Created temporary directory: /tmp/pip-unpack-qhmic3gc
2024-07-31T15:34:30,908 Created temporary directory: /tmp/pip-unpack-tdeyz4if
2024-07-31T15:34:30,909 Building wheels for collected packages: reframed
2024-07-31T15:34:30,913   Created temporary directory: /tmp/pip-wheel-r5kesnx2
2024-07-31T15:34:30,913   Building wheel for reframed (setup.py): started
2024-07-31T15:34:30,914   Destination directory: /tmp/pip-wheel-r5kesnx2
2024-07-31T15:34:30,915   Running command python setup.py bdist_wheel
2024-07-31T15:34:31,981   running bdist_wheel
2024-07-31T15:34:32,122   running build
2024-07-31T15:34:32,123   running build_py
2024-07-31T15:34:32,152   creating build
2024-07-31T15:34:32,153   creating build/lib
2024-07-31T15:34:32,153   creating build/lib/reframed
2024-07-31T15:34:32,155   copying reframed/__init__.py -> build/lib/reframed
2024-07-31T15:34:32,157   creating build/lib/tests
2024-07-31T15:34:32,158   copying tests/scip_carveme.py -> build/lib/tests
2024-07-31T15:34:32,160   copying tests/test_reframed.py -> build/lib/tests
2024-07-31T15:34:32,162   copying tests/__init__.py -> build/lib/tests
2024-07-31T15:34:32,164   creating build/lib/reframed/io
2024-07-31T15:34:32,165   copying reframed/io/cache.py -> build/lib/reframed/io
2024-07-31T15:34:32,167   copying reframed/io/__init__.py -> build/lib/reframed/io
2024-07-31T15:34:32,169   copying reframed/io/sbml.py -> build/lib/reframed/io
2024-07-31T15:34:32,172   creating build/lib/reframed/community
2024-07-31T15:34:32,173   copying reframed/community/solution.py -> build/lib/reframed/community
2024-07-31T15:34:32,175   copying reframed/community/__init__.py -> build/lib/reframed/community
2024-07-31T15:34:32,176   copying reframed/community/model.py -> build/lib/reframed/community
2024-07-31T15:34:32,178   copying reframed/community/SteadyCom.py -> build/lib/reframed/community
2024-07-31T15:34:32,181   creating build/lib/reframed/alpha
2024-07-31T15:34:32,182   copying reframed/alpha/geneswitch.py -> build/lib/reframed/alpha
2024-07-31T15:34:32,184   copying reframed/alpha/fluxutils.py -> build/lib/reframed/alpha
2024-07-31T15:34:32,186   copying reframed/alpha/gapMake.py -> build/lib/reframed/alpha
2024-07-31T15:34:32,188   copying reframed/alpha/__init__.py -> build/lib/reframed/alpha
2024-07-31T15:34:32,189   copying reframed/alpha/plotting.py -> build/lib/reframed/alpha
2024-07-31T15:34:32,191   copying reframed/alpha/sampling.py -> build/lib/reframed/alpha
2024-07-31T15:34:32,193   creating build/lib/reframed/core
2024-07-31T15:34:32,194   copying reframed/core/cbmodel.py -> build/lib/reframed/core
2024-07-31T15:34:32,197   copying reframed/core/environment.py -> build/lib/reframed/core
2024-07-31T15:34:32,199   copying reframed/core/transformation.py -> build/lib/reframed/core
2024-07-31T15:34:32,201   copying reframed/core/parser.py -> build/lib/reframed/core
2024-07-31T15:34:32,203   copying reframed/core/__init__.py -> build/lib/reframed/core
2024-07-31T15:34:32,204   copying reframed/core/model.py -> build/lib/reframed/core
2024-07-31T15:34:32,207   copying reframed/core/elements.py -> build/lib/reframed/core
2024-07-31T15:34:32,209   creating build/lib/reframed/cobra
2024-07-31T15:34:32,210   copying reframed/cobra/thermodynamics.py -> build/lib/reframed/cobra
2024-07-31T15:34:32,212   copying reframed/cobra/transcriptomics.py -> build/lib/reframed/cobra
2024-07-31T15:34:32,214   copying reframed/cobra/simulation.py -> build/lib/reframed/cobra
2024-07-31T15:34:32,217   copying reframed/cobra/medium.py -> build/lib/reframed/cobra
2024-07-31T15:34:32,219   copying reframed/cobra/ensemble.py -> build/lib/reframed/cobra
2024-07-31T15:34:32,221   copying reframed/cobra/knockout.py -> build/lib/reframed/cobra
2024-07-31T15:34:32,224   copying reframed/cobra/variability.py -> build/lib/reframed/cobra
2024-07-31T15:34:32,226   copying reframed/cobra/__init__.py -> build/lib/reframed/cobra
2024-07-31T15:34:32,227   copying reframed/cobra/plotting.py -> build/lib/reframed/cobra
2024-07-31T15:34:32,229   copying reframed/cobra/auxotrophy.py -> build/lib/reframed/cobra
2024-07-31T15:34:32,231   creating build/lib/reframed/solvers
2024-07-31T15:34:32,232   copying reframed/solvers/solver.py -> build/lib/reframed/solvers
2024-07-31T15:34:32,234   copying reframed/solvers/gurobi_solver.py -> build/lib/reframed/solvers
2024-07-31T15:34:32,236   copying reframed/solvers/solution.py -> build/lib/reframed/solvers
2024-07-31T15:34:32,238   copying reframed/solvers/__init__.py -> build/lib/reframed/solvers
2024-07-31T15:34:32,239   copying reframed/solvers/cplex_solver.py -> build/lib/reframed/solvers
2024-07-31T15:34:32,241   copying reframed/solvers/scip_solver.py -> build/lib/reframed/solvers
2024-07-31T15:34:32,244   creating build/lib/reframed/external
2024-07-31T15:34:32,245   copying reframed/external/escher.py -> build/lib/reframed/external
2024-07-31T15:34:32,247   copying reframed/external/cobrapy.py -> build/lib/reframed/external
2024-07-31T15:34:32,249   copying reframed/external/__init__.py -> build/lib/reframed/external
2024-07-31T15:34:32,250   running egg_info
2024-07-31T15:34:32,277   writing reframed.egg-info/PKG-INFO
2024-07-31T15:34:32,281   writing dependency_links to reframed.egg-info/dependency_links.txt
2024-07-31T15:34:32,282   writing requirements to reframed.egg-info/requires.txt
2024-07-31T15:34:32,284   writing top-level names to reframed.egg-info/top_level.txt
2024-07-31T15:34:32,319   reading manifest file 'reframed.egg-info/SOURCES.txt'
2024-07-31T15:34:32,323   reading manifest template 'MANIFEST.in'
2024-07-31T15:34:32,323   warning: no files found matching 'CONTRIBUTING.rst'
2024-07-31T15:34:32,324   warning: no files found matching 'HISTORY.rst'
2024-07-31T15:34:32,328   warning: no previously-included files matching '__pycache__' found under directory '*'
2024-07-31T15:34:32,329   warning: no previously-included files matching '*.py[co]' found under directory '*'
2024-07-31T15:34:32,359   warning: no files found matching '*.jpg' under directory 'docs'
2024-07-31T15:34:32,375   warning: no files found matching '*.gif' under directory 'docs'
2024-07-31T15:34:32,376   adding license file 'LICENSE'
2024-07-31T15:34:32,380   writing manifest file 'reframed.egg-info/SOURCES.txt'
2024-07-31T15:34:32,383   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'tests.data' is absent from the `packages` configuration.
2024-07-31T15:34:32,384   !!

2024-07-31T15:34:32,385           ********************************************************************************
2024-07-31T15:34:32,385           ############################
2024-07-31T15:34:32,386           # Package would be ignored #
2024-07-31T15:34:32,386           ############################
2024-07-31T15:34:32,387           Python recognizes 'tests.data' as an importable package[^1],
2024-07-31T15:34:32,387           but it is absent from setuptools' `packages` configuration.

2024-07-31T15:34:32,389           This leads to an ambiguous overall configuration. If you want to distribute this
2024-07-31T15:34:32,389           package, please make sure that 'tests.data' is explicitly added
2024-07-31T15:34:32,390           to the `packages` configuration field.

2024-07-31T15:34:32,390           Alternatively, you can also rely on setuptools' discovery methods
2024-07-31T15:34:32,391           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-07-31T15:34:32,391           instead of `find_packages(...)`/`find:`).

2024-07-31T15:34:32,392           You can read more about "package discovery" on setuptools documentation page:

2024-07-31T15:34:32,393           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-07-31T15:34:32,394           If you don't want 'tests.data' to be distributed and are
2024-07-31T15:34:32,394           already explicitly excluding 'tests.data' via
2024-07-31T15:34:32,395           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-07-31T15:34:32,395           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-07-31T15:34:32,396           combination with a more fine grained `package-data` configuration.

2024-07-31T15:34:32,399           You can read more about "package data files" on setuptools documentation page:

2024-07-31T15:34:32,402           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-07-31T15:34:32,405           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-07-31T15:34:32,406                 even if it does not contain any `.py` files.
2024-07-31T15:34:32,406                 On the other hand, currently there is no concept of package data
2024-07-31T15:34:32,407                 directory, all directories are treated like packages.
2024-07-31T15:34:32,408           ********************************************************************************

2024-07-31T15:34:32,410   !!
2024-07-31T15:34:32,410     check.warn(importable)
2024-07-31T15:34:32,411   creating build/lib/tests/data
2024-07-31T15:34:32,411   copying tests/data/e_coli_core.xml.gz -> build/lib/tests/data
2024-07-31T15:34:32,413   copying tests/data/iML1515.xml.gz -> build/lib/tests/data
2024-07-31T15:34:32,413   copying tests/data/model_cobra.xml.gz -> build/lib/tests/data
2024-07-31T15:34:32,414   copying tests/data/model_fbc2.xml.gz -> build/lib/tests/data
2024-07-31T15:34:32,443   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2024-07-31T15:34:32,444   !!

2024-07-31T15:34:32,445           ********************************************************************************
2024-07-31T15:34:32,445           Please avoid running ``setup.py`` directly.
2024-07-31T15:34:32,446           Instead, use pypa/build, pypa/installer or other
2024-07-31T15:34:32,447           standards-based tools.

2024-07-31T15:34:32,448           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2024-07-31T15:34:32,448           ********************************************************************************

2024-07-31T15:34:32,449   !!
2024-07-31T15:34:32,450     self.initialize_options()
2024-07-31T15:34:32,475   installing to build/bdist.linux-armv7l/wheel
2024-07-31T15:34:32,475   running install
2024-07-31T15:34:32,501   running install_lib
2024-07-31T15:34:32,528   creating build/bdist.linux-armv7l
2024-07-31T15:34:32,529   creating build/bdist.linux-armv7l/wheel
2024-07-31T15:34:32,531   creating build/bdist.linux-armv7l/wheel/reframed
2024-07-31T15:34:32,533   creating build/bdist.linux-armv7l/wheel/reframed/io
2024-07-31T15:34:32,534   copying build/lib/reframed/io/cache.py -> build/bdist.linux-armv7l/wheel/reframed/io
2024-07-31T15:34:32,536   copying build/lib/reframed/io/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/io
2024-07-31T15:34:32,538   copying build/lib/reframed/io/sbml.py -> build/bdist.linux-armv7l/wheel/reframed/io
2024-07-31T15:34:32,542   creating build/bdist.linux-armv7l/wheel/reframed/community
2024-07-31T15:34:32,543   copying build/lib/reframed/community/solution.py -> build/bdist.linux-armv7l/wheel/reframed/community
2024-07-31T15:34:32,545   copying build/lib/reframed/community/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/community
2024-07-31T15:34:32,547   copying build/lib/reframed/community/model.py -> build/bdist.linux-armv7l/wheel/reframed/community
2024-07-31T15:34:32,550   copying build/lib/reframed/community/SteadyCom.py -> build/bdist.linux-armv7l/wheel/reframed/community
2024-07-31T15:34:32,552   creating build/bdist.linux-armv7l/wheel/reframed/alpha
2024-07-31T15:34:32,554   copying build/lib/reframed/alpha/geneswitch.py -> build/bdist.linux-armv7l/wheel/reframed/alpha
2024-07-31T15:34:32,556   copying build/lib/reframed/alpha/fluxutils.py -> build/bdist.linux-armv7l/wheel/reframed/alpha
2024-07-31T15:34:32,558   copying build/lib/reframed/alpha/gapMake.py -> build/bdist.linux-armv7l/wheel/reframed/alpha
2024-07-31T15:34:32,560   copying build/lib/reframed/alpha/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/alpha
2024-07-31T15:34:32,562   copying build/lib/reframed/alpha/plotting.py -> build/bdist.linux-armv7l/wheel/reframed/alpha
2024-07-31T15:34:32,564   copying build/lib/reframed/alpha/sampling.py -> build/bdist.linux-armv7l/wheel/reframed/alpha
2024-07-31T15:34:32,567   creating build/bdist.linux-armv7l/wheel/reframed/core
2024-07-31T15:34:32,568   copying build/lib/reframed/core/cbmodel.py -> build/bdist.linux-armv7l/wheel/reframed/core
2024-07-31T15:34:32,571   copying build/lib/reframed/core/environment.py -> build/bdist.linux-armv7l/wheel/reframed/core
2024-07-31T15:34:32,573   copying build/lib/reframed/core/transformation.py -> build/bdist.linux-armv7l/wheel/reframed/core
2024-07-31T15:34:32,576   copying build/lib/reframed/core/parser.py -> build/bdist.linux-armv7l/wheel/reframed/core
2024-07-31T15:34:32,578   copying build/lib/reframed/core/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/core
2024-07-31T15:34:32,580   copying build/lib/reframed/core/model.py -> build/bdist.linux-armv7l/wheel/reframed/core
2024-07-31T15:34:32,583   copying build/lib/reframed/core/elements.py -> build/bdist.linux-armv7l/wheel/reframed/core
2024-07-31T15:34:32,585   creating build/bdist.linux-armv7l/wheel/reframed/cobra
2024-07-31T15:34:32,586   copying build/lib/reframed/cobra/thermodynamics.py -> build/bdist.linux-armv7l/wheel/reframed/cobra
2024-07-31T15:34:32,589   copying build/lib/reframed/cobra/transcriptomics.py -> build/bdist.linux-armv7l/wheel/reframed/cobra
2024-07-31T15:34:32,591   copying build/lib/reframed/cobra/simulation.py -> build/bdist.linux-armv7l/wheel/reframed/cobra
2024-07-31T15:34:32,593   copying build/lib/reframed/cobra/medium.py -> build/bdist.linux-armv7l/wheel/reframed/cobra
2024-07-31T15:34:32,596   copying build/lib/reframed/cobra/ensemble.py -> build/bdist.linux-armv7l/wheel/reframed/cobra
2024-07-31T15:34:32,598   copying build/lib/reframed/cobra/knockout.py -> build/bdist.linux-armv7l/wheel/reframed/cobra
2024-07-31T15:34:32,600   copying build/lib/reframed/cobra/variability.py -> build/bdist.linux-armv7l/wheel/reframed/cobra
2024-07-31T15:34:32,602   copying build/lib/reframed/cobra/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/cobra
2024-07-31T15:34:32,603   copying build/lib/reframed/cobra/plotting.py -> build/bdist.linux-armv7l/wheel/reframed/cobra
2024-07-31T15:34:32,605   copying build/lib/reframed/cobra/auxotrophy.py -> build/bdist.linux-armv7l/wheel/reframed/cobra
2024-07-31T15:34:32,607   creating build/bdist.linux-armv7l/wheel/reframed/solvers
2024-07-31T15:34:32,608   copying build/lib/reframed/solvers/solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers
2024-07-31T15:34:32,611   copying build/lib/reframed/solvers/gurobi_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers
2024-07-31T15:34:32,613   copying build/lib/reframed/solvers/solution.py -> build/bdist.linux-armv7l/wheel/reframed/solvers
2024-07-31T15:34:32,615   copying build/lib/reframed/solvers/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/solvers
2024-07-31T15:34:32,617   copying build/lib/reframed/solvers/cplex_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers
2024-07-31T15:34:32,619   copying build/lib/reframed/solvers/scip_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers
2024-07-31T15:34:32,621   copying build/lib/reframed/__init__.py -> build/bdist.linux-armv7l/wheel/reframed
2024-07-31T15:34:32,623   creating build/bdist.linux-armv7l/wheel/reframed/external
2024-07-31T15:34:32,624   copying build/lib/reframed/external/escher.py -> build/bdist.linux-armv7l/wheel/reframed/external
2024-07-31T15:34:32,626   copying build/lib/reframed/external/cobrapy.py -> build/bdist.linux-armv7l/wheel/reframed/external
2024-07-31T15:34:32,628   copying build/lib/reframed/external/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/external
2024-07-31T15:34:32,630   creating build/bdist.linux-armv7l/wheel/tests
2024-07-31T15:34:32,630   copying build/lib/tests/scip_carveme.py -> build/bdist.linux-armv7l/wheel/tests
2024-07-31T15:34:32,633   creating build/bdist.linux-armv7l/wheel/tests/data
2024-07-31T15:34:32,633   copying build/lib/tests/data/model_fbc2.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data
2024-07-31T15:34:32,636   copying build/lib/tests/data/e_coli_core.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data
2024-07-31T15:34:32,639   copying build/lib/tests/data/model_cobra.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data
2024-07-31T15:34:32,641   copying build/lib/tests/data/iML1515.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data
2024-07-31T15:34:32,652   copying build/lib/tests/test_reframed.py -> build/bdist.linux-armv7l/wheel/tests
2024-07-31T15:34:32,655   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests
2024-07-31T15:34:32,656   running install_egg_info
2024-07-31T15:34:32,689   Copying reframed.egg-info to build/bdist.linux-armv7l/wheel/reframed-1.5.3-py3.11.egg-info
2024-07-31T15:34:32,702   running install_scripts
2024-07-31T15:34:32,715   creating build/bdist.linux-armv7l/wheel/reframed-1.5.3.dist-info/WHEEL
2024-07-31T15:34:32,717   creating '/tmp/pip-wheel-r5kesnx2/reframed-1.5.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-07-31T15:34:32,719   adding 'reframed/__init__.py'
2024-07-31T15:34:32,721   adding 'reframed/alpha/__init__.py'
2024-07-31T15:34:32,722   adding 'reframed/alpha/fluxutils.py'
2024-07-31T15:34:32,724   adding 'reframed/alpha/gapMake.py'
2024-07-31T15:34:32,726   adding 'reframed/alpha/geneswitch.py'
2024-07-31T15:34:32,727   adding 'reframed/alpha/plotting.py'
2024-07-31T15:34:32,729   adding 'reframed/alpha/sampling.py'
2024-07-31T15:34:32,730   adding 'reframed/cobra/__init__.py'
2024-07-31T15:34:32,732   adding 'reframed/cobra/auxotrophy.py'
2024-07-31T15:34:32,733   adding 'reframed/cobra/ensemble.py'
2024-07-31T15:34:32,735   adding 'reframed/cobra/knockout.py'
2024-07-31T15:34:32,737   adding 'reframed/cobra/medium.py'
2024-07-31T15:34:32,738   adding 'reframed/cobra/plotting.py'
2024-07-31T15:34:32,740   adding 'reframed/cobra/simulation.py'
2024-07-31T15:34:32,743   adding 'reframed/cobra/thermodynamics.py'
2024-07-31T15:34:32,745   adding 'reframed/cobra/transcriptomics.py'
2024-07-31T15:34:32,746   adding 'reframed/cobra/variability.py'
2024-07-31T15:34:32,748   adding 'reframed/community/SteadyCom.py'
2024-07-31T15:34:32,750   adding 'reframed/community/__init__.py'
2024-07-31T15:34:32,751   adding 'reframed/community/model.py'
2024-07-31T15:34:32,753   adding 'reframed/community/solution.py'
2024-07-31T15:34:32,755   adding 'reframed/core/__init__.py'
2024-07-31T15:34:32,757   adding 'reframed/core/cbmodel.py'
2024-07-31T15:34:32,758   adding 'reframed/core/elements.py'
2024-07-31T15:34:32,760   adding 'reframed/core/environment.py'
2024-07-31T15:34:32,762   adding 'reframed/core/model.py'
2024-07-31T15:34:32,764   adding 'reframed/core/parser.py'
2024-07-31T15:34:32,766   adding 'reframed/core/transformation.py'
2024-07-31T15:34:32,768   adding 'reframed/external/__init__.py'
2024-07-31T15:34:32,770   adding 'reframed/external/cobrapy.py'
2024-07-31T15:34:32,771   adding 'reframed/external/escher.py'
2024-07-31T15:34:32,772   adding 'reframed/io/__init__.py'
2024-07-31T15:34:32,773   adding 'reframed/io/cache.py'
2024-07-31T15:34:32,777   adding 'reframed/io/sbml.py'
2024-07-31T15:34:32,779   adding 'reframed/solvers/__init__.py'
2024-07-31T15:34:32,780   adding 'reframed/solvers/cplex_solver.py'
2024-07-31T15:34:32,782   adding 'reframed/solvers/gurobi_solver.py'
2024-07-31T15:34:32,783   adding 'reframed/solvers/scip_solver.py'
2024-07-31T15:34:32,785   adding 'reframed/solvers/solution.py'
2024-07-31T15:34:32,786   adding 'reframed/solvers/solver.py'
2024-07-31T15:34:32,789   adding 'tests/__init__.py'
2024-07-31T15:34:32,790   adding 'tests/scip_carveme.py'
2024-07-31T15:34:32,791   adding 'tests/test_reframed.py'
2024-07-31T15:34:32,796   adding 'tests/data/e_coli_core.xml.gz'
2024-07-31T15:34:32,853   adding 'tests/data/iML1515.xml.gz'
2024-07-31T15:34:32,858   adding 'tests/data/model_cobra.xml.gz'
2024-07-31T15:34:32,860   adding 'tests/data/model_fbc2.xml.gz'
2024-07-31T15:34:32,861   adding 'reframed-1.5.3.dist-info/LICENSE'
2024-07-31T15:34:32,862   adding 'reframed-1.5.3.dist-info/METADATA'
2024-07-31T15:34:32,863   adding 'reframed-1.5.3.dist-info/WHEEL'
2024-07-31T15:34:32,864   adding 'reframed-1.5.3.dist-info/top_level.txt'
2024-07-31T15:34:32,865   adding 'reframed-1.5.3.dist-info/RECORD'
2024-07-31T15:34:32,878   removing build/bdist.linux-armv7l/wheel
2024-07-31T15:34:33,009   Building wheel for reframed (setup.py): finished with status 'done'
2024-07-31T15:34:33,017   Created wheel for reframed: filename=reframed-1.5.3-py3-none-any.whl size=587147 sha256=630d771b21d33250c364d0ece882de6fac5f7e11fda8d7eea559fa0275efa64e
2024-07-31T15:34:33,018   Stored in directory: /tmp/pip-ephem-wheel-cache-12badexo/wheels/4d/5e/6b/7144033f937d341400da0f967efe56139f76b3f48ceaf659ce
2024-07-31T15:34:33,029 Successfully built reframed
2024-07-31T15:34:33,045 Removed build tracker: '/tmp/pip-build-tracker-1hmr5z5a'