2023-11-10T19:45:50,124 Created temporary directory: /tmp/pip-build-tracker-kyhuevx7 2023-11-10T19:45:50,125 Initialized build tracking at /tmp/pip-build-tracker-kyhuevx7 2023-11-10T19:45:50,126 Created build tracker: /tmp/pip-build-tracker-kyhuevx7 2023-11-10T19:45:50,126 Entered build tracker: /tmp/pip-build-tracker-kyhuevx7 2023-11-10T19:45:50,127 Created temporary directory: /tmp/pip-wheel-rcfam___ 2023-11-10T19:45:50,130 Created temporary directory: /tmp/pip-ephem-wheel-cache-w2m7iu__ 2023-11-10T19:45:50,151 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-10T19:45:50,155 2 location(s) to search for versions of reframed: 2023-11-10T19:45:50,155 * https://pypi.org/simple/reframed/ 2023-11-10T19:45:50,155 * https://www.piwheels.org/simple/reframed/ 2023-11-10T19:45:50,156 Fetching project page and analyzing links: https://pypi.org/simple/reframed/ 2023-11-10T19:45:50,156 Getting page https://pypi.org/simple/reframed/ 2023-11-10T19:45:50,158 Found index url https://pypi.org/simple/ 2023-11-10T19:45:50,381 Fetched page https://pypi.org/simple/reframed/ as application/vnd.pypi.simple.v1+json 2023-11-10T19:45:50,385 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) 2023-11-10T19:45:50,386 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 2023-11-10T19:45:50,387 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) 2023-11-10T19:45:50,388 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 2023-11-10T19:45:50,388 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) 2023-11-10T19:45:50,390 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 2023-11-10T19:45:50,390 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) 2023-11-10T19:45:50,391 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 2023-11-10T19:45:50,392 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) 2023-11-10T19:45:50,393 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 2023-11-10T19:45:50,394 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) 2023-11-10T19:45:50,395 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 2023-11-10T19:45:50,395 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) 2023-11-10T19:45:50,396 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 2023-11-10T19:45:50,397 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) 2023-11-10T19:45:50,398 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 2023-11-10T19:45:50,398 Fetching project page and analyzing links: https://www.piwheels.org/simple/reframed/ 2023-11-10T19:45:50,399 Getting page https://www.piwheels.org/simple/reframed/ 2023-11-10T19:45:50,400 Found index url https://www.piwheels.org/simple/ 2023-11-10T19:45:50,567 Fetched page https://www.piwheels.org/simple/reframed/ as text/html 2023-11-10T19:45:50,571 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) 2023-11-10T19:45:50,571 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) 2023-11-10T19:45:50,572 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) 2023-11-10T19:45:50,572 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) 2023-11-10T19:45:50,573 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) 2023-11-10T19:45:50,574 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) 2023-11-10T19:45:50,574 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) 2023-11-10T19:45:50,575 Skipping link: not a file: https://www.piwheels.org/simple/reframed/ 2023-11-10T19:45:50,575 Skipping link: not a file: https://pypi.org/simple/reframed/ 2023-11-10T19:45:50,596 Given no hashes to check 1 links for project 'reframed': discarding no candidates 2023-11-10T19:45:50,616 Collecting reframed==1.5.0 2023-11-10T19:45:50,618 Created temporary directory: /tmp/pip-unpack-69jds31h 2023-11-10T19:45:50,837 Downloading reframed-1.5.0.tar.gz (587 kB) 2023-11-10T19:45:51,117 Added reframed==1.5.0 from https://files.pythonhosted.org/packages/fe/fb/98d4497abcb4c9637977e0c79c5bf722eeda37ce9815166b6b2ae2cbad3a/reframed-1.5.0.tar.gz to build tracker '/tmp/pip-build-tracker-kyhuevx7' 2023-11-10T19:45:51,119 Running setup.py (path:/tmp/pip-wheel-rcfam___/reframed_42616b0bc5004db190e6f71c33d44526/setup.py) egg_info for package reframed 2023-11-10T19:45:51,120 Created temporary directory: /tmp/pip-pip-egg-info-m4muvkyu 2023-11-10T19:45:51,120 Preparing metadata (setup.py): started 2023-11-10T19:45:51,122 Running command python setup.py egg_info 2023-11-10T19:45:52,196 running egg_info 2023-11-10T19:45:52,197 creating /tmp/pip-pip-egg-info-m4muvkyu/reframed.egg-info 2023-11-10T19:45:52,222 writing /tmp/pip-pip-egg-info-m4muvkyu/reframed.egg-info/PKG-INFO 2023-11-10T19:45:52,225 writing dependency_links to /tmp/pip-pip-egg-info-m4muvkyu/reframed.egg-info/dependency_links.txt 2023-11-10T19:45:52,227 writing requirements to /tmp/pip-pip-egg-info-m4muvkyu/reframed.egg-info/requires.txt 2023-11-10T19:45:52,228 writing top-level names to /tmp/pip-pip-egg-info-m4muvkyu/reframed.egg-info/top_level.txt 2023-11-10T19:45:52,229 writing manifest file '/tmp/pip-pip-egg-info-m4muvkyu/reframed.egg-info/SOURCES.txt' 2023-11-10T19:45:52,310 reading manifest file '/tmp/pip-pip-egg-info-m4muvkyu/reframed.egg-info/SOURCES.txt' 2023-11-10T19:45:52,311 reading manifest template 'MANIFEST.in' 2023-11-10T19:45:52,312 warning: no files found matching 'CONTRIBUTING.rst' 2023-11-10T19:45:52,313 warning: no files found matching 'HISTORY.rst' 2023-11-10T19:45:52,317 warning: no previously-included files matching '__pycache__' found under directory '*' 2023-11-10T19:45:52,318 warning: no previously-included files matching '*.py[co]' found under directory '*' 2023-11-10T19:45:52,337 warning: no files found matching '*.jpg' under directory 'docs' 2023-11-10T19:45:52,343 warning: no files found matching '*.png' under directory 'docs' 2023-11-10T19:45:52,348 warning: no files found matching '*.gif' under directory 'docs' 2023-11-10T19:45:52,348 adding license file 'LICENSE' 2023-11-10T19:45:52,351 writing manifest file '/tmp/pip-pip-egg-info-m4muvkyu/reframed.egg-info/SOURCES.txt' 2023-11-10T19:45:52,462 Preparing metadata (setup.py): finished with status 'done' 2023-11-10T19:45:52,466 Source in /tmp/pip-wheel-rcfam___/reframed_42616b0bc5004db190e6f71c33d44526 has version 1.5.0, which satisfies requirement reframed==1.5.0 from https://files.pythonhosted.org/packages/fe/fb/98d4497abcb4c9637977e0c79c5bf722eeda37ce9815166b6b2ae2cbad3a/reframed-1.5.0.tar.gz 2023-11-10T19:45:52,467 Removed reframed==1.5.0 from https://files.pythonhosted.org/packages/fe/fb/98d4497abcb4c9637977e0c79c5bf722eeda37ce9815166b6b2ae2cbad3a/reframed-1.5.0.tar.gz from build tracker '/tmp/pip-build-tracker-kyhuevx7' 2023-11-10T19:45:52,473 Created temporary directory: /tmp/pip-unpack-djuk3ikj 2023-11-10T19:45:52,474 Created temporary directory: /tmp/pip-unpack-nae4ueso 2023-11-10T19:45:52,481 Building wheels for collected packages: reframed 2023-11-10T19:45:52,485 Created temporary directory: /tmp/pip-wheel-niookrkn 2023-11-10T19:45:52,485 Building wheel for reframed (setup.py): started 2023-11-10T19:45:52,487 Destination directory: /tmp/pip-wheel-niookrkn 2023-11-10T19:45:52,487 Running command python setup.py bdist_wheel 2023-11-10T19:45:53,509 running bdist_wheel 2023-11-10T19:45:53,607 running build 2023-11-10T19:45:53,608 running build_py 2023-11-10T19:45:53,634 creating build 2023-11-10T19:45:53,635 creating build/lib 2023-11-10T19:45:53,636 creating build/lib/reframed 2023-11-10T19:45:53,638 copying reframed/__init__.py -> build/lib/reframed 2023-11-10T19:45:53,640 creating build/lib/tests 2023-11-10T19:45:53,641 copying tests/__init__.py -> build/lib/tests 2023-11-10T19:45:53,643 copying tests/scip_carveme.py -> build/lib/tests 2023-11-10T19:45:53,646 copying tests/test_reframed.py -> build/lib/tests 2023-11-10T19:45:53,649 creating build/lib/reframed/cobra 2023-11-10T19:45:53,650 copying reframed/cobra/__init__.py -> build/lib/reframed/cobra 2023-11-10T19:45:53,651 copying reframed/cobra/simulation.py -> build/lib/reframed/cobra 2023-11-10T19:45:53,654 copying reframed/cobra/ensemble.py -> build/lib/reframed/cobra 2023-11-10T19:45:53,656 copying reframed/cobra/plotting.py -> build/lib/reframed/cobra 2023-11-10T19:45:53,658 copying reframed/cobra/knockout.py -> build/lib/reframed/cobra 2023-11-10T19:45:53,660 copying reframed/cobra/variability.py -> build/lib/reframed/cobra 2023-11-10T19:45:53,662 copying reframed/cobra/transcriptomics.py -> build/lib/reframed/cobra 2023-11-10T19:45:53,664 copying reframed/cobra/thermodynamics.py -> build/lib/reframed/cobra 2023-11-10T19:45:53,667 copying reframed/cobra/auxotrophy.py -> build/lib/reframed/cobra 2023-11-10T19:45:53,669 copying reframed/cobra/medium.py -> build/lib/reframed/cobra 2023-11-10T19:45:53,672 creating build/lib/reframed/solvers 2023-11-10T19:45:53,673 copying reframed/solvers/__init__.py -> build/lib/reframed/solvers 2023-11-10T19:45:53,675 copying reframed/solvers/cplex_solver.py -> build/lib/reframed/solvers 2023-11-10T19:45:53,677 copying reframed/solvers/solver.py -> build/lib/reframed/solvers 2023-11-10T19:45:53,679 copying reframed/solvers/solution.py -> build/lib/reframed/solvers 2023-11-10T19:45:53,682 copying reframed/solvers/gurobi_solver.py -> build/lib/reframed/solvers 2023-11-10T19:45:53,684 copying reframed/solvers/pulp_solver.py -> build/lib/reframed/solvers 2023-11-10T19:45:53,687 copying reframed/solvers/optlang_solver.py -> build/lib/reframed/solvers 2023-11-10T19:45:53,689 copying reframed/solvers/scip_solver.py -> build/lib/reframed/solvers 2023-11-10T19:45:53,692 creating build/lib/reframed/alpha 2023-11-10T19:45:53,693 copying reframed/alpha/__init__.py -> build/lib/reframed/alpha 2023-11-10T19:45:53,694 copying reframed/alpha/geneswitch.py -> build/lib/reframed/alpha 2023-11-10T19:45:53,696 copying reframed/alpha/plotting.py -> build/lib/reframed/alpha 2023-11-10T19:45:53,698 copying reframed/alpha/fluxutils.py -> build/lib/reframed/alpha 2023-11-10T19:45:53,700 copying reframed/alpha/sampling.py -> build/lib/reframed/alpha 2023-11-10T19:45:53,702 copying reframed/alpha/gapMake.py -> build/lib/reframed/alpha 2023-11-10T19:45:53,704 creating build/lib/reframed/io 2023-11-10T19:45:53,705 copying reframed/io/__init__.py -> build/lib/reframed/io 2023-11-10T19:45:53,707 copying reframed/io/sbml.py -> build/lib/reframed/io 2023-11-10T19:45:53,710 copying reframed/io/cache.py -> build/lib/reframed/io 2023-11-10T19:45:53,712 creating build/lib/reframed/core 2023-11-10T19:45:53,713 copying reframed/core/__init__.py -> build/lib/reframed/core 2023-11-10T19:45:53,715 copying reframed/core/parser.py -> build/lib/reframed/core 2023-11-10T19:45:53,717 copying reframed/core/model.py -> build/lib/reframed/core 2023-11-10T19:45:53,719 copying reframed/core/environment.py -> build/lib/reframed/core 2023-11-10T19:45:53,721 copying reframed/core/transformation.py -> build/lib/reframed/core 2023-11-10T19:45:53,724 copying reframed/core/elements.py -> build/lib/reframed/core 2023-11-10T19:45:53,726 copying reframed/core/cbmodel.py -> build/lib/reframed/core 2023-11-10T19:45:53,729 creating build/lib/reframed/external 2023-11-10T19:45:53,730 copying reframed/external/__init__.py -> build/lib/reframed/external 2023-11-10T19:45:53,731 copying reframed/external/escher.py -> build/lib/reframed/external 2023-11-10T19:45:53,733 copying reframed/external/cobrapy.py -> build/lib/reframed/external 2023-11-10T19:45:53,735 creating build/lib/reframed/community 2023-11-10T19:45:53,736 copying reframed/community/__init__.py -> build/lib/reframed/community 2023-11-10T19:45:53,738 copying reframed/community/simulation.py -> build/lib/reframed/community 2023-11-10T19:45:53,740 copying reframed/community/solution.py -> build/lib/reframed/community 2023-11-10T19:45:53,742 copying reframed/community/SteadyCom.py -> build/lib/reframed/community 2023-11-10T19:45:53,744 copying reframed/community/simulation_old.py -> build/lib/reframed/community 2023-11-10T19:45:53,746 copying reframed/community/model.py -> build/lib/reframed/community 2023-11-10T19:45:53,749 running egg_info 2023-11-10T19:45:53,804 writing reframed.egg-info/PKG-INFO 2023-11-10T19:45:53,807 writing dependency_links to reframed.egg-info/dependency_links.txt 2023-11-10T19:45:53,809 writing requirements to reframed.egg-info/requires.txt 2023-11-10T19:45:53,810 writing top-level names to reframed.egg-info/top_level.txt 2023-11-10T19:45:53,840 reading manifest file 'reframed.egg-info/SOURCES.txt' 2023-11-10T19:45:53,843 reading manifest template 'MANIFEST.in' 2023-11-10T19:45:53,844 warning: no files found matching 'CONTRIBUTING.rst' 2023-11-10T19:45:53,844 warning: no files found matching 'HISTORY.rst' 2023-11-10T19:45:53,848 warning: no previously-included files matching '__pycache__' found under directory '*' 2023-11-10T19:45:53,849 warning: no previously-included files matching '*.py[co]' found under directory '*' 2023-11-10T19:45:53,868 warning: no files found matching '*.jpg' under directory 'docs' 2023-11-10T19:45:53,874 warning: no files found matching '*.png' under directory 'docs' 2023-11-10T19:45:53,879 warning: no files found matching '*.gif' under directory 'docs' 2023-11-10T19:45:53,879 adding license file 'LICENSE' 2023-11-10T19:45:53,883 writing manifest file 'reframed.egg-info/SOURCES.txt' 2023-11-10T19:45:53,886 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'tests.data' is absent from the `packages` configuration. 2023-11-10T19:45:53,886 !! 2023-11-10T19:45:53,887 ******************************************************************************** 2023-11-10T19:45:53,888 ############################ 2023-11-10T19:45:53,888 # Package would be ignored # 2023-11-10T19:45:53,889 ############################ 2023-11-10T19:45:53,889 Python recognizes 'tests.data' as an importable package[^1], 2023-11-10T19:45:53,890 but it is absent from setuptools' `packages` configuration. 2023-11-10T19:45:53,891 This leads to an ambiguous overall configuration. If you want to distribute this 2023-11-10T19:45:53,892 package, please make sure that 'tests.data' is explicitly added 2023-11-10T19:45:53,892 to the `packages` configuration field. 2023-11-10T19:45:53,893 Alternatively, you can also rely on setuptools' discovery methods 2023-11-10T19:45:53,894 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-11-10T19:45:53,895 instead of `find_packages(...)`/`find:`). 2023-11-10T19:45:53,897 You can read more about "package discovery" on setuptools documentation page: 2023-11-10T19:45:53,901 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-11-10T19:45:53,902 If you don't want 'tests.data' to be distributed and are 2023-11-10T19:45:53,903 already explicitly excluding 'tests.data' via 2023-11-10T19:45:53,903 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-11-10T19:45:53,904 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-11-10T19:45:53,904 combination with a more fine grained `package-data` configuration. 2023-11-10T19:45:53,905 You can read more about "package data files" on setuptools documentation page: 2023-11-10T19:45:53,906 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-11-10T19:45:53,908 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-11-10T19:45:53,908 even if it does not contain any `.py` files. 2023-11-10T19:45:53,909 On the other hand, currently there is no concept of package data 2023-11-10T19:45:53,909 directory, all directories are treated like packages. 2023-11-10T19:45:53,910 ******************************************************************************** 2023-11-10T19:45:53,911 !! 2023-11-10T19:45:53,911 check.warn(importable) 2023-11-10T19:45:53,912 creating build/lib/tests/data 2023-11-10T19:45:53,912 copying tests/data/e_coli_core.xml.gz -> build/lib/tests/data 2023-11-10T19:45:53,913 copying tests/data/iML1515.xml.gz -> build/lib/tests/data 2023-11-10T19:45:53,913 copying tests/data/model_cobra.xml.gz -> build/lib/tests/data 2023-11-10T19:45:53,914 copying tests/data/model_fbc2.xml.gz -> build/lib/tests/data 2023-11-10T19:45:53,936 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-11-10T19:45:53,937 !! 2023-11-10T19:45:53,938 ******************************************************************************** 2023-11-10T19:45:53,938 Please avoid running ``setup.py`` directly. 2023-11-10T19:45:53,939 Instead, use pypa/build, pypa/installer or other 2023-11-10T19:45:53,939 standards-based tools. 2023-11-10T19:45:53,940 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-11-10T19:45:53,940 ******************************************************************************** 2023-11-10T19:45:53,941 !! 2023-11-10T19:45:53,942 self.initialize_options() 2023-11-10T19:45:53,960 installing to build/bdist.linux-armv7l/wheel 2023-11-10T19:45:53,960 running install 2023-11-10T19:45:53,984 running install_lib 2023-11-10T19:45:54,007 creating build/bdist.linux-armv7l 2023-11-10T19:45:54,008 creating build/bdist.linux-armv7l/wheel 2023-11-10T19:45:54,009 creating build/bdist.linux-armv7l/wheel/reframed 2023-11-10T19:45:54,010 copying build/lib/reframed/__init__.py -> build/bdist.linux-armv7l/wheel/reframed 2023-11-10T19:45:54,012 creating build/bdist.linux-armv7l/wheel/reframed/cobra 2023-11-10T19:45:54,013 copying build/lib/reframed/cobra/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2023-11-10T19:45:54,015 copying build/lib/reframed/cobra/simulation.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2023-11-10T19:45:54,017 copying build/lib/reframed/cobra/ensemble.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2023-11-10T19:45:54,019 copying build/lib/reframed/cobra/plotting.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2023-11-10T19:45:54,021 copying build/lib/reframed/cobra/knockout.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2023-11-10T19:45:54,024 copying build/lib/reframed/cobra/variability.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2023-11-10T19:45:54,025 copying build/lib/reframed/cobra/transcriptomics.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2023-11-10T19:45:54,027 copying build/lib/reframed/cobra/thermodynamics.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2023-11-10T19:45:54,030 copying build/lib/reframed/cobra/auxotrophy.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2023-11-10T19:45:54,031 copying build/lib/reframed/cobra/medium.py -> build/bdist.linux-armv7l/wheel/reframed/cobra 2023-11-10T19:45:54,034 creating build/bdist.linux-armv7l/wheel/reframed/solvers 2023-11-10T19:45:54,035 copying build/lib/reframed/solvers/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2023-11-10T19:45:54,037 copying build/lib/reframed/solvers/cplex_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2023-11-10T19:45:54,039 copying build/lib/reframed/solvers/solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2023-11-10T19:45:54,041 copying build/lib/reframed/solvers/solution.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2023-11-10T19:45:54,043 copying build/lib/reframed/solvers/gurobi_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2023-11-10T19:45:54,046 copying build/lib/reframed/solvers/pulp_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2023-11-10T19:45:54,048 copying build/lib/reframed/solvers/optlang_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2023-11-10T19:45:54,050 copying build/lib/reframed/solvers/scip_solver.py -> build/bdist.linux-armv7l/wheel/reframed/solvers 2023-11-10T19:45:54,053 creating build/bdist.linux-armv7l/wheel/reframed/alpha 2023-11-10T19:45:54,053 copying build/lib/reframed/alpha/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2023-11-10T19:45:54,055 copying build/lib/reframed/alpha/geneswitch.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2023-11-10T19:45:54,057 copying build/lib/reframed/alpha/plotting.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2023-11-10T19:45:54,058 copying build/lib/reframed/alpha/fluxutils.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2023-11-10T19:45:54,060 copying build/lib/reframed/alpha/sampling.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2023-11-10T19:45:54,062 copying build/lib/reframed/alpha/gapMake.py -> build/bdist.linux-armv7l/wheel/reframed/alpha 2023-11-10T19:45:54,064 creating build/bdist.linux-armv7l/wheel/reframed/io 2023-11-10T19:45:54,065 copying build/lib/reframed/io/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/io 2023-11-10T19:45:54,066 copying build/lib/reframed/io/sbml.py -> build/bdist.linux-armv7l/wheel/reframed/io 2023-11-10T19:45:54,069 copying build/lib/reframed/io/cache.py -> build/bdist.linux-armv7l/wheel/reframed/io 2023-11-10T19:45:54,071 creating build/bdist.linux-armv7l/wheel/reframed/core 2023-11-10T19:45:54,071 copying build/lib/reframed/core/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/core 2023-11-10T19:45:54,073 copying build/lib/reframed/core/parser.py -> build/bdist.linux-armv7l/wheel/reframed/core 2023-11-10T19:45:54,075 copying build/lib/reframed/core/model.py -> build/bdist.linux-armv7l/wheel/reframed/core 2023-11-10T19:45:54,077 copying build/lib/reframed/core/environment.py -> build/bdist.linux-armv7l/wheel/reframed/core 2023-11-10T19:45:54,079 copying build/lib/reframed/core/transformation.py -> build/bdist.linux-armv7l/wheel/reframed/core 2023-11-10T19:45:54,081 copying build/lib/reframed/core/elements.py -> build/bdist.linux-armv7l/wheel/reframed/core 2023-11-10T19:45:54,083 copying build/lib/reframed/core/cbmodel.py -> build/bdist.linux-armv7l/wheel/reframed/core 2023-11-10T19:45:54,086 creating build/bdist.linux-armv7l/wheel/reframed/external 2023-11-10T19:45:54,086 copying build/lib/reframed/external/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/external 2023-11-10T19:45:54,088 copying build/lib/reframed/external/escher.py -> build/bdist.linux-armv7l/wheel/reframed/external 2023-11-10T19:45:54,090 copying build/lib/reframed/external/cobrapy.py -> build/bdist.linux-armv7l/wheel/reframed/external 2023-11-10T19:45:54,092 creating build/bdist.linux-armv7l/wheel/reframed/community 2023-11-10T19:45:54,093 copying build/lib/reframed/community/__init__.py -> build/bdist.linux-armv7l/wheel/reframed/community 2023-11-10T19:45:54,094 copying build/lib/reframed/community/simulation.py -> build/bdist.linux-armv7l/wheel/reframed/community 2023-11-10T19:45:54,096 copying build/lib/reframed/community/solution.py -> build/bdist.linux-armv7l/wheel/reframed/community 2023-11-10T19:45:54,098 copying build/lib/reframed/community/SteadyCom.py -> build/bdist.linux-armv7l/wheel/reframed/community 2023-11-10T19:45:54,100 copying build/lib/reframed/community/simulation_old.py -> build/bdist.linux-armv7l/wheel/reframed/community 2023-11-10T19:45:54,103 copying build/lib/reframed/community/model.py -> build/bdist.linux-armv7l/wheel/reframed/community 2023-11-10T19:45:54,105 creating build/bdist.linux-armv7l/wheel/tests 2023-11-10T19:45:54,107 creating build/bdist.linux-armv7l/wheel/tests/data 2023-11-10T19:45:54,108 copying build/lib/tests/data/e_coli_core.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data 2023-11-10T19:45:54,111 copying build/lib/tests/data/iML1515.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data 2023-11-10T19:45:54,119 copying build/lib/tests/data/model_cobra.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data 2023-11-10T19:45:54,121 copying build/lib/tests/data/model_fbc2.xml.gz -> build/bdist.linux-armv7l/wheel/tests/data 2023-11-10T19:45:54,124 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests 2023-11-10T19:45:54,125 copying build/lib/tests/scip_carveme.py -> build/bdist.linux-armv7l/wheel/tests 2023-11-10T19:45:54,127 copying build/lib/tests/test_reframed.py -> build/bdist.linux-armv7l/wheel/tests 2023-11-10T19:45:54,129 running install_egg_info 2023-11-10T19:45:54,159 Copying reframed.egg-info to build/bdist.linux-armv7l/wheel/reframed-1.5.0-py3.11.egg-info 2023-11-10T19:45:54,169 running install_scripts 2023-11-10T19:45:54,182 creating build/bdist.linux-armv7l/wheel/reframed-1.5.0.dist-info/WHEEL 2023-11-10T19:45:54,185 creating '/tmp/pip-wheel-niookrkn/reframed-1.5.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-11-10T19:45:54,187 adding 'reframed/__init__.py' 2023-11-10T19:45:54,189 adding 'reframed/alpha/__init__.py' 2023-11-10T19:45:54,190 adding 'reframed/alpha/fluxutils.py' 2023-11-10T19:45:54,191 adding 'reframed/alpha/gapMake.py' 2023-11-10T19:45:54,193 adding 'reframed/alpha/geneswitch.py' 2023-11-10T19:45:54,194 adding 'reframed/alpha/plotting.py' 2023-11-10T19:45:54,195 adding 'reframed/alpha/sampling.py' 2023-11-10T19:45:54,197 adding 'reframed/cobra/__init__.py' 2023-11-10T19:45:54,198 adding 'reframed/cobra/auxotrophy.py' 2023-11-10T19:45:54,200 adding 'reframed/cobra/ensemble.py' 2023-11-10T19:45:54,201 adding 'reframed/cobra/knockout.py' 2023-11-10T19:45:54,203 adding 'reframed/cobra/medium.py' 2023-11-10T19:45:54,204 adding 'reframed/cobra/plotting.py' 2023-11-10T19:45:54,206 adding 'reframed/cobra/simulation.py' 2023-11-10T19:45:54,208 adding 'reframed/cobra/thermodynamics.py' 2023-11-10T19:45:54,210 adding 'reframed/cobra/transcriptomics.py' 2023-11-10T19:45:54,212 adding 'reframed/cobra/variability.py' 2023-11-10T19:45:54,214 adding 'reframed/community/SteadyCom.py' 2023-11-10T19:45:54,215 adding 'reframed/community/__init__.py' 2023-11-10T19:45:54,216 adding 'reframed/community/model.py' 2023-11-10T19:45:54,218 adding 'reframed/community/simulation.py' 2023-11-10T19:45:54,220 adding 'reframed/community/simulation_old.py' 2023-11-10T19:45:54,221 adding 'reframed/community/solution.py' 2023-11-10T19:45:54,223 adding 'reframed/core/__init__.py' 2023-11-10T19:45:54,225 adding 'reframed/core/cbmodel.py' 2023-11-10T19:45:54,226 adding 'reframed/core/elements.py' 2023-11-10T19:45:54,228 adding 'reframed/core/environment.py' 2023-11-10T19:45:54,230 adding 'reframed/core/model.py' 2023-11-10T19:45:54,232 adding 'reframed/core/parser.py' 2023-11-10T19:45:54,234 adding 'reframed/core/transformation.py' 2023-11-10T19:45:54,235 adding 'reframed/external/__init__.py' 2023-11-10T19:45:54,237 adding 'reframed/external/cobrapy.py' 2023-11-10T19:45:54,238 adding 'reframed/external/escher.py' 2023-11-10T19:45:54,239 adding 'reframed/io/__init__.py' 2023-11-10T19:45:54,241 adding 'reframed/io/cache.py' 2023-11-10T19:45:54,244 adding 'reframed/io/sbml.py' 2023-11-10T19:45:54,246 adding 'reframed/solvers/__init__.py' 2023-11-10T19:45:54,249 adding 'reframed/solvers/cplex_solver.py' 2023-11-10T19:45:54,251 adding 'reframed/solvers/gurobi_solver.py' 2023-11-10T19:45:54,253 adding 'reframed/solvers/optlang_solver.py' 2023-11-10T19:45:54,255 adding 'reframed/solvers/pulp_solver.py' 2023-11-10T19:45:54,257 adding 'reframed/solvers/scip_solver.py' 2023-11-10T19:45:54,258 adding 'reframed/solvers/solution.py' 2023-11-10T19:45:54,260 adding 'reframed/solvers/solver.py' 2023-11-10T19:45:54,262 adding 'tests/__init__.py' 2023-11-10T19:45:54,264 adding 'tests/scip_carveme.py' 2023-11-10T19:45:54,265 adding 'tests/test_reframed.py' 2023-11-10T19:45:54,270 adding 'tests/data/e_coli_core.xml.gz' 2023-11-10T19:45:54,328 adding 'tests/data/iML1515.xml.gz' 2023-11-10T19:45:54,333 adding 'tests/data/model_cobra.xml.gz' 2023-11-10T19:45:54,335 adding 'tests/data/model_fbc2.xml.gz' 2023-11-10T19:45:54,336 adding 'reframed-1.5.0.dist-info/LICENSE' 2023-11-10T19:45:54,337 adding 'reframed-1.5.0.dist-info/METADATA' 2023-11-10T19:45:54,338 adding 'reframed-1.5.0.dist-info/WHEEL' 2023-11-10T19:45:54,339 adding 'reframed-1.5.0.dist-info/top_level.txt' 2023-11-10T19:45:54,340 adding 'reframed-1.5.0.dist-info/RECORD' 2023-11-10T19:45:54,347 removing build/bdist.linux-armv7l/wheel 2023-11-10T19:45:54,475 Building wheel for reframed (setup.py): finished with status 'done' 2023-11-10T19:45:54,485 Created wheel for reframed: filename=reframed-1.5.0-py3-none-any.whl size=602567 sha256=fb599b43bd5101cd2f6669892af2463bab8d5e3bc9897ca062c077ff4fabb794 2023-11-10T19:45:54,486 Stored in directory: /tmp/pip-ephem-wheel-cache-w2m7iu__/wheels/d8/17/d0/69107666e36d6f1d089c3da2181468cc7ce5ac4a3a26643d4d 2023-11-10T19:45:54,497 Successfully built reframed 2023-11-10T19:45:54,523 Removed build tracker: '/tmp/pip-build-tracker-kyhuevx7'