2025-06-01T01:53:45,815 Created temporary directory: /tmp/pip-build-tracker-u2x2xagz
2025-06-01T01:53:45,816 Initialized build tracking at /tmp/pip-build-tracker-u2x2xagz
2025-06-01T01:53:45,816 Created build tracker: /tmp/pip-build-tracker-u2x2xagz
2025-06-01T01:53:45,817 Entered build tracker: /tmp/pip-build-tracker-u2x2xagz
2025-06-01T01:53:45,818 Created temporary directory: /tmp/pip-wheel-k0wl09_s
2025-06-01T01:53:45,822 Created temporary directory: /tmp/pip-ephem-wheel-cache-6x1evf0x
2025-06-01T01:53:45,870 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-01T01:53:45,873 2 location(s) to search for versions of reframed:
2025-06-01T01:53:45,873 * https://pypi.org/simple/reframed/
2025-06-01T01:53:45,873 * https://www.piwheels.org/simple/reframed/
2025-06-01T01:53:45,873 Fetching project page and analyzing links: https://pypi.org/simple/reframed/
2025-06-01T01:53:45,874 Getting page https://pypi.org/simple/reframed/
2025-06-01T01:53:45,876 Found index url https://pypi.org/simple/
2025-06-01T01:53:46,098 Fetched page https://pypi.org/simple/reframed/ as application/vnd.pypi.simple.v1+json
2025-06-01T01:53:46,102   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)
2025-06-01T01:53:46,103   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
2025-06-01T01:53:46,104   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)
2025-06-01T01:53:46,104   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
2025-06-01T01:53:46,105   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)
2025-06-01T01:53:46,106   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
2025-06-01T01:53:46,106   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)
2025-06-01T01:53:46,107   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
2025-06-01T01:53:46,108   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)
2025-06-01T01:53:46,109   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
2025-06-01T01:53:46,109   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)
2025-06-01T01:53:46,110   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
2025-06-01T01:53:46,110   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)
2025-06-01T01:53:46,111   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
2025-06-01T01:53:46,112   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)
2025-06-01T01:53:46,112   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
2025-06-01T01:53:46,113   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)
2025-06-01T01:53:46,113   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
2025-06-01T01:53:46,114   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)
2025-06-01T01:53:46,115   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
2025-06-01T01:53:46,115   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)
2025-06-01T01:53:46,116   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
2025-06-01T01:53:46,116   Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/20/34/8bd95c6f8a99d52e8603a91195e1725d4b4bac65962722ea7cec9908bd3f/reframed-1.5.4-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.8)
2025-06-01T01:53:46,117   Found link https://files.pythonhosted.org/packages/69/cc/86552c9e883191ef39cd3c344b712260ac01d5932c19d977f9eb19d66922/reframed-1.5.4.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.8), version: 1.5.4
2025-06-01T01:53:46,118   Skipping link: No binaries permitted for reframed: https://files.pythonhosted.org/packages/85/14/35130655198ceb33b45115abcfb442624cebd06bd29f05cd3b134f67b180/reframed-1.6.0-py3-none-any.whl (from https://pypi.org/simple/reframed/) (requires-python:>=3.8)
2025-06-01T01:53:46,119   Found link https://files.pythonhosted.org/packages/3f/91/7f9702e191c5c2d728701cd5ec3b885ad732b2380f6bb11cf46de6f68aed/reframed-1.6.0.tar.gz (from https://pypi.org/simple/reframed/) (requires-python:>=3.8), version: 1.6.0
2025-06-01T01:53:46,119 Fetching project page and analyzing links: https://www.piwheels.org/simple/reframed/
2025-06-01T01:53:46,120 Getting page https://www.piwheels.org/simple/reframed/
2025-06-01T01:53:46,121 Found index url https://www.piwheels.org/simple/
2025-06-01T01:53:46,272 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/reframed/
2025-06-01T01:53:46,921 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/reframed/
2025-06-01T01:53:48,136 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/reframed/
2025-06-01T01:53:50,352 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/reframed/
2025-06-01T01:53:54,562 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/reframed/
2025-06-01T01:53:54,777 Could not fetch URL https://www.piwheels.org/simple/reframed/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/reframed/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping
2025-06-01T01:53:54,779 Skipping link: not a file: https://www.piwheels.org/simple/reframed/
2025-06-01T01:53:54,780 Skipping link: not a file: https://pypi.org/simple/reframed/
2025-06-01T01:53:54,806 Given no hashes to check 1 links for project 'reframed': discarding no candidates
2025-06-01T01:53:54,809 Collecting reframed==1.5.4
2025-06-01T01:53:55,028   Created temporary directory: /tmp/pip-unpack-ua85pdfc
2025-06-01T01:53:55,258   Downloading reframed-1.5.4.tar.gz (662 kB)
2025-06-01T01:53:55,949   Added reframed==1.5.4 from https://files.pythonhosted.org/packages/69/cc/86552c9e883191ef39cd3c344b712260ac01d5932c19d977f9eb19d66922/reframed-1.5.4.tar.gz to build tracker '/tmp/pip-build-tracker-u2x2xagz'
2025-06-01T01:53:55,952   Running setup.py (path:/tmp/pip-wheel-k0wl09_s/reframed_18938ab0aeaf4b1b9161a67b556b4abf/setup.py) egg_info for package reframed
2025-06-01T01:53:55,953   Created temporary directory: /tmp/pip-pip-egg-info-6cn21bv7
2025-06-01T01:53:55,953   Preparing metadata (setup.py): started
2025-06-01T01:53:55,955   Running command python setup.py egg_info
2025-06-01T01:53:57,242   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
2025-06-01T01:53:57,243     warnings.warn(msg)
2025-06-01T01:53:57,243   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
2025-06-01T01:53:57,244     warnings.warn(msg)
2025-06-01T01:53:57,542   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-01T01:53:57,543   !!

2025-06-01T01:53:57,544           ********************************************************************************
2025-06-01T01:53:57,544           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-01T01:53:57,546           License :: OSI Approved :: Apache Software License

2025-06-01T01:53:57,547           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-01T01:53:57,548           ********************************************************************************

2025-06-01T01:53:57,549   !!
2025-06-01T01:53:57,549     self._finalize_license_expression()
2025-06-01T01:53:57,570   running egg_info
2025-06-01T01:53:57,596   creating /tmp/pip-pip-egg-info-6cn21bv7/reframed.egg-info
2025-06-01T01:53:57,597   writing /tmp/pip-pip-egg-info-6cn21bv7/reframed.egg-info/PKG-INFO
2025-06-01T01:53:57,601   writing dependency_links to /tmp/pip-pip-egg-info-6cn21bv7/reframed.egg-info/dependency_links.txt
2025-06-01T01:53:57,603   writing requirements to /tmp/pip-pip-egg-info-6cn21bv7/reframed.egg-info/requires.txt
2025-06-01T01:53:57,604   writing top-level names to /tmp/pip-pip-egg-info-6cn21bv7/reframed.egg-info/top_level.txt
2025-06-01T01:53:57,606   writing manifest file '/tmp/pip-pip-egg-info-6cn21bv7/reframed.egg-info/SOURCES.txt'
2025-06-01T01:53:57,696   reading manifest file '/tmp/pip-pip-egg-info-6cn21bv7/reframed.egg-info/SOURCES.txt'
2025-06-01T01:53:57,698   reading manifest template 'MANIFEST.in'
2025-06-01T01:53:57,699   warning: no files found matching 'CONTRIBUTING.rst'
2025-06-01T01:53:57,699   warning: no files found matching 'HISTORY.rst'
2025-06-01T01:53:57,704   warning: no previously-included files matching '__pycache__' found under directory '*'
2025-06-01T01:53:57,704   warning: no previously-included files matching '*.py[co]' found under directory '*'
2025-06-01T01:53:57,737   warning: no files found matching '*.jpg' under directory 'docs'
2025-06-01T01:53:57,754   warning: no files found matching '*.gif' under directory 'docs'
2025-06-01T01:53:57,754   adding license file 'LICENSE'
2025-06-01T01:53:57,758   writing manifest file '/tmp/pip-pip-egg-info-6cn21bv7/reframed.egg-info/SOURCES.txt'
2025-06-01T01:53:57,863   Preparing metadata (setup.py): finished with status 'done'
2025-06-01T01:53:57,868   Source in /tmp/pip-wheel-k0wl09_s/reframed_18938ab0aeaf4b1b9161a67b556b4abf has version 1.5.4, which satisfies requirement reframed==1.5.4 from https://files.pythonhosted.org/packages/69/cc/86552c9e883191ef39cd3c344b712260ac01d5932c19d977f9eb19d66922/reframed-1.5.4.tar.gz
2025-06-01T01:53:57,869   Removed reframed==1.5.4 from https://files.pythonhosted.org/packages/69/cc/86552c9e883191ef39cd3c344b712260ac01d5932c19d977f9eb19d66922/reframed-1.5.4.tar.gz from build tracker '/tmp/pip-build-tracker-u2x2xagz'
2025-06-01T01:53:57,875 Created temporary directory: /tmp/pip-unpack-yxxf9cpf
2025-06-01T01:53:57,876 Created temporary directory: /tmp/pip-unpack-2rm_3d6n
2025-06-01T01:53:57,877 Building wheels for collected packages: reframed
2025-06-01T01:53:57,880   Created temporary directory: /tmp/pip-wheel-x7uuiso7
2025-06-01T01:53:57,881   DEPRECATION: Building 'reframed' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'reframed'. Discussion can be found at https://github.com/pypa/pip/issues/6334
2025-06-01T01:53:57,882   Building wheel for reframed (setup.py): started
2025-06-01T01:53:57,883   Destination directory: /tmp/pip-wheel-x7uuiso7
2025-06-01T01:53:57,884   Running command python setup.py bdist_wheel
2025-06-01T01:53:58,635   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
2025-06-01T01:53:58,635     warnings.warn(msg)
2025-06-01T01:53:58,635   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
2025-06-01T01:53:58,636     warnings.warn(msg)
2025-06-01T01:53:58,944   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-01T01:53:58,945   !!

2025-06-01T01:53:58,946           ********************************************************************************
2025-06-01T01:53:58,947           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-01T01:53:58,948           License :: OSI Approved :: Apache Software License

2025-06-01T01:53:58,949           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-01T01:53:58,949           ********************************************************************************

2025-06-01T01:53:58,950   !!
2025-06-01T01:53:58,951     self._finalize_license_expression()
2025-06-01T01:53:58,951   running bdist_wheel
2025-06-01T01:53:59,076   running build
2025-06-01T01:53:59,076   running build_py
2025-06-01T01:53:59,105   creating build/lib/reframed
2025-06-01T01:53:59,107   copying reframed/__init__.py -> build/lib/reframed
2025-06-01T01:53:59,109   creating build/lib/tests
2025-06-01T01:53:59,110   copying tests/test_reframed.py -> build/lib/tests
2025-06-01T01:53:59,112   copying tests/__init__.py -> build/lib/tests
2025-06-01T01:53:59,114   copying tests/scip_carveme.py -> build/lib/tests
2025-06-01T01:53:59,117   creating build/lib/reframed/cobra
2025-06-01T01:53:59,118   copying reframed/cobra/ensemble.py -> build/lib/reframed/cobra
2025-06-01T01:53:59,120   copying reframed/cobra/thermodynamics.py -> build/lib/reframed/cobra
2025-06-01T01:53:59,123   copying reframed/cobra/transcriptomics.py -> build/lib/reframed/cobra
2025-06-01T01:53:59,126   copying reframed/cobra/plotting.py -> build/lib/reframed/cobra
2025-06-01T01:53:59,127   copying reframed/cobra/variability.py -> build/lib/reframed/cobra
2025-06-01T01:53:59,129   copying reframed/cobra/__init__.py -> build/lib/reframed/cobra
2025-06-01T01:53:59,131   copying reframed/cobra/simulation.py -> build/lib/reframed/cobra
2025-06-01T01:53:59,133   copying reframed/cobra/medium.py -> build/lib/reframed/cobra
2025-06-01T01:53:59,136   copying reframed/cobra/knockout.py -> build/lib/reframed/cobra
2025-06-01T01:53:59,138   copying reframed/cobra/auxotrophy.py -> build/lib/reframed/cobra
2025-06-01T01:53:59,140   creating build/lib/reframed/solvers
2025-06-01T01:53:59,142   copying reframed/solvers/scip_solver.py -> build/lib/reframed/solvers
2025-06-01T01:53:59,144   copying reframed/solvers/solver.py -> build/lib/reframed/solvers
2025-06-01T01:53:59,146   copying reframed/solvers/__init__.py -> build/lib/reframed/solvers
2025-06-01T01:53:59,148   copying reframed/solvers/cplex_solver.py -> build/lib/reframed/solvers
2025-06-01T01:53:59,151   copying reframed/solvers/solution.py -> build/lib/reframed/solvers
2025-06-01T01:53:59,153   copying reframed/solvers/gurobi_solver.py -> build/lib/reframed/solvers
2025-06-01T01:53:59,156   creating build/lib/reframed/io
2025-06-01T01:53:59,157   copying reframed/io/__init__.py -> build/lib/reframed/io
2025-06-01T01:53:59,159   copying reframed/io/cache.py -> build/lib/reframed/io
2025-06-01T01:53:59,161   copying reframed/io/sbml.py -> build/lib/reframed/io
2025-06-01T01:53:59,164   creating build/lib/reframed/core
2025-06-01T01:53:59,165   copying reframed/core/transformation.py -> build/lib/reframed/core
2025-06-01T01:53:59,168   copying reframed/core/__init__.py -> build/lib/reframed/core
2025-06-01T01:53:59,169   copying reframed/core/model.py -> build/lib/reframed/core
2025-06-01T01:53:59,172   copying reframed/core/cbmodel.py -> build/lib/reframed/core
2025-06-01T01:53:59,174   copying reframed/core/environment.py -> build/lib/reframed/core
2025-06-01T01:53:59,177   copying reframed/core/elements.py -> build/lib/reframed/core
2025-06-01T01:53:59,179   copying reframed/core/parser.py -> build/lib/reframed/core
2025-06-01T01:53:59,181   creating build/lib/reframed/alpha
2025-06-01T01:53:59,182   copying reframed/alpha/fluxutils.py -> build/lib/reframed/alpha
2025-06-01T01:53:59,184   copying reframed/alpha/sampling.py -> build/lib/reframed/alpha
2025-06-01T01:53:59,186   copying reframed/alpha/plotting.py -> build/lib/reframed/alpha
2025-06-01T01:53:59,188   copying reframed/alpha/geneswitch.py -> build/lib/reframed/alpha
2025-06-01T01:53:59,190   copying reframed/alpha/__init__.py -> build/lib/reframed/alpha
2025-06-01T01:53:59,192   copying reframed/alpha/gapMake.py -> build/lib/reframed/alpha
2025-06-01T01:53:59,194   creating build/lib/reframed/external
2025-06-01T01:53:59,195   copying reframed/external/__init__.py -> build/lib/reframed/external
2025-06-01T01:53:59,197   copying reframed/external/cobrapy.py -> build/lib/reframed/external
2025-06-01T01:53:59,199   copying reframed/external/escher.py -> build/lib/reframed/external
2025-06-01T01:53:59,201   creating build/lib/reframed/community
2025-06-01T01:53:59,202   copying reframed/community/SteadyCom.py -> build/lib/reframed/community
2025-06-01T01:53:59,204   copying reframed/community/__init__.py -> build/lib/reframed/community
2025-06-01T01:53:59,205   copying reframed/community/model.py -> build/lib/reframed/community
2025-06-01T01:53:59,207   copying reframed/community/solution.py -> build/lib/reframed/community
2025-06-01T01:53:59,209   running egg_info
2025-06-01T01:53:59,235   writing reframed.egg-info/PKG-INFO
2025-06-01T01:53:59,239   writing dependency_links to reframed.egg-info/dependency_links.txt
2025-06-01T01:53:59,240   writing requirements to reframed.egg-info/requires.txt
2025-06-01T01:53:59,242   writing top-level names to reframed.egg-info/top_level.txt
2025-06-01T01:53:59,279   reading manifest file 'reframed.egg-info/SOURCES.txt'
2025-06-01T01:53:59,284   reading manifest template 'MANIFEST.in'
2025-06-01T01:53:59,285   warning: no files found matching 'CONTRIBUTING.rst'
2025-06-01T01:53:59,285   warning: no files found matching 'HISTORY.rst'
2025-06-01T01:53:59,290   warning: no previously-included files matching '__pycache__' found under directory '*'
2025-06-01T01:53:59,291   warning: no previously-included files matching '*.py[co]' found under directory '*'
2025-06-01T01:53:59,327   warning: no files found matching '*.jpg' under directory 'docs'
2025-06-01T01:53:59,351   warning: no files found matching '*.gif' under directory 'docs'
2025-06-01T01:53:59,352   adding license file 'LICENSE'
2025-06-01T01:53:59,357   writing manifest file 'reframed.egg-info/SOURCES.txt'
2025-06-01T01:53:59,360   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tests.data' is absent from the `packages` configuration.
2025-06-01T01:53:59,361   !!

2025-06-01T01:53:59,362           ********************************************************************************
2025-06-01T01:53:59,362           ############################
2025-06-01T01:53:59,363           # Package would be ignored #
2025-06-01T01:53:59,363           ############################
2025-06-01T01:53:59,364           Python recognizes 'tests.data' as an importable package[^1],
2025-06-01T01:53:59,364           but it is absent from setuptools' `packages` configuration.

2025-06-01T01:53:59,365           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-01T01:53:59,366           package, please make sure that 'tests.data' is explicitly added
2025-06-01T01:53:59,366           to the `packages` configuration field.

2025-06-01T01:53:59,367           Alternatively, you can also rely on setuptools' discovery methods
2025-06-01T01:53:59,368           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-01T01:53:59,368           instead of `find_packages(...)`/`find:`).

2025-06-01T01:53:59,369           You can read more about "package discovery" on setuptools documentation page:

2025-06-01T01:53:59,371           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-01T01:53:59,372           If you don't want 'tests.data' to be distributed and are
2025-06-01T01:53:59,373           already explicitly excluding 'tests.data' via
2025-06-01T01:53:59,373           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-01T01:53:59,374           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-01T01:53:59,375           combination with a more fine grained `package-data` configuration.

2025-06-01T01:53:59,381           You can read more about "package data files" on setuptools documentation page:

2025-06-01T01:53:59,382           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-01T01:53:59,383           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-01T01:53:59,384                 even if it does not contain any `.py` files.
2025-06-01T01:53:59,384                 On the other hand, currently there is no concept of package data
2025-06-01T01:53:59,385                 directory, all directories are treated like packages.
2025-06-01T01:53:59,385           ********************************************************************************

2025-06-01T01:53:59,386   !!
2025-06-01T01:53:59,386     check.warn(importable)
2025-06-01T01:53:59,387   creating build/lib/tests/data
2025-06-01T01:53:59,387   copying tests/data/e_coli_core.xml.gz -> build/lib/tests/data
2025-06-01T01:53:59,388   copying tests/data/iML1515.xml.gz -> build/lib/tests/data
2025-06-01T01:53:59,389   copying tests/data/model_cobra.xml.gz -> build/lib/tests/data
2025-06-01T01:53:59,389   copying tests/data/model_fbc2.xml.gz -> build/lib/tests/data
2025-06-01T01:53:59,419   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-01T01:53:59,420   !!

2025-06-01T01:53:59,421           ********************************************************************************
2025-06-01T01:53:59,421           Please avoid running ``setup.py`` directly.
2025-06-01T01:53:59,422           Instead, use pypa/build, pypa/installer or other
2025-06-01T01:53:59,422           standards-based tools.

2025-06-01T01:53:59,424           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-01T01:53:59,424           or your builds will no longer be supported.

2025-06-01T01:53:59,425           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-01T01:53:59,426           ********************************************************************************

2025-06-01T01:53:59,427   !!
2025-06-01T01:53:59,428     self.initialize_options()
2025-06-01T01:53:59,449   installing to build/bdist.linux-armv7l/wheel
2025-06-01T01:53:59,450   running install
2025-06-01T01:53:59,473   running install_lib
2025-06-01T01:53:59,500   creating build/bdist.linux-armv7l/wheel
2025-06-01T01:53:59,502   creating build/bdist.linux-armv7l/wheel/reframed
2025-06-01T01:53:59,504   creating build/bdist.linux-armv7l/wheel/reframed/cobra
2025-06-01T01:53:59,505   copying build/lib/reframed/cobra/ensemble.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra
2025-06-01T01:53:59,507   copying build/lib/reframed/cobra/thermodynamics.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra
2025-06-01T01:53:59,510   copying build/lib/reframed/cobra/transcriptomics.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra
2025-06-01T01:53:59,512   copying build/lib/reframed/cobra/plotting.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra
2025-06-01T01:53:59,514   copying build/lib/reframed/cobra/variability.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra
2025-06-01T01:53:59,516   copying build/lib/reframed/cobra/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra
2025-06-01T01:53:59,518   copying build/lib/reframed/cobra/simulation.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra
2025-06-01T01:53:59,520   copying build/lib/reframed/cobra/medium.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra
2025-06-01T01:53:59,522   copying build/lib/reframed/cobra/knockout.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra
2025-06-01T01:53:59,525   copying build/lib/reframed/cobra/auxotrophy.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra
2025-06-01T01:53:59,527   creating build/bdist.linux-armv7l/wheel/reframed/solvers
2025-06-01T01:53:59,528   copying build/lib/reframed/solvers/scip_solver.py -> build/bdist.linux-armv7l/wheel/./reframed/solvers
2025-06-01T01:53:59,531   copying build/lib/reframed/solvers/solver.py -> build/bdist.linux-armv7l/wheel/./reframed/solvers
2025-06-01T01:53:59,533   copying build/lib/reframed/solvers/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/solvers
2025-06-01T01:53:59,535   copying build/lib/reframed/solvers/cplex_solver.py -> build/bdist.linux-armv7l/wheel/./reframed/solvers
2025-06-01T01:53:59,537   copying build/lib/reframed/solvers/solution.py -> build/bdist.linux-armv7l/wheel/./reframed/solvers
2025-06-01T01:53:59,539   copying build/lib/reframed/solvers/gurobi_solver.py -> build/bdist.linux-armv7l/wheel/./reframed/solvers
2025-06-01T01:53:59,541   creating build/bdist.linux-armv7l/wheel/reframed/io
2025-06-01T01:53:59,542   copying build/lib/reframed/io/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/io
2025-06-01T01:53:59,544   copying build/lib/reframed/io/cache.py -> build/bdist.linux-armv7l/wheel/./reframed/io
2025-06-01T01:53:59,546   copying build/lib/reframed/io/sbml.py -> build/bdist.linux-armv7l/wheel/./reframed/io
2025-06-01T01:53:59,549   creating build/bdist.linux-armv7l/wheel/reframed/core
2025-06-01T01:53:59,550   copying build/lib/reframed/core/transformation.py -> build/bdist.linux-armv7l/wheel/./reframed/core
2025-06-01T01:53:59,552   copying build/lib/reframed/core/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/core
2025-06-01T01:53:59,554   copying build/lib/reframed/core/model.py -> build/bdist.linux-armv7l/wheel/./reframed/core
2025-06-01T01:53:59,556   copying build/lib/reframed/core/cbmodel.py -> build/bdist.linux-armv7l/wheel/./reframed/core
2025-06-01T01:53:59,558   copying build/lib/reframed/core/environment.py -> build/bdist.linux-armv7l/wheel/./reframed/core
2025-06-01T01:53:59,561   copying build/lib/reframed/core/elements.py -> build/bdist.linux-armv7l/wheel/./reframed/core
2025-06-01T01:53:59,562   copying build/lib/reframed/core/parser.py -> build/bdist.linux-armv7l/wheel/./reframed/core
2025-06-01T01:53:59,564   copying build/lib/reframed/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed
2025-06-01T01:53:59,566   creating build/bdist.linux-armv7l/wheel/reframed/alpha
2025-06-01T01:53:59,567   copying build/lib/reframed/alpha/fluxutils.py -> build/bdist.linux-armv7l/wheel/./reframed/alpha
2025-06-01T01:53:59,570   copying build/lib/reframed/alpha/sampling.py -> build/bdist.linux-armv7l/wheel/./reframed/alpha
2025-06-01T01:53:59,571   copying build/lib/reframed/alpha/plotting.py -> build/bdist.linux-armv7l/wheel/./reframed/alpha
2025-06-01T01:53:59,573   copying build/lib/reframed/alpha/geneswitch.py -> build/bdist.linux-armv7l/wheel/./reframed/alpha
2025-06-01T01:53:59,575   copying build/lib/reframed/alpha/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/alpha
2025-06-01T01:53:59,577   copying build/lib/reframed/alpha/gapMake.py -> build/bdist.linux-armv7l/wheel/./reframed/alpha
2025-06-01T01:53:59,579   creating build/bdist.linux-armv7l/wheel/reframed/external
2025-06-01T01:53:59,580   copying build/lib/reframed/external/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/external
2025-06-01T01:53:59,582   copying build/lib/reframed/external/cobrapy.py -> build/bdist.linux-armv7l/wheel/./reframed/external
2025-06-01T01:53:59,584   copying build/lib/reframed/external/escher.py -> build/bdist.linux-armv7l/wheel/./reframed/external
2025-06-01T01:53:59,586   creating build/bdist.linux-armv7l/wheel/reframed/community
2025-06-01T01:53:59,587   copying build/lib/reframed/community/SteadyCom.py -> build/bdist.linux-armv7l/wheel/./reframed/community
2025-06-01T01:53:59,589   copying build/lib/reframed/community/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/community
2025-06-01T01:53:59,591   copying build/lib/reframed/community/model.py -> build/bdist.linux-armv7l/wheel/./reframed/community
2025-06-01T01:53:59,593   copying build/lib/reframed/community/solution.py -> build/bdist.linux-armv7l/wheel/./reframed/community
2025-06-01T01:53:59,596   creating build/bdist.linux-armv7l/wheel/tests
2025-06-01T01:53:59,597   copying build/lib/tests/test_reframed.py -> build/bdist.linux-armv7l/wheel/./tests
2025-06-01T01:53:59,600   creating build/bdist.linux-armv7l/wheel/tests/data
2025-06-01T01:53:59,601   copying build/lib/tests/data/model_cobra.xml.gz -> build/bdist.linux-armv7l/wheel/./tests/data
2025-06-01T01:53:59,604   copying build/lib/tests/data/model_fbc2.xml.gz -> build/bdist.linux-armv7l/wheel/./tests/data
2025-06-01T01:53:59,608   copying build/lib/tests/data/iML1515.xml.gz -> build/bdist.linux-armv7l/wheel/./tests/data
2025-06-01T01:53:59,619   copying build/lib/tests/data/e_coli_core.xml.gz -> build/bdist.linux-armv7l/wheel/./tests/data
2025-06-01T01:53:59,623   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests
2025-06-01T01:53:59,624   copying build/lib/tests/scip_carveme.py -> build/bdist.linux-armv7l/wheel/./tests
2025-06-01T01:53:59,626   running install_egg_info
2025-06-01T01:53:59,660   Copying reframed.egg-info to build/bdist.linux-armv7l/wheel/./reframed-1.5.4-py3.11.egg-info
2025-06-01T01:53:59,674   running install_scripts
2025-06-01T01:53:59,686   creating build/bdist.linux-armv7l/wheel/reframed-1.5.4.dist-info/WHEEL
2025-06-01T01:53:59,689   creating '/tmp/pip-wheel-x7uuiso7/reframed-1.5.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-01T01:53:59,691   adding 'reframed/__init__.py'
2025-06-01T01:53:59,693   adding 'reframed/alpha/__init__.py'
2025-06-01T01:53:59,694   adding 'reframed/alpha/fluxutils.py'
2025-06-01T01:53:59,695   adding 'reframed/alpha/gapMake.py'
2025-06-01T01:53:59,697   adding 'reframed/alpha/geneswitch.py'
2025-06-01T01:53:59,698   adding 'reframed/alpha/plotting.py'
2025-06-01T01:53:59,700   adding 'reframed/alpha/sampling.py'
2025-06-01T01:53:59,702   adding 'reframed/cobra/__init__.py'
2025-06-01T01:53:59,703   adding 'reframed/cobra/auxotrophy.py'
2025-06-01T01:53:59,704   adding 'reframed/cobra/ensemble.py'
2025-06-01T01:53:59,706   adding 'reframed/cobra/knockout.py'
2025-06-01T01:53:59,707   adding 'reframed/cobra/medium.py'
2025-06-01T01:53:59,709   adding 'reframed/cobra/plotting.py'
2025-06-01T01:53:59,711   adding 'reframed/cobra/simulation.py'
2025-06-01T01:53:59,713   adding 'reframed/cobra/thermodynamics.py'
2025-06-01T01:53:59,715   adding 'reframed/cobra/transcriptomics.py'
2025-06-01T01:53:59,716   adding 'reframed/cobra/variability.py'
2025-06-01T01:53:59,718   adding 'reframed/community/SteadyCom.py'
2025-06-01T01:53:59,938   adding 'reframed/community/__init__.py'
2025-06-01T01:53:59,940   adding 'reframed/community/model.py'
2025-06-01T01:53:59,942   adding 'reframed/community/solution.py'
2025-06-01T01:53:59,943   adding 'reframed/core/__init__.py'
2025-06-01T01:53:59,946   adding 'reframed/core/cbmodel.py'
2025-06-01T01:53:59,947   adding 'reframed/core/elements.py'
2025-06-01T01:53:59,949   adding 'reframed/core/environment.py'
2025-06-01T01:53:59,952   adding 'reframed/core/model.py'
2025-06-01T01:53:59,953   adding 'reframed/core/parser.py'
2025-06-01T01:53:59,956   adding 'reframed/core/transformation.py'
2025-06-01T01:53:59,958   adding 'reframed/external/__init__.py'
2025-06-01T01:53:59,960   adding 'reframed/external/cobrapy.py'
2025-06-01T01:53:59,961   adding 'reframed/external/escher.py'
2025-06-01T01:54:00,179   adding 'reframed/io/__init__.py'
2025-06-01T01:54:00,181   adding 'reframed/io/cache.py'
2025-06-01T01:54:00,190   adding 'reframed/io/sbml.py'
2025-06-01T01:54:00,194   adding 'reframed/solvers/__init__.py'
2025-06-01T01:54:00,197   adding 'reframed/solvers/cplex_solver.py'
2025-06-01T01:54:00,200   adding 'reframed/solvers/gurobi_solver.py'
2025-06-01T01:54:00,204   adding 'reframed/solvers/scip_solver.py'
2025-06-01T01:54:00,207   adding 'reframed/solvers/solution.py'
2025-06-01T01:54:00,210   adding 'reframed/solvers/solver.py'
2025-06-01T01:54:00,215   adding 'reframed-1.5.4.dist-info/licenses/LICENSE'
2025-06-01T01:54:00,218   adding 'tests/__init__.py'
2025-06-01T01:54:00,221   adding 'tests/scip_carveme.py'
2025-06-01T01:54:00,224   adding 'tests/test_reframed.py'
2025-06-01T01:54:00,236   adding 'tests/data/e_coli_core.xml.gz'
2025-06-01T01:54:00,323   adding 'tests/data/iML1515.xml.gz'
2025-06-01T01:54:00,331   adding 'tests/data/model_cobra.xml.gz'
2025-06-01T01:54:00,336   adding 'tests/data/model_fbc2.xml.gz'
2025-06-01T01:54:00,339   adding 'reframed-1.5.4.dist-info/METADATA'
2025-06-01T01:54:00,341   adding 'reframed-1.5.4.dist-info/WHEEL'
2025-06-01T01:54:00,343   adding 'reframed-1.5.4.dist-info/top_level.txt'
2025-06-01T01:54:00,344   adding 'reframed-1.5.4.dist-info/RECORD'
2025-06-01T01:54:00,821   removing build/bdist.linux-armv7l/wheel
2025-06-01T01:54:01,186   Building wheel for reframed (setup.py): finished with status 'done'
2025-06-01T01:54:01,220   Created wheel for reframed: filename=reframed-1.5.4-py3-none-any.whl size=642782 sha256=87c23385a6a40fc08504bf311f2c0fa217f1923c4f363e5de4d3da7e569911d5
2025-06-01T01:54:01,222   Stored in directory: /tmp/pip-ephem-wheel-cache-6x1evf0x/wheels/82/ed/5f/0156e0812317451ef1c2dedff2abd1635c38b69deedbc6985e
2025-06-01T01:54:01,239 Successfully built reframed
2025-06-01T01:54:01,260 Removed build tracker: '/tmp/pip-build-tracker-u2x2xagz'