2025-06-05T11:44:36,721 Created temporary directory: /tmp/pip-build-tracker-x3b8j5z9 2025-06-05T11:44:36,722 Initialized build tracking at /tmp/pip-build-tracker-x3b8j5z9 2025-06-05T11:44:36,722 Created build tracker: /tmp/pip-build-tracker-x3b8j5z9 2025-06-05T11:44:36,723 Entered build tracker: /tmp/pip-build-tracker-x3b8j5z9 2025-06-05T11:44:36,724 Created temporary directory: /tmp/pip-wheel-nt6hnod3 2025-06-05T11:44:36,728 Created temporary directory: /tmp/pip-ephem-wheel-cache-18cfvyc5 2025-06-05T11:44:36,778 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-05T11:44:36,780 2 location(s) to search for versions of reframed: 2025-06-05T11:44:36,780 * https://pypi.org/simple/reframed/ 2025-06-05T11:44:36,780 * https://www.piwheels.org/simple/reframed/ 2025-06-05T11:44:36,781 Fetching project page and analyzing links: https://pypi.org/simple/reframed/ 2025-06-05T11:44:36,782 Getting page https://pypi.org/simple/reframed/ 2025-06-05T11:44:36,783 Found index url https://pypi.org/simple/ 2025-06-05T11:44:37,009 Fetched page https://pypi.org/simple/reframed/ as application/vnd.pypi.simple.v1+json 2025-06-05T11:44:37,018 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) 2025-06-05T11:44:37,021 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 2025-06-05T11:44:37,022 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) 2025-06-05T11:44:37,023 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 2025-06-05T11:44:37,024 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) 2025-06-05T11:44:37,025 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 2025-06-05T11:44:37,027 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) 2025-06-05T11:44:37,028 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 2025-06-05T11:44:37,029 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) 2025-06-05T11:44:37,030 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 2025-06-05T11:44:37,031 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) 2025-06-05T11:44:37,032 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 2025-06-05T11:44:37,032 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) 2025-06-05T11:44:37,033 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 2025-06-05T11:44:37,034 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) 2025-06-05T11:44:37,035 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 2025-06-05T11:44:37,035 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) 2025-06-05T11:44:37,036 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 2025-06-05T11:44:37,036 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) 2025-06-05T11:44:37,037 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 2025-06-05T11:44:37,038 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) 2025-06-05T11:44:37,039 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 2025-06-05T11:44:37,039 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) 2025-06-05T11:44:37,040 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 2025-06-05T11:44:37,040 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) 2025-06-05T11:44:37,041 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 2025-06-05T11:44:37,042 Fetching project page and analyzing links: https://www.piwheels.org/simple/reframed/ 2025-06-05T11:44:37,042 Getting page https://www.piwheels.org/simple/reframed/ 2025-06-05T11:44:37,044 Found index url https://www.piwheels.org/simple/ 2025-06-05T11:44:37,213 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/ 2025-06-05T11:44:37,874 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/ 2025-06-05T11:44:39,047 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/ 2025-06-05T11:44:41,214 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/ 2025-06-05T11:44:45,417 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/ 2025-06-05T11:44:45,586 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 2025-06-05T11:44:45,588 Skipping link: not a file: https://www.piwheels.org/simple/reframed/ 2025-06-05T11:44:45,589 Skipping link: not a file: https://pypi.org/simple/reframed/ 2025-06-05T11:44:45,612 Given no hashes to check 1 links for project 'reframed': discarding no candidates 2025-06-05T11:44:45,614 Collecting reframed==1.6.0 2025-06-05T11:44:45,616 Created temporary directory: /tmp/pip-unpack-cfuazjvk 2025-06-05T11:44:46,069 Downloading reframed-1.6.0.tar.gz (665 kB) 2025-06-05T11:44:46,401 Added reframed==1.6.0 from https://files.pythonhosted.org/packages/3f/91/7f9702e191c5c2d728701cd5ec3b885ad732b2380f6bb11cf46de6f68aed/reframed-1.6.0.tar.gz to build tracker '/tmp/pip-build-tracker-x3b8j5z9' 2025-06-05T11:44:46,403 Running setup.py (path:/tmp/pip-wheel-nt6hnod3/reframed_df870d05f30a4d6bafb4ec32e485ecd6/setup.py) egg_info for package reframed 2025-06-05T11:44:46,404 Created temporary directory: /tmp/pip-pip-egg-info-wiboim0m 2025-06-05T11:44:46,405 Preparing metadata (setup.py): started 2025-06-05T11:44:46,406 Running command python setup.py egg_info 2025-06-05T11:44:47,016 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-06-05T11:44:47,017 warnings.warn(msg) 2025-06-05T11:44:47,017 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-06-05T11:44:47,018 warnings.warn(msg) 2025-06-05T11:44:47,332 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-05T11:44:47,333 !! 2025-06-05T11:44:47,334 ******************************************************************************** 2025-06-05T11:44:47,335 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-05T11:44:47,337 License :: OSI Approved :: Apache Software License 2025-06-05T11:44:47,338 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-05T11:44:47,339 ******************************************************************************** 2025-06-05T11:44:47,340 !! 2025-06-05T11:44:47,340 self._finalize_license_expression() 2025-06-05T11:44:47,364 running egg_info 2025-06-05T11:44:47,395 creating /tmp/pip-pip-egg-info-wiboim0m/reframed.egg-info 2025-06-05T11:44:47,396 writing /tmp/pip-pip-egg-info-wiboim0m/reframed.egg-info/PKG-INFO 2025-06-05T11:44:47,400 writing dependency_links to /tmp/pip-pip-egg-info-wiboim0m/reframed.egg-info/dependency_links.txt 2025-06-05T11:44:47,401 writing entry points to /tmp/pip-pip-egg-info-wiboim0m/reframed.egg-info/entry_points.txt 2025-06-05T11:44:47,403 writing requirements to /tmp/pip-pip-egg-info-wiboim0m/reframed.egg-info/requires.txt 2025-06-05T11:44:47,404 writing top-level names to /tmp/pip-pip-egg-info-wiboim0m/reframed.egg-info/top_level.txt 2025-06-05T11:44:47,406 writing manifest file '/tmp/pip-pip-egg-info-wiboim0m/reframed.egg-info/SOURCES.txt' 2025-06-05T11:44:47,510 reading manifest file '/tmp/pip-pip-egg-info-wiboim0m/reframed.egg-info/SOURCES.txt' 2025-06-05T11:44:47,512 reading manifest template 'MANIFEST.in' 2025-06-05T11:44:47,513 warning: no files found matching 'CONTRIBUTING.rst' 2025-06-05T11:44:47,514 warning: no files found matching 'HISTORY.rst' 2025-06-05T11:44:47,519 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-06-05T11:44:47,519 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-06-05T11:44:47,561 warning: no files found matching '*.jpg' under directory 'docs' 2025-06-05T11:44:47,583 warning: no files found matching '*.gif' under directory 'docs' 2025-06-05T11:44:47,584 adding license file 'LICENSE' 2025-06-05T11:44:47,589 writing manifest file '/tmp/pip-pip-egg-info-wiboim0m/reframed.egg-info/SOURCES.txt' 2025-06-05T11:44:47,697 Preparing metadata (setup.py): finished with status 'done' 2025-06-05T11:44:47,701 Source in /tmp/pip-wheel-nt6hnod3/reframed_df870d05f30a4d6bafb4ec32e485ecd6 has version 1.6.0, which satisfies requirement reframed==1.6.0 from https://files.pythonhosted.org/packages/3f/91/7f9702e191c5c2d728701cd5ec3b885ad732b2380f6bb11cf46de6f68aed/reframed-1.6.0.tar.gz 2025-06-05T11:44:47,702 Removed reframed==1.6.0 from https://files.pythonhosted.org/packages/3f/91/7f9702e191c5c2d728701cd5ec3b885ad732b2380f6bb11cf46de6f68aed/reframed-1.6.0.tar.gz from build tracker '/tmp/pip-build-tracker-x3b8j5z9' 2025-06-05T11:44:47,709 Created temporary directory: /tmp/pip-unpack-cbrhfoz7 2025-06-05T11:44:47,710 Created temporary directory: /tmp/pip-unpack-tykfvmbt 2025-06-05T11:44:47,711 Building wheels for collected packages: reframed 2025-06-05T11:44:47,715 Created temporary directory: /tmp/pip-wheel-8ihlw1w1 2025-06-05T11:44:47,716 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 2025-06-05T11:44:47,718 Building wheel for reframed (setup.py): started 2025-06-05T11:44:47,719 Destination directory: /tmp/pip-wheel-8ihlw1w1 2025-06-05T11:44:47,720 Running command python setup.py bdist_wheel 2025-06-05T11:44:48,281 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-06-05T11:44:48,281 warnings.warn(msg) 2025-06-05T11:44:48,282 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-06-05T11:44:48,282 warnings.warn(msg) 2025-06-05T11:44:48,585 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-05T11:44:48,585 !! 2025-06-05T11:44:48,587 ******************************************************************************** 2025-06-05T11:44:48,587 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-05T11:44:48,588 License :: OSI Approved :: Apache Software License 2025-06-05T11:44:48,589 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-05T11:44:48,590 ******************************************************************************** 2025-06-05T11:44:48,591 !! 2025-06-05T11:44:48,591 self._finalize_license_expression() 2025-06-05T11:44:48,592 running bdist_wheel 2025-06-05T11:44:48,727 running build 2025-06-05T11:44:48,728 running build_py 2025-06-05T11:44:48,759 creating build/lib/reframed 2025-06-05T11:44:48,761 copying reframed/__init__.py -> build/lib/reframed 2025-06-05T11:44:48,764 creating build/lib/tests 2025-06-05T11:44:48,765 copying tests/scip_carveme.py -> build/lib/tests 2025-06-05T11:44:48,767 copying tests/__init__.py -> build/lib/tests 2025-06-05T11:44:48,769 copying tests/test_reframed.py -> build/lib/tests 2025-06-05T11:44:48,772 creating build/lib/reframed/external 2025-06-05T11:44:48,773 copying reframed/external/cobrapy.py -> build/lib/reframed/external 2025-06-05T11:44:48,775 copying reframed/external/escher.py -> build/lib/reframed/external 2025-06-05T11:44:48,777 copying reframed/external/__init__.py -> build/lib/reframed/external 2025-06-05T11:44:48,779 creating build/lib/reframed/cobra 2025-06-05T11:44:48,780 copying reframed/cobra/auxotrophy.py -> build/lib/reframed/cobra 2025-06-05T11:44:48,783 copying reframed/cobra/thermodynamics.py -> build/lib/reframed/cobra 2025-06-05T11:44:48,786 copying reframed/cobra/variability.py -> build/lib/reframed/cobra 2025-06-05T11:44:48,789 copying reframed/cobra/knockout.py -> build/lib/reframed/cobra 2025-06-05T11:44:48,792 copying reframed/cobra/ensemble.py -> build/lib/reframed/cobra 2025-06-05T11:44:48,794 copying reframed/cobra/plotting.py -> build/lib/reframed/cobra 2025-06-05T11:44:48,796 copying reframed/cobra/transcriptomics.py -> build/lib/reframed/cobra 2025-06-05T11:44:48,799 copying reframed/cobra/__init__.py -> build/lib/reframed/cobra 2025-06-05T11:44:48,801 copying reframed/cobra/medium.py -> build/lib/reframed/cobra 2025-06-05T11:44:48,804 copying reframed/cobra/simulation.py -> build/lib/reframed/cobra 2025-06-05T11:44:48,808 creating build/lib/reframed/alpha 2025-06-05T11:44:48,809 copying reframed/alpha/fluxutils.py -> build/lib/reframed/alpha 2025-06-05T11:44:48,811 copying reframed/alpha/sampling.py -> build/lib/reframed/alpha 2025-06-05T11:44:48,813 copying reframed/alpha/plotting.py -> build/lib/reframed/alpha 2025-06-05T11:44:48,815 copying reframed/alpha/__init__.py -> build/lib/reframed/alpha 2025-06-05T11:44:48,817 copying reframed/alpha/gapMake.py -> build/lib/reframed/alpha 2025-06-05T11:44:48,820 copying reframed/alpha/geneswitch.py -> build/lib/reframed/alpha 2025-06-05T11:44:48,823 creating build/lib/reframed/community 2025-06-05T11:44:48,824 copying reframed/community/SteadyCom.py -> build/lib/reframed/community 2025-06-05T11:44:48,826 copying reframed/community/__init__.py -> build/lib/reframed/community 2025-06-05T11:44:48,828 copying reframed/community/model.py -> build/lib/reframed/community 2025-06-05T11:44:48,831 copying reframed/community/solution.py -> build/lib/reframed/community 2025-06-05T11:44:48,834 creating build/lib/reframed/cli 2025-06-05T11:44:48,835 copying reframed/cli/__init__.py -> build/lib/reframed/cli 2025-06-05T11:44:48,838 copying reframed/cli/cli.py -> build/lib/reframed/cli 2025-06-05T11:44:48,841 creating build/lib/reframed/core 2025-06-05T11:44:48,842 copying reframed/core/environment.py -> build/lib/reframed/core 2025-06-05T11:44:48,845 copying reframed/core/cbmodel.py -> build/lib/reframed/core 2025-06-05T11:44:48,848 copying reframed/core/transformation.py -> build/lib/reframed/core 2025-06-05T11:44:48,851 copying reframed/core/__init__.py -> build/lib/reframed/core 2025-06-05T11:44:48,853 copying reframed/core/elements.py -> build/lib/reframed/core 2025-06-05T11:44:48,855 copying reframed/core/model.py -> build/lib/reframed/core 2025-06-05T11:44:48,858 copying reframed/core/parser.py -> build/lib/reframed/core 2025-06-05T11:44:48,861 creating build/lib/reframed/io 2025-06-05T11:44:48,862 copying reframed/io/cache.py -> build/lib/reframed/io 2025-06-05T11:44:48,864 copying reframed/io/sbml.py -> build/lib/reframed/io 2025-06-05T11:44:48,868 copying reframed/io/__init__.py -> build/lib/reframed/io 2025-06-05T11:44:48,870 creating build/lib/reframed/solvers 2025-06-05T11:44:48,871 copying reframed/solvers/solver.py -> build/lib/reframed/solvers 2025-06-05T11:44:48,874 copying reframed/solvers/cplex_solver.py -> build/lib/reframed/solvers 2025-06-05T11:44:48,877 copying reframed/solvers/scip_solver.py -> build/lib/reframed/solvers 2025-06-05T11:44:48,880 copying reframed/solvers/__init__.py -> build/lib/reframed/solvers 2025-06-05T11:44:48,882 copying reframed/solvers/gurobi_solver.py -> build/lib/reframed/solvers 2025-06-05T11:44:48,885 copying reframed/solvers/solution.py -> build/lib/reframed/solvers 2025-06-05T11:44:48,887 running egg_info 2025-06-05T11:44:48,919 writing reframed.egg-info/PKG-INFO 2025-06-05T11:44:48,923 writing dependency_links to reframed.egg-info/dependency_links.txt 2025-06-05T11:44:48,925 writing entry points to reframed.egg-info/entry_points.txt 2025-06-05T11:44:48,926 writing requirements to reframed.egg-info/requires.txt 2025-06-05T11:44:48,927 writing top-level names to reframed.egg-info/top_level.txt 2025-06-05T11:44:48,969 reading manifest file 'reframed.egg-info/SOURCES.txt' 2025-06-05T11:44:48,976 reading manifest template 'MANIFEST.in' 2025-06-05T11:44:48,976 warning: no files found matching 'CONTRIBUTING.rst' 2025-06-05T11:44:48,977 warning: no files found matching 'HISTORY.rst' 2025-06-05T11:44:48,982 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-06-05T11:44:48,983 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-06-05T11:44:49,022 warning: no files found matching '*.jpg' under directory 'docs' 2025-06-05T11:44:49,044 warning: no files found matching '*.gif' under directory 'docs' 2025-06-05T11:44:49,045 adding license file 'LICENSE' 2025-06-05T11:44:49,052 writing manifest file 'reframed.egg-info/SOURCES.txt' 2025-06-05T11:44:49,056 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tests.data' is absent from the `packages` configuration. 2025-06-05T11:44:49,056 !! 2025-06-05T11:44:49,058 ******************************************************************************** 2025-06-05T11:44:49,058 ############################ 2025-06-05T11:44:49,059 # Package would be ignored # 2025-06-05T11:44:49,060 ############################ 2025-06-05T11:44:49,060 Python recognizes 'tests.data' as an importable package[^1], 2025-06-05T11:44:49,061 but it is absent from setuptools' `packages` configuration. 2025-06-05T11:44:49,062 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-05T11:44:49,063 package, please make sure that 'tests.data' is explicitly added 2025-06-05T11:44:49,063 to the `packages` configuration field. 2025-06-05T11:44:49,065 Alternatively, you can also rely on setuptools' discovery methods 2025-06-05T11:44:49,065 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-05T11:44:49,066 instead of `find_packages(...)`/`find:`). 2025-06-05T11:44:49,067 You can read more about "package discovery" on setuptools documentation page: 2025-06-05T11:44:49,068 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-05T11:44:49,070 If you don't want 'tests.data' to be distributed and are 2025-06-05T11:44:49,070 already explicitly excluding 'tests.data' via 2025-06-05T11:44:49,071 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-05T11:44:49,071 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-05T11:44:49,072 combination with a more fine grained `package-data` configuration. 2025-06-05T11:44:49,073 You can read more about "package data files" on setuptools documentation page: 2025-06-05T11:44:49,074 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-05T11:44:49,075 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-05T11:44:49,076 even if it does not contain any `.py` files. 2025-06-05T11:44:49,076 On the other hand, currently there is no concept of package data 2025-06-05T11:44:49,077 directory, all directories are treated like packages. 2025-06-05T11:44:49,078 ******************************************************************************** 2025-06-05T11:44:49,079 !! 2025-06-05T11:44:49,080 check.warn(importable) 2025-06-05T11:44:49,080 creating build/lib/tests/data 2025-06-05T11:44:49,081 copying tests/data/e_coli_core.xml.gz -> build/lib/tests/data 2025-06-05T11:44:49,082 copying tests/data/iML1515.xml.gz -> build/lib/tests/data 2025-06-05T11:44:49,087 copying tests/data/model_cobra.xml.gz -> build/lib/tests/data 2025-06-05T11:44:49,091 copying tests/data/model_fbc2.xml.gz -> build/lib/tests/data 2025-06-05T11:44:49,128 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-05T11:44:49,129 !! 2025-06-05T11:44:49,130 ******************************************************************************** 2025-06-05T11:44:49,130 Please avoid running ``setup.py`` directly. 2025-06-05T11:44:49,131 Instead, use pypa/build, pypa/installer or other 2025-06-05T11:44:49,132 standards-based tools. 2025-06-05T11:44:49,133 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-05T11:44:49,133 or your builds will no longer be supported. 2025-06-05T11:44:49,135 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-05T11:44:49,135 ******************************************************************************** 2025-06-05T11:44:49,136 !! 2025-06-05T11:44:49,137 self.initialize_options() 2025-06-05T11:44:49,157 installing to build/bdist.linux-armv7l/wheel 2025-06-05T11:44:49,158 running install 2025-06-05T11:44:49,184 running install_lib 2025-06-05T11:44:49,212 creating build/bdist.linux-armv7l/wheel 2025-06-05T11:44:49,214 creating build/bdist.linux-armv7l/wheel/reframed 2025-06-05T11:44:49,216 creating build/bdist.linux-armv7l/wheel/reframed/external 2025-06-05T11:44:49,217 copying build/lib/reframed/external/cobrapy.py -> build/bdist.linux-armv7l/wheel/./reframed/external 2025-06-05T11:44:49,219 copying build/lib/reframed/external/escher.py -> build/bdist.linux-armv7l/wheel/./reframed/external 2025-06-05T11:44:49,221 copying build/lib/reframed/external/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/external 2025-06-05T11:44:49,223 creating build/bdist.linux-armv7l/wheel/reframed/cobra 2025-06-05T11:44:49,225 copying build/lib/reframed/cobra/auxotrophy.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra 2025-06-05T11:44:49,227 copying build/lib/reframed/cobra/thermodynamics.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra 2025-06-05T11:44:49,229 copying build/lib/reframed/cobra/variability.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra 2025-06-05T11:44:49,232 copying build/lib/reframed/cobra/knockout.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra 2025-06-05T11:44:49,234 copying build/lib/reframed/cobra/ensemble.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra 2025-06-05T11:44:49,237 copying build/lib/reframed/cobra/plotting.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra 2025-06-05T11:44:49,239 copying build/lib/reframed/cobra/transcriptomics.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra 2025-06-05T11:44:49,242 copying build/lib/reframed/cobra/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra 2025-06-05T11:44:49,244 copying build/lib/reframed/cobra/medium.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra 2025-06-05T11:44:49,246 copying build/lib/reframed/cobra/simulation.py -> build/bdist.linux-armv7l/wheel/./reframed/cobra 2025-06-05T11:44:49,250 creating build/bdist.linux-armv7l/wheel/reframed/alpha 2025-06-05T11:44:49,251 copying build/lib/reframed/alpha/fluxutils.py -> build/bdist.linux-armv7l/wheel/./reframed/alpha 2025-06-05T11:44:49,253 copying build/lib/reframed/alpha/sampling.py -> build/bdist.linux-armv7l/wheel/./reframed/alpha 2025-06-05T11:44:49,256 copying build/lib/reframed/alpha/plotting.py -> build/bdist.linux-armv7l/wheel/./reframed/alpha 2025-06-05T11:44:49,258 copying build/lib/reframed/alpha/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/alpha 2025-06-05T11:44:49,260 copying build/lib/reframed/alpha/gapMake.py -> build/bdist.linux-armv7l/wheel/./reframed/alpha 2025-06-05T11:44:49,262 copying build/lib/reframed/alpha/geneswitch.py -> build/bdist.linux-armv7l/wheel/./reframed/alpha 2025-06-05T11:44:49,265 creating build/bdist.linux-armv7l/wheel/reframed/community 2025-06-05T11:44:49,266 copying build/lib/reframed/community/SteadyCom.py -> build/bdist.linux-armv7l/wheel/./reframed/community 2025-06-05T11:44:49,269 copying build/lib/reframed/community/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/community 2025-06-05T11:44:49,271 copying build/lib/reframed/community/model.py -> build/bdist.linux-armv7l/wheel/./reframed/community 2025-06-05T11:44:49,274 copying build/lib/reframed/community/solution.py -> build/bdist.linux-armv7l/wheel/./reframed/community 2025-06-05T11:44:49,277 creating build/bdist.linux-armv7l/wheel/reframed/cli 2025-06-05T11:44:49,278 copying build/lib/reframed/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/cli 2025-06-05T11:44:49,280 copying build/lib/reframed/cli/cli.py -> build/bdist.linux-armv7l/wheel/./reframed/cli 2025-06-05T11:44:49,284 creating build/bdist.linux-armv7l/wheel/reframed/core 2025-06-05T11:44:49,285 copying build/lib/reframed/core/environment.py -> build/bdist.linux-armv7l/wheel/./reframed/core 2025-06-05T11:44:49,288 copying build/lib/reframed/core/cbmodel.py -> build/bdist.linux-armv7l/wheel/./reframed/core 2025-06-05T11:44:49,291 copying build/lib/reframed/core/transformation.py -> build/bdist.linux-armv7l/wheel/./reframed/core 2025-06-05T11:44:49,294 copying build/lib/reframed/core/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/core 2025-06-05T11:44:49,296 copying build/lib/reframed/core/elements.py -> build/bdist.linux-armv7l/wheel/./reframed/core 2025-06-05T11:44:49,298 copying build/lib/reframed/core/model.py -> build/bdist.linux-armv7l/wheel/./reframed/core 2025-06-05T11:44:49,301 copying build/lib/reframed/core/parser.py -> build/bdist.linux-armv7l/wheel/./reframed/core 2025-06-05T11:44:49,304 copying build/lib/reframed/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed 2025-06-05T11:44:49,306 creating build/bdist.linux-armv7l/wheel/reframed/io 2025-06-05T11:44:49,308 copying build/lib/reframed/io/cache.py -> build/bdist.linux-armv7l/wheel/./reframed/io 2025-06-05T11:44:49,310 copying build/lib/reframed/io/sbml.py -> build/bdist.linux-armv7l/wheel/./reframed/io 2025-06-05T11:44:49,314 copying build/lib/reframed/io/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/io 2025-06-05T11:44:49,316 creating build/bdist.linux-armv7l/wheel/reframed/solvers 2025-06-05T11:44:49,318 copying build/lib/reframed/solvers/solver.py -> build/bdist.linux-armv7l/wheel/./reframed/solvers 2025-06-05T11:44:49,321 copying build/lib/reframed/solvers/cplex_solver.py -> build/bdist.linux-armv7l/wheel/./reframed/solvers 2025-06-05T11:44:49,324 copying build/lib/reframed/solvers/scip_solver.py -> build/bdist.linux-armv7l/wheel/./reframed/solvers 2025-06-05T11:44:49,327 copying build/lib/reframed/solvers/__init__.py -> build/bdist.linux-armv7l/wheel/./reframed/solvers 2025-06-05T11:44:49,329 copying build/lib/reframed/solvers/gurobi_solver.py -> build/bdist.linux-armv7l/wheel/./reframed/solvers 2025-06-05T11:44:49,332 copying build/lib/reframed/solvers/solution.py -> build/bdist.linux-armv7l/wheel/./reframed/solvers 2025-06-05T11:44:49,335 creating build/bdist.linux-armv7l/wheel/tests 2025-06-05T11:44:49,337 copying build/lib/tests/scip_carveme.py -> build/bdist.linux-armv7l/wheel/./tests 2025-06-05T11:44:49,339 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2025-06-05T11:44:49,341 copying build/lib/tests/test_reframed.py -> build/bdist.linux-armv7l/wheel/./tests 2025-06-05T11:44:49,345 creating build/bdist.linux-armv7l/wheel/tests/data 2025-06-05T11:44:49,346 copying build/lib/tests/data/model_fbc2.xml.gz -> build/bdist.linux-armv7l/wheel/./tests/data 2025-06-05T11:44:49,350 copying build/lib/tests/data/iML1515.xml.gz -> build/bdist.linux-armv7l/wheel/./tests/data 2025-06-05T11:44:49,364 copying build/lib/tests/data/e_coli_core.xml.gz -> build/bdist.linux-armv7l/wheel/./tests/data 2025-06-05T11:44:49,367 copying build/lib/tests/data/model_cobra.xml.gz -> build/bdist.linux-armv7l/wheel/./tests/data 2025-06-05T11:44:49,370 running install_egg_info 2025-06-05T11:44:49,411 Copying reframed.egg-info to build/bdist.linux-armv7l/wheel/./reframed-1.6.0-py3.11.egg-info 2025-06-05T11:44:49,426 running install_scripts 2025-06-05T11:44:49,443 creating build/bdist.linux-armv7l/wheel/reframed-1.6.0.dist-info/WHEEL 2025-06-05T11:44:49,446 creating '/tmp/pip-wheel-8ihlw1w1/reframed-1.6.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-05T11:44:49,449 adding 'reframed/__init__.py' 2025-06-05T11:44:49,451 adding 'reframed/alpha/__init__.py' 2025-06-05T11:44:49,453 adding 'reframed/alpha/fluxutils.py' 2025-06-05T11:44:49,455 adding 'reframed/alpha/gapMake.py' 2025-06-05T11:44:49,457 adding 'reframed/alpha/geneswitch.py' 2025-06-05T11:44:49,458 adding 'reframed/alpha/plotting.py' 2025-06-05T11:44:49,460 adding 'reframed/alpha/sampling.py' 2025-06-05T11:44:49,462 adding 'reframed/cli/__init__.py' 2025-06-05T11:44:49,464 adding 'reframed/cli/cli.py' 2025-06-05T11:44:49,466 adding 'reframed/cobra/__init__.py' 2025-06-05T11:44:49,468 adding 'reframed/cobra/auxotrophy.py' 2025-06-05T11:44:49,469 adding 'reframed/cobra/ensemble.py' 2025-06-05T11:44:49,471 adding 'reframed/cobra/knockout.py' 2025-06-05T11:44:49,473 adding 'reframed/cobra/medium.py' 2025-06-05T11:44:49,474 adding 'reframed/cobra/plotting.py' 2025-06-05T11:44:49,477 adding 'reframed/cobra/simulation.py' 2025-06-05T11:44:49,479 adding 'reframed/cobra/thermodynamics.py' 2025-06-05T11:44:49,481 adding 'reframed/cobra/transcriptomics.py' 2025-06-05T11:44:49,483 adding 'reframed/cobra/variability.py' 2025-06-05T11:44:49,485 adding 'reframed/community/SteadyCom.py' 2025-06-05T11:44:49,486 adding 'reframed/community/__init__.py' 2025-06-05T11:44:49,488 adding 'reframed/community/model.py' 2025-06-05T11:44:49,489 adding 'reframed/community/solution.py' 2025-06-05T11:44:49,491 adding 'reframed/core/__init__.py' 2025-06-05T11:44:49,494 adding 'reframed/core/cbmodel.py' 2025-06-05T11:44:49,495 adding 'reframed/core/elements.py' 2025-06-05T11:44:49,497 adding 'reframed/core/environment.py' 2025-06-05T11:44:49,500 adding 'reframed/core/model.py' 2025-06-05T11:44:49,501 adding 'reframed/core/parser.py' 2025-06-05T11:44:49,504 adding 'reframed/core/transformation.py' 2025-06-05T11:44:49,506 adding 'reframed/external/__init__.py' 2025-06-05T11:44:49,507 adding 'reframed/external/cobrapy.py' 2025-06-05T11:44:49,508 adding 'reframed/external/escher.py' 2025-06-05T11:44:49,510 adding 'reframed/io/__init__.py' 2025-06-05T11:44:49,511 adding 'reframed/io/cache.py' 2025-06-05T11:44:49,516 adding 'reframed/io/sbml.py' 2025-06-05T11:44:49,518 adding 'reframed/solvers/__init__.py' 2025-06-05T11:44:49,520 adding 'reframed/solvers/cplex_solver.py' 2025-06-05T11:44:49,521 adding 'reframed/solvers/gurobi_solver.py' 2025-06-05T11:44:49,524 adding 'reframed/solvers/scip_solver.py' 2025-06-05T11:44:49,526 adding 'reframed/solvers/solution.py' 2025-06-05T11:44:49,527 adding 'reframed/solvers/solver.py' 2025-06-05T11:44:49,530 adding 'reframed-1.6.0.dist-info/licenses/LICENSE' 2025-06-05T11:44:49,532 adding 'tests/__init__.py' 2025-06-05T11:44:49,533 adding 'tests/scip_carveme.py' 2025-06-05T11:44:49,534 adding 'tests/test_reframed.py' 2025-06-05T11:44:49,540 adding 'tests/data/e_coli_core.xml.gz' 2025-06-05T11:44:49,597 adding 'tests/data/iML1515.xml.gz' 2025-06-05T11:44:49,603 adding 'tests/data/model_cobra.xml.gz' 2025-06-05T11:44:49,607 adding 'tests/data/model_fbc2.xml.gz' 2025-06-05T11:44:49,609 adding 'reframed-1.6.0.dist-info/METADATA' 2025-06-05T11:44:49,610 adding 'reframed-1.6.0.dist-info/WHEEL' 2025-06-05T11:44:49,611 adding 'reframed-1.6.0.dist-info/entry_points.txt' 2025-06-05T11:44:49,612 adding 'reframed-1.6.0.dist-info/top_level.txt' 2025-06-05T11:44:49,613 adding 'reframed-1.6.0.dist-info/RECORD' 2025-06-05T11:44:49,623 removing build/bdist.linux-armv7l/wheel 2025-06-05T11:44:49,753 Building wheel for reframed (setup.py): finished with status 'done' 2025-06-05T11:44:49,762 Created wheel for reframed: filename=reframed-1.6.0-py3-none-any.whl size=646152 sha256=217c5748266f23c281c8f31293555abdbef614b8033b4e8fd567af5c482e6670 2025-06-05T11:44:49,763 Stored in directory: /tmp/pip-ephem-wheel-cache-18cfvyc5/wheels/4d/09/65/99a88a9fb94c964c2709c186302a1deaaaa25e6ced5ed40a39 2025-06-05T11:44:49,777 Successfully built reframed 2025-06-05T11:44:49,801 Removed build tracker: '/tmp/pip-build-tracker-x3b8j5z9'