2026-04-04T23:57:10,733 Created temporary directory: /tmp/pip-ephem-wheel-cache-hc5tsm18 2026-04-04T23:57:10,735 Created temporary directory: /tmp/pip-build-tracker-z0l2lfc1 2026-04-04T23:57:10,736 Initialized build tracking at /tmp/pip-build-tracker-z0l2lfc1 2026-04-04T23:57:10,737 Created build tracker: /tmp/pip-build-tracker-z0l2lfc1 2026-04-04T23:57:10,737 Entered build tracker: /tmp/pip-build-tracker-z0l2lfc1 2026-04-04T23:57:10,738 Created temporary directory: /tmp/pip-wheel-2zhtf3a2 2026-04-04T23:57:10,741 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-04-04T23:57:10,744 Created temporary directory: /tmp/pip-ephem-wheel-cache-nobu0zr8 2026-04-04T23:57:10,767 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-04T23:57:10,771 2 location(s) to search for versions of pirlygenes: 2026-04-04T23:57:10,771 * https://pypi.org/simple/pirlygenes/ 2026-04-04T23:57:10,771 * https://www.piwheels.org/simple/pirlygenes/ 2026-04-04T23:57:10,772 Fetching project page and analyzing links: https://pypi.org/simple/pirlygenes/ 2026-04-04T23:57:10,773 Getting page https://pypi.org/simple/pirlygenes/ 2026-04-04T23:57:10,774 Found index url https://pypi.org/simple 2026-04-04T23:57:11,000 Fetched page https://pypi.org/simple/pirlygenes/ as application/vnd.pypi.simple.v1+json 2026-04-04T23:57:11,003 Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/2e/66/a994711ece0c32dc4037b2c20acb069375f8eb2c80bdcca3a9efa47fdaee/pirlygenes-1.7.0-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9) 2026-04-04T23:57:11,004 Found link https://files.pythonhosted.org/packages/17/fe/bcdacc3535105e4aed789ffd67937b0a725f5eaf16e19e2d70d7d9994985/pirlygenes-1.7.0.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 1.7.0 2026-04-04T23:57:11,005 Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/59/b0/3e2df98a4c7e570e430d5a43b78c4325669dc94f670df919535730ad97e4/pirlygenes-1.8.0-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9) 2026-04-04T23:57:11,006 Found link https://files.pythonhosted.org/packages/4b/7c/57808dd823cb43e0775fef54e28607a61d6e34549ef6c21f02e85567e13a/pirlygenes-1.8.0.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 1.8.0 2026-04-04T23:57:11,006 Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/9a/8d/f18f1d145c3cc415d28137493c5cb8e758516d9ac9633fc74cb4f86a318a/pirlygenes-1.8.1-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9) 2026-04-04T23:57:11,007 Found link https://files.pythonhosted.org/packages/61/0c/c3f0aff27c3758ba3f3ee1f4a63a05238e02043251af230032d9ba555624/pirlygenes-1.8.1.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 1.8.1 2026-04-04T23:57:11,008 Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/24/35/2c1111a823202625bf5719038d745faaa60ed3613bc790db7a365d0d9e91/pirlygenes-1.9.0-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9) 2026-04-04T23:57:11,009 Found link https://files.pythonhosted.org/packages/00/21/33762d0e1497cb8f52920f8804591991b077145275a9bb472d54cb34bd3b/pirlygenes-1.9.0.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 1.9.0 2026-04-04T23:57:11,010 Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/da/14/c0e64534396352276e63b247458c9b5db4f43c4d36ecba3f447203f1bed8/pirlygenes-2.0.0-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9) 2026-04-04T23:57:11,011 Found link https://files.pythonhosted.org/packages/1a/15/da113c10028ce6cef9359672f0d6309ef13174410f74bd641ab56fe968e1/pirlygenes-2.0.0.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 2.0.0 2026-04-04T23:57:11,012 Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/ef/67/1ca24d76bbfbb8547103f0c887d0215b8689b9d68ca03b8e63245446d85f/pirlygenes-2.0.1-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9) 2026-04-04T23:57:11,013 Found link https://files.pythonhosted.org/packages/f0/57/519f98c3e3ce7414973c34a35b56e0123e63c2397c1c28a40f52096110e8/pirlygenes-2.0.1.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 2.0.1 2026-04-04T23:57:11,014 Fetching project page and analyzing links: https://www.piwheels.org/simple/pirlygenes/ 2026-04-04T23:57:11,014 Getting page https://www.piwheels.org/simple/pirlygenes/ 2026-04-04T23:57:11,015 Found index url https://www.piwheels.org/simple 2026-04-04T23:57:11,186 Fetched page https://www.piwheels.org/simple/pirlygenes/ as text/html 2026-04-04T23:57:11,188 Skipping link: No binaries permitted for pirlygenes: https://www.piwheels.org/simple/pirlygenes/pirlygenes-1.9.0-py3-none-any.whl#sha256=3be90370a11cc9b33de80e02b84f99700133addc5994e35bcb8b80b76f09f8ae (from https://www.piwheels.org/simple/pirlygenes/) (requires-python:>=3.9) 2026-04-04T23:57:11,189 Skipping link: No binaries permitted for pirlygenes: https://www.piwheels.org/simple/pirlygenes/pirlygenes-1.8.1-py3-none-any.whl#sha256=35f8427ceac3714bb6339609b7f3602ea81ea8b5642c4e760931e9a28263a28b (from https://www.piwheels.org/simple/pirlygenes/) (requires-python:>=3.9) 2026-04-04T23:57:11,189 Skipping link: No binaries permitted for pirlygenes: https://www.piwheels.org/simple/pirlygenes/pirlygenes-1.8.0-py3-none-any.whl#sha256=202a232caf63d7ad6c6d202e8d8c6c3f52bb57aa7bd124b14be89597a4637f02 (from https://www.piwheels.org/simple/pirlygenes/) (requires-python:>=3.9) 2026-04-04T23:57:11,190 Skipping link: No binaries permitted for pirlygenes: https://www.piwheels.org/simple/pirlygenes/pirlygenes-1.7.0-py3-none-any.whl#sha256=01a45cdf8948ae1d8a8034363ecd9357088d1df4c99ffb9370f8d68432ff4fa7 (from https://www.piwheels.org/simple/pirlygenes/) (requires-python:>=3.9) 2026-04-04T23:57:11,191 Skipping link: not a file: https://www.piwheels.org/simple/pirlygenes/ 2026-04-04T23:57:11,192 Skipping link: not a file: https://pypi.org/simple/pirlygenes/ 2026-04-04T23:57:11,213 Given no hashes to check 1 links for project 'pirlygenes': discarding no candidates 2026-04-04T23:57:11,232 Collecting pirlygenes==2.0.1 2026-04-04T23:57:11,235 Created temporary directory: /tmp/pip-unpack-8v1sm_4p 2026-04-04T23:57:11,461 Downloading pirlygenes-2.0.1.tar.gz (667 kB) 2026-04-04T23:57:11,761 Added pirlygenes==2.0.1 from https://files.pythonhosted.org/packages/f0/57/519f98c3e3ce7414973c34a35b56e0123e63c2397c1c28a40f52096110e8/pirlygenes-2.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-z0l2lfc1' 2026-04-04T23:57:11,767 Created temporary directory: /tmp/pip-build-env-e9iete1d 2026-04-04T23:57:11,771 Installing build dependencies: started 2026-04-04T23:57:11,773 Running command pip subprocess to install build dependencies 2026-04-04T23:57:12,922 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-04T23:57:13,344 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-04-04T23:57:13,367 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-04T23:57:15,148 Collecting setuptools>=60 2026-04-04T23:57:15,269 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-04T23:57:15,649 Collecting setuptools-scm>=8.0 2026-04-04T23:57:15,665 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-10.0.5-py3-none-any.whl (21 kB) 2026-04-04T23:57:15,749 Collecting vcs-versioning>=1.0.0.dev0 2026-04-04T23:57:15,766 Using cached https://www.piwheels.org/simple/vcs-versioning/vcs_versioning-1.1.1-py3-none-any.whl (79 kB) 2026-04-04T23:57:15,953 Collecting packaging>=20 2026-04-04T23:57:15,971 Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB) 2026-04-04T23:57:18,966 Installing collected packages: setuptools, packaging, vcs-versioning, setuptools-scm 2026-04-04T23:57:22,690 Creating /tmp/pip-build-env-e9iete1d/overlay/local/bin 2026-04-04T23:57:22,692 changing mode of /tmp/pip-build-env-e9iete1d/overlay/local/bin/vcs-versioning to 755 2026-04-04T23:57:22,808 changing mode of /tmp/pip-build-env-e9iete1d/overlay/local/bin/setuptools-scm to 755 2026-04-04T23:57:22,837 Successfully installed packaging-26.0 setuptools-82.0.1 setuptools-scm-10.0.5 vcs-versioning-1.1.1 2026-04-04T23:57:23,122 Installing build dependencies: finished with status 'done' 2026-04-04T23:57:23,137 Getting requirements to build wheel: started 2026-04-04T23:57:23,139 Running command Getting requirements to build wheel 2026-04-04T23:57:23,854 toml section missing PosixPath('pyproject.toml') does not contain any of the tool sections: ['setuptools_scm', 'vcs-versioning'] 2026-04-04T23:57:23,975 /tmp/pip-build-env-e9iete1d/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-04T23:57:23,975 !! 2026-04-04T23:57:23,977 ******************************************************************************** 2026-04-04T23:57:23,977 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-04T23:57:23,978 License :: OSI Approved :: Apache Software License 2026-04-04T23:57:23,980 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-04T23:57:23,980 ******************************************************************************** 2026-04-04T23:57:23,982 !! 2026-04-04T23:57:23,982 dist._finalize_license_expression() 2026-04-04T23:57:23,983 /tmp/pip-build-env-e9iete1d/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-04T23:57:23,984 !! 2026-04-04T23:57:23,985 ******************************************************************************** 2026-04-04T23:57:23,986 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-04T23:57:23,987 License :: OSI Approved :: Apache Software License 2026-04-04T23:57:23,988 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-04T23:57:23,989 ******************************************************************************** 2026-04-04T23:57:23,990 !! 2026-04-04T23:57:23,991 self._finalize_license_expression() 2026-04-04T23:57:23,992 running egg_info 2026-04-04T23:57:23,999 writing pirlygenes.egg-info/PKG-INFO 2026-04-04T23:57:24,003 writing dependency_links to pirlygenes.egg-info/dependency_links.txt 2026-04-04T23:57:24,005 writing entry points to pirlygenes.egg-info/entry_points.txt 2026-04-04T23:57:24,006 writing requirements to pirlygenes.egg-info/requires.txt 2026-04-04T23:57:24,008 writing top-level names to pirlygenes.egg-info/top_level.txt 2026-04-04T23:57:24,050 /tmp/pip-build-env-e9iete1d/overlay/local/lib/python3.11/dist-packages/vcs_versioning/overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly. 2026-04-04T23:57:24,051 return get_active_overrides().subprocess_timeout 2026-04-04T23:57:24,058 listing git files failed - pretending there aren't any 2026-04-04T23:57:24,068 reading manifest file 'pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:57:24,076 adding license file 'LICENSE' 2026-04-04T23:57:24,081 writing manifest file 'pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:57:24,185 Getting requirements to build wheel: finished with status 'done' 2026-04-04T23:57:24,189 Created temporary directory: /tmp/pip-modern-metadata-nbfp1f5k 2026-04-04T23:57:24,192 Preparing metadata (pyproject.toml): started 2026-04-04T23:57:24,193 Running command Preparing metadata (pyproject.toml) 2026-04-04T23:57:24,840 toml section missing PosixPath('pyproject.toml') does not contain any of the tool sections: ['setuptools_scm', 'vcs-versioning'] 2026-04-04T23:57:24,947 /tmp/pip-build-env-e9iete1d/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-04T23:57:24,947 !! 2026-04-04T23:57:24,948 ******************************************************************************** 2026-04-04T23:57:24,949 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-04T23:57:24,950 License :: OSI Approved :: Apache Software License 2026-04-04T23:57:24,951 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-04T23:57:24,951 ******************************************************************************** 2026-04-04T23:57:24,952 !! 2026-04-04T23:57:24,953 dist._finalize_license_expression() 2026-04-04T23:57:24,954 /tmp/pip-build-env-e9iete1d/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-04T23:57:24,954 !! 2026-04-04T23:57:24,955 ******************************************************************************** 2026-04-04T23:57:24,956 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-04T23:57:24,957 License :: OSI Approved :: Apache Software License 2026-04-04T23:57:24,959 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-04T23:57:24,959 ******************************************************************************** 2026-04-04T23:57:24,961 !! 2026-04-04T23:57:24,961 self._finalize_license_expression() 2026-04-04T23:57:24,962 running dist_info 2026-04-04T23:57:24,976 creating /tmp/pip-modern-metadata-nbfp1f5k/pirlygenes.egg-info 2026-04-04T23:57:24,977 writing /tmp/pip-modern-metadata-nbfp1f5k/pirlygenes.egg-info/PKG-INFO 2026-04-04T23:57:24,981 writing dependency_links to /tmp/pip-modern-metadata-nbfp1f5k/pirlygenes.egg-info/dependency_links.txt 2026-04-04T23:57:24,982 writing entry points to /tmp/pip-modern-metadata-nbfp1f5k/pirlygenes.egg-info/entry_points.txt 2026-04-04T23:57:24,984 writing requirements to /tmp/pip-modern-metadata-nbfp1f5k/pirlygenes.egg-info/requires.txt 2026-04-04T23:57:24,985 writing top-level names to /tmp/pip-modern-metadata-nbfp1f5k/pirlygenes.egg-info/top_level.txt 2026-04-04T23:57:24,986 writing manifest file '/tmp/pip-modern-metadata-nbfp1f5k/pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:57:25,024 /tmp/pip-build-env-e9iete1d/overlay/local/lib/python3.11/dist-packages/vcs_versioning/overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly. 2026-04-04T23:57:25,024 return get_active_overrides().subprocess_timeout 2026-04-04T23:57:25,031 listing git files failed - pretending there aren't any 2026-04-04T23:57:25,039 reading manifest file '/tmp/pip-modern-metadata-nbfp1f5k/pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:57:25,041 adding license file 'LICENSE' 2026-04-04T23:57:25,044 writing manifest file '/tmp/pip-modern-metadata-nbfp1f5k/pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:57:25,045 creating '/tmp/pip-modern-metadata-nbfp1f5k/pirlygenes-2.0.1.dist-info' 2026-04-04T23:57:25,182 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-04T23:57:25,187 Source in /tmp/pip-wheel-2zhtf3a2/pirlygenes_7ce774071a1c43fc85df274b4d2b7be6 has version 2.0.1, which satisfies requirement pirlygenes==2.0.1 from https://files.pythonhosted.org/packages/f0/57/519f98c3e3ce7414973c34a35b56e0123e63c2397c1c28a40f52096110e8/pirlygenes-2.0.1.tar.gz 2026-04-04T23:57:25,188 Removed pirlygenes==2.0.1 from https://files.pythonhosted.org/packages/f0/57/519f98c3e3ce7414973c34a35b56e0123e63c2397c1c28a40f52096110e8/pirlygenes-2.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-z0l2lfc1' 2026-04-04T23:57:25,195 Created temporary directory: /tmp/pip-unpack-9ph2nq2_ 2026-04-04T23:57:25,196 Building wheels for collected packages: pirlygenes 2026-04-04T23:57:25,200 Created temporary directory: /tmp/pip-wheel-xm92ckm9 2026-04-04T23:57:25,201 Destination directory: /tmp/pip-wheel-xm92ckm9 2026-04-04T23:57:25,203 Building wheel for pirlygenes (pyproject.toml): started 2026-04-04T23:57:25,205 Running command Building wheel for pirlygenes (pyproject.toml) 2026-04-04T23:57:25,825 toml section missing PosixPath('pyproject.toml') does not contain any of the tool sections: ['setuptools_scm', 'vcs-versioning'] 2026-04-04T23:57:25,923 /tmp/pip-build-env-e9iete1d/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-04T23:57:25,923 !! 2026-04-04T23:57:25,924 ******************************************************************************** 2026-04-04T23:57:25,925 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-04T23:57:25,926 License :: OSI Approved :: Apache Software License 2026-04-04T23:57:25,927 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-04T23:57:25,928 ******************************************************************************** 2026-04-04T23:57:25,929 !! 2026-04-04T23:57:25,930 dist._finalize_license_expression() 2026-04-04T23:57:25,930 /tmp/pip-build-env-e9iete1d/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-04T23:57:25,931 !! 2026-04-04T23:57:25,932 ******************************************************************************** 2026-04-04T23:57:25,933 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-04T23:57:25,934 License :: OSI Approved :: Apache Software License 2026-04-04T23:57:25,935 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-04T23:57:25,936 ******************************************************************************** 2026-04-04T23:57:25,937 !! 2026-04-04T23:57:25,938 self._finalize_license_expression() 2026-04-04T23:57:25,938 running bdist_wheel 2026-04-04T23:57:25,959 running build 2026-04-04T23:57:25,960 running build_py 2026-04-04T23:57:25,962 creating build/lib/pirlygenes 2026-04-04T23:57:25,964 copying pirlygenes/gene_sets_old.py -> build/lib/pirlygenes 2026-04-04T23:57:25,966 copying pirlygenes/gene_ids.py -> build/lib/pirlygenes 2026-04-04T23:57:25,968 copying pirlygenes/plot_data_helpers.py -> build/lib/pirlygenes 2026-04-04T23:57:25,971 copying pirlygenes/__init__.py -> build/lib/pirlygenes 2026-04-04T23:57:25,972 copying pirlygenes/aggregate_gene_expression.py -> build/lib/pirlygenes 2026-04-04T23:57:25,975 copying pirlygenes/version.py -> build/lib/pirlygenes 2026-04-04T23:57:25,976 copying pirlygenes/load_dataset.py -> build/lib/pirlygenes 2026-04-04T23:57:25,978 copying pirlygenes/gene_names.py -> build/lib/pirlygenes 2026-04-04T23:57:25,980 copying pirlygenes/transcript_to_gene.py -> build/lib/pirlygenes 2026-04-04T23:57:25,982 copying pirlygenes/plot.py -> build/lib/pirlygenes 2026-04-04T23:57:25,984 copying pirlygenes/common.py -> build/lib/pirlygenes 2026-04-04T23:57:25,986 copying pirlygenes/gene_sets_cancer.py -> build/lib/pirlygenes 2026-04-04T23:57:25,988 copying pirlygenes/cli.py -> build/lib/pirlygenes 2026-04-04T23:57:25,990 copying pirlygenes/load_expression.py -> build/lib/pirlygenes 2026-04-04T23:57:25,992 running egg_info 2026-04-04T23:57:26,007 writing pirlygenes.egg-info/PKG-INFO 2026-04-04T23:57:26,010 writing dependency_links to pirlygenes.egg-info/dependency_links.txt 2026-04-04T23:57:26,011 writing entry points to pirlygenes.egg-info/entry_points.txt 2026-04-04T23:57:26,013 writing requirements to pirlygenes.egg-info/requires.txt 2026-04-04T23:57:26,014 writing top-level names to pirlygenes.egg-info/top_level.txt 2026-04-04T23:57:26,043 /tmp/pip-build-env-e9iete1d/overlay/local/lib/python3.11/dist-packages/vcs_versioning/overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly. 2026-04-04T23:57:26,043 return get_active_overrides().subprocess_timeout 2026-04-04T23:57:26,049 listing git files failed - pretending there aren't any 2026-04-04T23:57:26,056 reading manifest file 'pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:57:26,061 adding license file 'LICENSE' 2026-04-04T23:57:26,066 writing manifest file 'pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:57:26,069 /tmp/pip-build-env-e9iete1d/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pirlygenes.data' is absent from the `packages` configuration. 2026-04-04T23:57:26,069 !! 2026-04-04T23:57:26,071 ******************************************************************************** 2026-04-04T23:57:26,071 ############################ 2026-04-04T23:57:26,072 # Package would be ignored # 2026-04-04T23:57:26,072 ############################ 2026-04-04T23:57:26,073 Python recognizes 'pirlygenes.data' as an importable package[^1], 2026-04-04T23:57:26,073 but it is absent from setuptools' `packages` configuration. 2026-04-04T23:57:26,074 This leads to an ambiguous overall configuration. If you want to distribute this 2026-04-04T23:57:26,075 package, please make sure that 'pirlygenes.data' is explicitly added 2026-04-04T23:57:26,075 to the `packages` configuration field. 2026-04-04T23:57:26,077 Alternatively, you can also rely on setuptools' discovery methods 2026-04-04T23:57:26,077 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2026-04-04T23:57:26,078 instead of `find_packages(...)`/`find:`). 2026-04-04T23:57:26,079 You can read more about "package discovery" on setuptools documentation page: 2026-04-04T23:57:26,080 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2026-04-04T23:57:26,081 If you don't want 'pirlygenes.data' to be distributed and are 2026-04-04T23:57:26,081 already explicitly excluding 'pirlygenes.data' via 2026-04-04T23:57:26,082 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2026-04-04T23:57:26,083 you can try to use `exclude_package_data`, or `include-package-data=False` in 2026-04-04T23:57:26,083 combination with a more fine grained `package-data` configuration. 2026-04-04T23:57:26,084 You can read more about "package data files" on setuptools documentation page: 2026-04-04T23:57:26,085 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2026-04-04T23:57:26,087 [^1]: For Python, any directory (with suitable naming) can be imported, 2026-04-04T23:57:26,088 even if it does not contain any `.py` files. 2026-04-04T23:57:26,088 On the other hand, currently there is no concept of package data 2026-04-04T23:57:26,089 directory, all directories are treated like packages. 2026-04-04T23:57:26,089 ******************************************************************************** 2026-04-04T23:57:26,090 !! 2026-04-04T23:57:26,090 check.warn(importable) 2026-04-04T23:57:26,091 copying pirlygenes/PLAN-1.4.0-radioligand.md -> build/lib/pirlygenes 2026-04-04T23:57:26,091 creating build/lib/pirlygenes/data 2026-04-04T23:57:26,092 copying pirlygenes/data/ADC-approved.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,092 copying pirlygenes/data/ADC-trials.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,092 copying pirlygenes/data/ADC-withdrawn.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,093 copying pirlygenes/data/CAR-T-approved.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,093 copying pirlygenes/data/TCR-T-approved.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,094 copying pirlygenes/data/TCR-T-trials.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,095 copying pirlygenes/data/bispecific-antibodies-approved.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,097 copying pirlygenes/data/cancer-driver-genes.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,101 copying pirlygenes/data/cancer-driver-variants.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,104 copying pirlygenes/data/cancer-testis-antigens.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,108 copying pirlygenes/data/class1-mhc-presentation-pathway.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,110 copying pirlygenes/data/interferon-response.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,112 copying pirlygenes/data/multispecific-tcell-engager-trials.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,114 copying pirlygenes/data/radioligand-targets.csv -> build/lib/pirlygenes/data 2026-04-04T23:57:26,130 installing to build/bdist.linux-armv7l/wheel 2026-04-04T23:57:26,131 running install 2026-04-04T23:57:26,155 running install_lib 2026-04-04T23:57:26,163 creating build/bdist.linux-armv7l/wheel 2026-04-04T23:57:26,165 creating build/bdist.linux-armv7l/wheel/pirlygenes 2026-04-04T23:57:26,167 copying build/lib/pirlygenes/gene_sets_old.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,169 copying build/lib/pirlygenes/gene_ids.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,172 copying build/lib/pirlygenes/plot_data_helpers.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,174 copying build/lib/pirlygenes/__init__.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,176 copying build/lib/pirlygenes/aggregate_gene_expression.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,179 copying build/lib/pirlygenes/PLAN-1.4.0-radioligand.md -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,181 copying build/lib/pirlygenes/version.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,183 copying build/lib/pirlygenes/load_dataset.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,185 copying build/lib/pirlygenes/gene_names.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,187 copying build/lib/pirlygenes/transcript_to_gene.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,189 copying build/lib/pirlygenes/plot.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,192 creating build/bdist.linux-armv7l/wheel/pirlygenes/data 2026-04-04T23:57:26,194 copying build/lib/pirlygenes/data/class1-mhc-presentation-pathway.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,196 copying build/lib/pirlygenes/data/ADC-trials.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,199 copying build/lib/pirlygenes/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,203 copying build/lib/pirlygenes/data/TCR-T-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,205 copying build/lib/pirlygenes/data/ADC-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,207 copying build/lib/pirlygenes/data/bispecific-antibodies-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,209 copying build/lib/pirlygenes/data/radioligand-targets.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,211 copying build/lib/pirlygenes/data/CAR-T-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,213 copying build/lib/pirlygenes/data/interferon-response.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,215 copying build/lib/pirlygenes/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,218 copying build/lib/pirlygenes/data/TCR-T-trials.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,221 copying build/lib/pirlygenes/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,226 copying build/lib/pirlygenes/data/ADC-withdrawn.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,228 copying build/lib/pirlygenes/data/multispecific-tcell-engager-trials.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:57:26,231 copying build/lib/pirlygenes/common.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,234 copying build/lib/pirlygenes/gene_sets_cancer.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,237 copying build/lib/pirlygenes/cli.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,240 copying build/lib/pirlygenes/load_expression.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:57:26,243 running install_egg_info 2026-04-04T23:57:26,251 Copying pirlygenes.egg-info to build/bdist.linux-armv7l/wheel/./pirlygenes-2.0.1-py3.11.egg-info 2026-04-04T23:57:26,266 running install_scripts 2026-04-04T23:57:26,281 creating build/bdist.linux-armv7l/wheel/pirlygenes-2.0.1.dist-info/WHEEL 2026-04-04T23:57:26,285 creating '/tmp/pip-wheel-xm92ckm9/.tmp-ezbqqamh/pirlygenes-2.0.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-04T23:57:26,288 adding 'pirlygenes/PLAN-1.4.0-radioligand.md' 2026-04-04T23:57:26,289 adding 'pirlygenes/__init__.py' 2026-04-04T23:57:26,291 adding 'pirlygenes/aggregate_gene_expression.py' 2026-04-04T23:57:26,293 adding 'pirlygenes/cli.py' 2026-04-04T23:57:26,295 adding 'pirlygenes/common.py' 2026-04-04T23:57:26,296 adding 'pirlygenes/gene_ids.py' 2026-04-04T23:57:26,298 adding 'pirlygenes/gene_names.py' 2026-04-04T23:57:26,301 adding 'pirlygenes/gene_sets_cancer.py' 2026-04-04T23:57:26,303 adding 'pirlygenes/gene_sets_old.py' 2026-04-04T23:57:26,305 adding 'pirlygenes/load_dataset.py' 2026-04-04T23:57:26,306 adding 'pirlygenes/load_expression.py' 2026-04-04T23:57:26,309 adding 'pirlygenes/plot.py' 2026-04-04T23:57:26,311 adding 'pirlygenes/plot_data_helpers.py' 2026-04-04T23:57:26,313 adding 'pirlygenes/transcript_to_gene.py' 2026-04-04T23:57:26,314 adding 'pirlygenes/version.py' 2026-04-04T23:57:26,317 adding 'pirlygenes/data/ADC-approved.csv' 2026-04-04T23:57:26,321 adding 'pirlygenes/data/ADC-trials.csv' 2026-04-04T23:57:26,323 adding 'pirlygenes/data/ADC-withdrawn.csv' 2026-04-04T23:57:26,324 adding 'pirlygenes/data/CAR-T-approved.csv' 2026-04-04T23:57:26,326 adding 'pirlygenes/data/TCR-T-approved.csv' 2026-04-04T23:57:26,329 adding 'pirlygenes/data/TCR-T-trials.csv' 2026-04-04T23:57:26,331 adding 'pirlygenes/data/bispecific-antibodies-approved.csv' 2026-04-04T23:57:26,337 adding 'pirlygenes/data/cancer-driver-genes.csv' 2026-04-04T23:57:26,340 adding 'pirlygenes/data/cancer-driver-variants.csv' 2026-04-04T23:57:26,346 adding 'pirlygenes/data/cancer-testis-antigens.csv' 2026-04-04T23:57:26,349 adding 'pirlygenes/data/class1-mhc-presentation-pathway.csv' 2026-04-04T23:57:26,350 adding 'pirlygenes/data/interferon-response.csv' 2026-04-04T23:57:26,352 adding 'pirlygenes/data/multispecific-tcell-engager-trials.csv' 2026-04-04T23:57:26,354 adding 'pirlygenes/data/radioligand-targets.csv' 2026-04-04T23:57:26,357 adding 'pirlygenes-2.0.1.dist-info/licenses/LICENSE' 2026-04-04T23:57:26,360 adding 'pirlygenes-2.0.1.dist-info/METADATA' 2026-04-04T23:57:26,361 adding 'pirlygenes-2.0.1.dist-info/WHEEL' 2026-04-04T23:57:26,363 adding 'pirlygenes-2.0.1.dist-info/entry_points.txt' 2026-04-04T23:57:26,364 adding 'pirlygenes-2.0.1.dist-info/top_level.txt' 2026-04-04T23:57:26,366 adding 'pirlygenes-2.0.1.dist-info/RECORD' 2026-04-04T23:57:26,369 removing build/bdist.linux-armv7l/wheel 2026-04-04T23:57:26,484 Building wheel for pirlygenes (pyproject.toml): finished with status 'done' 2026-04-04T23:57:26,491 Created wheel for pirlygenes: filename=pirlygenes-2.0.1-py3-none-any.whl size=90490 sha256=0956b5fd3f21d43dea90b38bbc06628b327c49504aa0fc53d3d81d55208c6f5f 2026-04-04T23:57:26,492 Stored in directory: /tmp/pip-ephem-wheel-cache-nobu0zr8/wheels/1c/a9/a6/9cad0430c6261f493853651616eba6d3b7f1d2fe6f688d2d9f 2026-04-04T23:57:26,505 Successfully built pirlygenes 2026-04-04T23:57:26,511 Removed build tracker: '/tmp/pip-build-tracker-z0l2lfc1'