2026-04-04T23:56:32,506 Created temporary directory: /tmp/pip-ephem-wheel-cache-mmcsk530 2026-04-04T23:56:32,508 Created temporary directory: /tmp/pip-build-tracker-50wzfql3 2026-04-04T23:56:32,508 Initialized build tracking at /tmp/pip-build-tracker-50wzfql3 2026-04-04T23:56:32,509 Created build tracker: /tmp/pip-build-tracker-50wzfql3 2026-04-04T23:56:32,509 Entered build tracker: /tmp/pip-build-tracker-50wzfql3 2026-04-04T23:56:32,510 Created temporary directory: /tmp/pip-wheel-lf4r_tfh 2026-04-04T23:56:32,513 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 2026-04-04T23:56:32,516 Created temporary directory: /tmp/pip-ephem-wheel-cache-_aodlj5p 2026-04-04T23:56:32,538 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-04T23:56:32,541 2 location(s) to search for versions of pirlygenes: 2026-04-04T23:56:32,541 * https://pypi.org/simple/pirlygenes/ 2026-04-04T23:56:32,541 * https://www.piwheels.org/simple/pirlygenes/ 2026-04-04T23:56:32,542 Fetching project page and analyzing links: https://pypi.org/simple/pirlygenes/ 2026-04-04T23:56:32,543 Getting page https://pypi.org/simple/pirlygenes/ 2026-04-04T23:56:32,544 Found index url https://pypi.org/simple 2026-04-04T23:56:32,771 Fetched page https://pypi.org/simple/pirlygenes/ as application/vnd.pypi.simple.v1+json 2026-04-04T23:56:32,774 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) 2026-04-04T23:56:32,775 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 2026-04-04T23:56:32,776 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) 2026-04-04T23:56:32,777 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 2026-04-04T23:56:32,778 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) 2026-04-04T23:56:32,779 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 2026-04-04T23:56:32,780 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) 2026-04-04T23:56:32,780 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 2026-04-04T23:56:32,781 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) 2026-04-04T23:56:32,782 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 2026-04-04T23:56:32,783 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) 2026-04-04T23:56:32,784 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 2026-04-04T23:56:32,785 Fetching project page and analyzing links: https://www.piwheels.org/simple/pirlygenes/ 2026-04-04T23:56:32,785 Getting page https://www.piwheels.org/simple/pirlygenes/ 2026-04-04T23:56:32,787 Found index url https://www.piwheels.org/simple 2026-04-04T23:56:33,173 Fetched page https://www.piwheels.org/simple/pirlygenes/ as text/html 2026-04-04T23:56:33,175 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) 2026-04-04T23:56:33,176 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) 2026-04-04T23:56:33,177 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) 2026-04-04T23:56:33,177 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) 2026-04-04T23:56:33,178 Skipping link: not a file: https://www.piwheels.org/simple/pirlygenes/ 2026-04-04T23:56:33,179 Skipping link: not a file: https://pypi.org/simple/pirlygenes/ 2026-04-04T23:56:33,198 Given no hashes to check 1 links for project 'pirlygenes': discarding no candidates 2026-04-04T23:56:33,216 Collecting pirlygenes==2.0.0 2026-04-04T23:56:33,219 Created temporary directory: /tmp/pip-unpack-wa92bcfm 2026-04-04T23:56:33,445 Downloading pirlygenes-2.0.0.tar.gz (667 kB) 2026-04-04T23:56:33,764 Added pirlygenes==2.0.0 from https://files.pythonhosted.org/packages/1a/15/da113c10028ce6cef9359672f0d6309ef13174410f74bd641ab56fe968e1/pirlygenes-2.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-50wzfql3' 2026-04-04T23:56:33,770 Created temporary directory: /tmp/pip-build-env-6yeqqpkv 2026-04-04T23:56:33,775 Installing build dependencies: started 2026-04-04T23:56:33,776 Running command pip subprocess to install build dependencies 2026-04-04T23:56:34,932 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-04T23:56:35,424 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 2026-04-04T23:56:35,447 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-04T23:56:37,205 Collecting setuptools>=60 2026-04-04T23:56:37,299 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-04T23:56:37,688 Collecting setuptools-scm>=8.0 2026-04-04T23:56:37,703 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-10.0.5-py3-none-any.whl (21 kB) 2026-04-04T23:56:37,785 Collecting vcs-versioning>=1.0.0.dev0 2026-04-04T23:56:37,803 Using cached https://www.piwheels.org/simple/vcs-versioning/vcs_versioning-1.1.1-py3-none-any.whl (79 kB) 2026-04-04T23:56:37,986 Collecting packaging>=20 2026-04-04T23:56:38,002 Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB) 2026-04-04T23:56:41,009 Installing collected packages: setuptools, packaging, vcs-versioning, setuptools-scm 2026-04-04T23:56:44,776 Creating /tmp/pip-build-env-6yeqqpkv/overlay/local/bin 2026-04-04T23:56:44,778 changing mode of /tmp/pip-build-env-6yeqqpkv/overlay/local/bin/vcs-versioning to 755 2026-04-04T23:56:44,892 changing mode of /tmp/pip-build-env-6yeqqpkv/overlay/local/bin/setuptools-scm to 755 2026-04-04T23:56:44,919 Successfully installed packaging-26.0 setuptools-82.0.1 setuptools-scm-10.0.5 vcs-versioning-1.1.1 2026-04-04T23:56:45,211 Installing build dependencies: finished with status 'done' 2026-04-04T23:56:45,229 Getting requirements to build wheel: started 2026-04-04T23:56:45,230 Running command Getting requirements to build wheel 2026-04-04T23:56:45,913 toml section missing PosixPath('pyproject.toml') does not contain any of the tool sections: ['setuptools_scm', 'vcs-versioning'] 2026-04-04T23:56:46,029 /tmp/pip-build-env-6yeqqpkv/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-04T23:56:46,030 !! 2026-04-04T23:56:46,031 ******************************************************************************** 2026-04-04T23:56:46,031 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-04T23:56:46,032 License :: OSI Approved :: Apache Software License 2026-04-04T23:56:46,034 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-04T23:56:46,034 ******************************************************************************** 2026-04-04T23:56:46,036 !! 2026-04-04T23:56:46,036 dist._finalize_license_expression() 2026-04-04T23:56:46,037 /tmp/pip-build-env-6yeqqpkv/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-04T23:56:46,038 !! 2026-04-04T23:56:46,039 ******************************************************************************** 2026-04-04T23:56:46,040 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-04T23:56:46,041 License :: OSI Approved :: Apache Software License 2026-04-04T23:56:46,042 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-04T23:56:46,043 ******************************************************************************** 2026-04-04T23:56:46,044 !! 2026-04-04T23:56:46,044 self._finalize_license_expression() 2026-04-04T23:56:46,045 running egg_info 2026-04-04T23:56:46,053 writing pirlygenes.egg-info/PKG-INFO 2026-04-04T23:56:46,057 writing dependency_links to pirlygenes.egg-info/dependency_links.txt 2026-04-04T23:56:46,059 writing entry points to pirlygenes.egg-info/entry_points.txt 2026-04-04T23:56:46,061 writing requirements to pirlygenes.egg-info/requires.txt 2026-04-04T23:56:46,062 writing top-level names to pirlygenes.egg-info/top_level.txt 2026-04-04T23:56:46,103 /tmp/pip-build-env-6yeqqpkv/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. 2026-04-04T23:56:46,104 return get_active_overrides().subprocess_timeout 2026-04-04T23:56:46,111 listing git files failed - pretending there aren't any 2026-04-04T23:56:46,121 reading manifest file 'pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:56:46,128 adding license file 'LICENSE' 2026-04-04T23:56:46,133 writing manifest file 'pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:56:46,239 Getting requirements to build wheel: finished with status 'done' 2026-04-04T23:56:46,243 Created temporary directory: /tmp/pip-modern-metadata-rxicgmdm 2026-04-04T23:56:46,245 Preparing metadata (pyproject.toml): started 2026-04-04T23:56:46,246 Running command Preparing metadata (pyproject.toml) 2026-04-04T23:56:46,887 toml section missing PosixPath('pyproject.toml') does not contain any of the tool sections: ['setuptools_scm', 'vcs-versioning'] 2026-04-04T23:56:47,002 /tmp/pip-build-env-6yeqqpkv/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-04T23:56:47,002 !! 2026-04-04T23:56:47,004 ******************************************************************************** 2026-04-04T23:56:47,004 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-04T23:56:47,005 License :: OSI Approved :: Apache Software License 2026-04-04T23:56:47,006 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-04T23:56:47,007 ******************************************************************************** 2026-04-04T23:56:47,008 !! 2026-04-04T23:56:47,008 dist._finalize_license_expression() 2026-04-04T23:56:47,009 /tmp/pip-build-env-6yeqqpkv/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-04T23:56:47,010 !! 2026-04-04T23:56:47,011 ******************************************************************************** 2026-04-04T23:56:47,012 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-04T23:56:47,013 License :: OSI Approved :: Apache Software License 2026-04-04T23:56:47,014 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-04T23:56:47,015 ******************************************************************************** 2026-04-04T23:56:47,016 !! 2026-04-04T23:56:47,017 self._finalize_license_expression() 2026-04-04T23:56:47,019 running dist_info 2026-04-04T23:56:47,034 creating /tmp/pip-modern-metadata-rxicgmdm/pirlygenes.egg-info 2026-04-04T23:56:47,035 writing /tmp/pip-modern-metadata-rxicgmdm/pirlygenes.egg-info/PKG-INFO 2026-04-04T23:56:47,039 writing dependency_links to /tmp/pip-modern-metadata-rxicgmdm/pirlygenes.egg-info/dependency_links.txt 2026-04-04T23:56:47,041 writing entry points to /tmp/pip-modern-metadata-rxicgmdm/pirlygenes.egg-info/entry_points.txt 2026-04-04T23:56:47,042 writing requirements to /tmp/pip-modern-metadata-rxicgmdm/pirlygenes.egg-info/requires.txt 2026-04-04T23:56:47,043 writing top-level names to /tmp/pip-modern-metadata-rxicgmdm/pirlygenes.egg-info/top_level.txt 2026-04-04T23:56:47,045 writing manifest file '/tmp/pip-modern-metadata-rxicgmdm/pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:56:47,082 /tmp/pip-build-env-6yeqqpkv/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. 2026-04-04T23:56:47,083 return get_active_overrides().subprocess_timeout 2026-04-04T23:56:47,089 listing git files failed - pretending there aren't any 2026-04-04T23:56:47,097 reading manifest file '/tmp/pip-modern-metadata-rxicgmdm/pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:56:47,099 adding license file 'LICENSE' 2026-04-04T23:56:47,103 writing manifest file '/tmp/pip-modern-metadata-rxicgmdm/pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:56:47,104 creating '/tmp/pip-modern-metadata-rxicgmdm/pirlygenes-2.0.0.dist-info' 2026-04-04T23:56:47,241 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-04T23:56:47,247 Source in /tmp/pip-wheel-lf4r_tfh/pirlygenes_3d990e9259374ea29d382c0b475e0e8c has version 2.0.0, which satisfies requirement pirlygenes==2.0.0 from https://files.pythonhosted.org/packages/1a/15/da113c10028ce6cef9359672f0d6309ef13174410f74bd641ab56fe968e1/pirlygenes-2.0.0.tar.gz 2026-04-04T23:56:47,248 Removed pirlygenes==2.0.0 from https://files.pythonhosted.org/packages/1a/15/da113c10028ce6cef9359672f0d6309ef13174410f74bd641ab56fe968e1/pirlygenes-2.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-50wzfql3' 2026-04-04T23:56:47,254 Created temporary directory: /tmp/pip-unpack-su0qm0tt 2026-04-04T23:56:47,255 Building wheels for collected packages: pirlygenes 2026-04-04T23:56:47,259 Created temporary directory: /tmp/pip-wheel-o0ba0dza 2026-04-04T23:56:47,260 Destination directory: /tmp/pip-wheel-o0ba0dza 2026-04-04T23:56:47,262 Building wheel for pirlygenes (pyproject.toml): started 2026-04-04T23:56:47,263 Running command Building wheel for pirlygenes (pyproject.toml) 2026-04-04T23:56:47,895 toml section missing PosixPath('pyproject.toml') does not contain any of the tool sections: ['setuptools_scm', 'vcs-versioning'] 2026-04-04T23:56:48,003 /tmp/pip-build-env-6yeqqpkv/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-04T23:56:48,003 !! 2026-04-04T23:56:48,005 ******************************************************************************** 2026-04-04T23:56:48,005 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-04T23:56:48,007 License :: OSI Approved :: Apache Software License 2026-04-04T23:56:48,008 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-04T23:56:48,008 ******************************************************************************** 2026-04-04T23:56:48,010 !! 2026-04-04T23:56:48,010 dist._finalize_license_expression() 2026-04-04T23:56:48,011 /tmp/pip-build-env-6yeqqpkv/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-04T23:56:48,012 !! 2026-04-04T23:56:48,013 ******************************************************************************** 2026-04-04T23:56:48,014 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-04T23:56:48,015 License :: OSI Approved :: Apache Software License 2026-04-04T23:56:48,016 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-04T23:56:48,017 ******************************************************************************** 2026-04-04T23:56:48,018 !! 2026-04-04T23:56:48,018 self._finalize_license_expression() 2026-04-04T23:56:48,019 running bdist_wheel 2026-04-04T23:56:48,040 running build 2026-04-04T23:56:48,040 running build_py 2026-04-04T23:56:48,042 creating build/lib/pirlygenes 2026-04-04T23:56:48,045 copying pirlygenes/version.py -> build/lib/pirlygenes 2026-04-04T23:56:48,048 copying pirlygenes/plot_data_helpers.py -> build/lib/pirlygenes 2026-04-04T23:56:48,051 copying pirlygenes/aggregate_gene_expression.py -> build/lib/pirlygenes 2026-04-04T23:56:48,053 copying pirlygenes/cli.py -> build/lib/pirlygenes 2026-04-04T23:56:48,055 copying pirlygenes/gene_sets_old.py -> build/lib/pirlygenes 2026-04-04T23:56:48,057 copying pirlygenes/plot.py -> build/lib/pirlygenes 2026-04-04T23:56:48,060 copying pirlygenes/gene_names.py -> build/lib/pirlygenes 2026-04-04T23:56:48,062 copying pirlygenes/gene_sets_cancer.py -> build/lib/pirlygenes 2026-04-04T23:56:48,065 copying pirlygenes/gene_ids.py -> build/lib/pirlygenes 2026-04-04T23:56:48,067 copying pirlygenes/common.py -> build/lib/pirlygenes 2026-04-04T23:56:48,069 copying pirlygenes/__init__.py -> build/lib/pirlygenes 2026-04-04T23:56:48,071 copying pirlygenes/load_dataset.py -> build/lib/pirlygenes 2026-04-04T23:56:48,072 copying pirlygenes/load_expression.py -> build/lib/pirlygenes 2026-04-04T23:56:48,074 copying pirlygenes/transcript_to_gene.py -> build/lib/pirlygenes 2026-04-04T23:56:48,076 running egg_info 2026-04-04T23:56:48,092 writing pirlygenes.egg-info/PKG-INFO 2026-04-04T23:56:48,095 writing dependency_links to pirlygenes.egg-info/dependency_links.txt 2026-04-04T23:56:48,096 writing entry points to pirlygenes.egg-info/entry_points.txt 2026-04-04T23:56:48,098 writing requirements to pirlygenes.egg-info/requires.txt 2026-04-04T23:56:48,099 writing top-level names to pirlygenes.egg-info/top_level.txt 2026-04-04T23:56:48,129 /tmp/pip-build-env-6yeqqpkv/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. 2026-04-04T23:56:48,130 return get_active_overrides().subprocess_timeout 2026-04-04T23:56:48,136 listing git files failed - pretending there aren't any 2026-04-04T23:56:48,144 reading manifest file 'pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:56:48,149 adding license file 'LICENSE' 2026-04-04T23:56:48,154 writing manifest file 'pirlygenes.egg-info/SOURCES.txt' 2026-04-04T23:56:48,156 /tmp/pip-build-env-6yeqqpkv/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pirlygenes.data' is absent from the `packages` configuration. 2026-04-04T23:56:48,157 !! 2026-04-04T23:56:48,158 ******************************************************************************** 2026-04-04T23:56:48,159 ############################ 2026-04-04T23:56:48,160 # Package would be ignored # 2026-04-04T23:56:48,160 ############################ 2026-04-04T23:56:48,161 Python recognizes 'pirlygenes.data' as an importable package[^1], 2026-04-04T23:56:48,161 but it is absent from setuptools' `packages` configuration. 2026-04-04T23:56:48,162 This leads to an ambiguous overall configuration. If you want to distribute this 2026-04-04T23:56:48,163 package, please make sure that 'pirlygenes.data' is explicitly added 2026-04-04T23:56:48,164 to the `packages` configuration field. 2026-04-04T23:56:48,165 Alternatively, you can also rely on setuptools' discovery methods 2026-04-04T23:56:48,165 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2026-04-04T23:56:48,166 instead of `find_packages(...)`/`find:`). 2026-04-04T23:56:48,167 You can read more about "package discovery" on setuptools documentation page: 2026-04-04T23:56:48,168 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2026-04-04T23:56:48,169 If you don't want 'pirlygenes.data' to be distributed and are 2026-04-04T23:56:48,169 already explicitly excluding 'pirlygenes.data' via 2026-04-04T23:56:48,170 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2026-04-04T23:56:48,171 you can try to use `exclude_package_data`, or `include-package-data=False` in 2026-04-04T23:56:48,171 combination with a more fine grained `package-data` configuration. 2026-04-04T23:56:48,173 You can read more about "package data files" on setuptools documentation page: 2026-04-04T23:56:48,174 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2026-04-04T23:56:48,176 [^1]: For Python, any directory (with suitable naming) can be imported, 2026-04-04T23:56:48,176 even if it does not contain any `.py` files. 2026-04-04T23:56:48,177 On the other hand, currently there is no concept of package data 2026-04-04T23:56:48,177 directory, all directories are treated like packages. 2026-04-04T23:56:48,178 ******************************************************************************** 2026-04-04T23:56:48,179 !! 2026-04-04T23:56:48,179 check.warn(importable) 2026-04-04T23:56:48,180 copying pirlygenes/PLAN-1.4.0-radioligand.md -> build/lib/pirlygenes 2026-04-04T23:56:48,180 creating build/lib/pirlygenes/data 2026-04-04T23:56:48,181 copying pirlygenes/data/ADC-approved.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,181 copying pirlygenes/data/ADC-trials.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,181 copying pirlygenes/data/ADC-withdrawn.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,182 copying pirlygenes/data/CAR-T-approved.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,182 copying pirlygenes/data/TCR-T-approved.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,183 copying pirlygenes/data/TCR-T-trials.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,185 copying pirlygenes/data/bispecific-antibodies-approved.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,188 copying pirlygenes/data/cancer-driver-genes.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,191 copying pirlygenes/data/cancer-driver-variants.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,195 copying pirlygenes/data/cancer-testis-antigens.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,198 copying pirlygenes/data/class1-mhc-presentation-pathway.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,201 copying pirlygenes/data/interferon-response.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,203 copying pirlygenes/data/multispecific-tcell-engager-trials.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,206 copying pirlygenes/data/radioligand-targets.csv -> build/lib/pirlygenes/data 2026-04-04T23:56:48,222 installing to build/bdist.linux-armv7l/wheel 2026-04-04T23:56:48,223 running install 2026-04-04T23:56:48,246 running install_lib 2026-04-04T23:56:48,254 creating build/bdist.linux-armv7l/wheel 2026-04-04T23:56:48,256 creating build/bdist.linux-armv7l/wheel/pirlygenes 2026-04-04T23:56:48,257 copying build/lib/pirlygenes/version.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,259 copying build/lib/pirlygenes/plot_data_helpers.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,262 copying build/lib/pirlygenes/aggregate_gene_expression.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,264 copying build/lib/pirlygenes/cli.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,266 copying build/lib/pirlygenes/PLAN-1.4.0-radioligand.md -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,269 creating build/bdist.linux-armv7l/wheel/pirlygenes/data 2026-04-04T23:56:48,270 copying build/lib/pirlygenes/data/ADC-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,272 copying build/lib/pirlygenes/data/class1-mhc-presentation-pathway.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,274 copying build/lib/pirlygenes/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,277 copying build/lib/pirlygenes/data/TCR-T-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,279 copying build/lib/pirlygenes/data/TCR-T-trials.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,282 copying build/lib/pirlygenes/data/interferon-response.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,284 copying build/lib/pirlygenes/data/CAR-T-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,286 copying build/lib/pirlygenes/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,289 copying build/lib/pirlygenes/data/ADC-withdrawn.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,291 copying build/lib/pirlygenes/data/ADC-trials.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,295 copying build/lib/pirlygenes/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,298 copying build/lib/pirlygenes/data/radioligand-targets.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,300 copying build/lib/pirlygenes/data/bispecific-antibodies-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,302 copying build/lib/pirlygenes/data/multispecific-tcell-engager-trials.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-04T23:56:48,305 copying build/lib/pirlygenes/gene_sets_old.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,307 copying build/lib/pirlygenes/plot.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,309 copying build/lib/pirlygenes/gene_names.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,311 copying build/lib/pirlygenes/gene_sets_cancer.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,314 copying build/lib/pirlygenes/gene_ids.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,316 copying build/lib/pirlygenes/common.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,318 copying build/lib/pirlygenes/__init__.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,320 copying build/lib/pirlygenes/load_dataset.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,322 copying build/lib/pirlygenes/load_expression.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,325 copying build/lib/pirlygenes/transcript_to_gene.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-04T23:56:48,327 running install_egg_info 2026-04-04T23:56:48,334 Copying pirlygenes.egg-info to build/bdist.linux-armv7l/wheel/./pirlygenes-2.0.0-py3.11.egg-info 2026-04-04T23:56:48,348 running install_scripts 2026-04-04T23:56:48,361 creating build/bdist.linux-armv7l/wheel/pirlygenes-2.0.0.dist-info/WHEEL 2026-04-04T23:56:48,364 creating '/tmp/pip-wheel-o0ba0dza/.tmp-t6hxvc7b/pirlygenes-2.0.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-04T23:56:48,367 adding 'pirlygenes/PLAN-1.4.0-radioligand.md' 2026-04-04T23:56:48,368 adding 'pirlygenes/__init__.py' 2026-04-04T23:56:48,370 adding 'pirlygenes/aggregate_gene_expression.py' 2026-04-04T23:56:48,371 adding 'pirlygenes/cli.py' 2026-04-04T23:56:48,373 adding 'pirlygenes/common.py' 2026-04-04T23:56:48,375 adding 'pirlygenes/gene_ids.py' 2026-04-04T23:56:48,376 adding 'pirlygenes/gene_names.py' 2026-04-04T23:56:48,379 adding 'pirlygenes/gene_sets_cancer.py' 2026-04-04T23:56:48,380 adding 'pirlygenes/gene_sets_old.py' 2026-04-04T23:56:48,382 adding 'pirlygenes/load_dataset.py' 2026-04-04T23:56:48,383 adding 'pirlygenes/load_expression.py' 2026-04-04T23:56:48,385 adding 'pirlygenes/plot.py' 2026-04-04T23:56:48,387 adding 'pirlygenes/plot_data_helpers.py' 2026-04-04T23:56:48,389 adding 'pirlygenes/transcript_to_gene.py' 2026-04-04T23:56:48,390 adding 'pirlygenes/version.py' 2026-04-04T23:56:48,392 adding 'pirlygenes/data/ADC-approved.csv' 2026-04-04T23:56:48,396 adding 'pirlygenes/data/ADC-trials.csv' 2026-04-04T23:56:48,398 adding 'pirlygenes/data/ADC-withdrawn.csv' 2026-04-04T23:56:48,399 adding 'pirlygenes/data/CAR-T-approved.csv' 2026-04-04T23:56:48,400 adding 'pirlygenes/data/TCR-T-approved.csv' 2026-04-04T23:56:48,404 adding 'pirlygenes/data/TCR-T-trials.csv' 2026-04-04T23:56:48,406 adding 'pirlygenes/data/bispecific-antibodies-approved.csv' 2026-04-04T23:56:48,411 adding 'pirlygenes/data/cancer-driver-genes.csv' 2026-04-04T23:56:48,413 adding 'pirlygenes/data/cancer-driver-variants.csv' 2026-04-04T23:56:48,420 adding 'pirlygenes/data/cancer-testis-antigens.csv' 2026-04-04T23:56:48,421 adding 'pirlygenes/data/class1-mhc-presentation-pathway.csv' 2026-04-04T23:56:48,423 adding 'pirlygenes/data/interferon-response.csv' 2026-04-04T23:56:48,424 adding 'pirlygenes/data/multispecific-tcell-engager-trials.csv' 2026-04-04T23:56:48,425 adding 'pirlygenes/data/radioligand-targets.csv' 2026-04-04T23:56:48,429 adding 'pirlygenes-2.0.0.dist-info/licenses/LICENSE' 2026-04-04T23:56:48,432 adding 'pirlygenes-2.0.0.dist-info/METADATA' 2026-04-04T23:56:48,433 adding 'pirlygenes-2.0.0.dist-info/WHEEL' 2026-04-04T23:56:48,434 adding 'pirlygenes-2.0.0.dist-info/entry_points.txt' 2026-04-04T23:56:48,434 adding 'pirlygenes-2.0.0.dist-info/top_level.txt' 2026-04-04T23:56:48,435 adding 'pirlygenes-2.0.0.dist-info/RECORD' 2026-04-04T23:56:48,438 removing build/bdist.linux-armv7l/wheel 2026-04-04T23:56:48,555 Building wheel for pirlygenes (pyproject.toml): finished with status 'done' 2026-04-04T23:56:48,562 Created wheel for pirlygenes: filename=pirlygenes-2.0.0-py3-none-any.whl size=90443 sha256=de738501d014cdb6760b96e01afa7d18cb8dac3d863d433e9ce8fce0172641f5 2026-04-04T23:56:48,563 Stored in directory: /tmp/pip-ephem-wheel-cache-_aodlj5p/wheels/25/cc/74/361af17313c4b2d84c63981f804c378de18c9a2adfc3b97917 2026-04-04T23:56:48,576 Successfully built pirlygenes 2026-04-04T23:56:48,583 Removed build tracker: '/tmp/pip-build-tracker-50wzfql3'