2026-04-03T17:57:32,269 Created temporary directory: /tmp/pip-ephem-wheel-cache-bktotlvv 2026-04-03T17:57:32,271 Created temporary directory: /tmp/pip-build-tracker-dc295aqe 2026-04-03T17:57:32,272 Initialized build tracking at /tmp/pip-build-tracker-dc295aqe 2026-04-03T17:57:32,272 Created build tracker: /tmp/pip-build-tracker-dc295aqe 2026-04-03T17:57:32,273 Entered build tracker: /tmp/pip-build-tracker-dc295aqe 2026-04-03T17:57:32,273 Created temporary directory: /tmp/pip-wheel-_e1de1ik 2026-04-03T17:57:32,276 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 2026-04-03T17:57:32,279 Created temporary directory: /tmp/pip-ephem-wheel-cache-4rh9xg73 2026-04-03T17:57:32,301 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-03T17:57:32,304 2 location(s) to search for versions of pirlygenes: 2026-04-03T17:57:32,304 * https://pypi.org/simple/pirlygenes/ 2026-04-03T17:57:32,304 * https://www.piwheels.org/simple/pirlygenes/ 2026-04-03T17:57:32,305 Fetching project page and analyzing links: https://pypi.org/simple/pirlygenes/ 2026-04-03T17:57:32,306 Getting page https://pypi.org/simple/pirlygenes/ 2026-04-03T17:57:32,307 Found index url https://pypi.org/simple 2026-04-03T17:57:32,534 Fetched page https://pypi.org/simple/pirlygenes/ as application/vnd.pypi.simple.v1+json 2026-04-03T17:57:32,536 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) 2026-04-03T17:57:32,537 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 2026-04-03T17:57:32,538 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) 2026-04-03T17:57:32,539 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 2026-04-03T17:57:32,540 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) 2026-04-03T17:57:32,541 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 2026-04-03T17:57:32,541 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) 2026-04-03T17:57:32,542 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 2026-04-03T17:57:32,543 Fetching project page and analyzing links: https://www.piwheels.org/simple/pirlygenes/ 2026-04-03T17:57:32,544 Getting page https://www.piwheels.org/simple/pirlygenes/ 2026-04-03T17:57:32,545 Found index url https://www.piwheels.org/simple 2026-04-03T17:57:32,712 Fetched page https://www.piwheels.org/simple/pirlygenes/ as text/html 2026-04-03T17:57:32,715 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) 2026-04-03T17:57:32,715 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) 2026-04-03T17:57:32,716 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) 2026-04-03T17:57:32,716 Skipping link: not a file: https://www.piwheels.org/simple/pirlygenes/ 2026-04-03T17:57:32,717 Skipping link: not a file: https://pypi.org/simple/pirlygenes/ 2026-04-03T17:57:32,736 Given no hashes to check 1 links for project 'pirlygenes': discarding no candidates 2026-04-03T17:57:32,754 Collecting pirlygenes==1.9.0 2026-04-03T17:57:32,756 Created temporary directory: /tmp/pip-unpack-hb813bof 2026-04-03T17:57:32,980 Downloading pirlygenes-1.9.0.tar.gz (666 kB) 2026-04-03T17:57:33,285 Added pirlygenes==1.9.0 from https://files.pythonhosted.org/packages/00/21/33762d0e1497cb8f52920f8804591991b077145275a9bb472d54cb34bd3b/pirlygenes-1.9.0.tar.gz to build tracker '/tmp/pip-build-tracker-dc295aqe' 2026-04-03T17:57:33,291 Created temporary directory: /tmp/pip-build-env-kvaupzjl 2026-04-03T17:57:33,296 Installing build dependencies: started 2026-04-03T17:57:33,297 Running command pip subprocess to install build dependencies 2026-04-03T17:57:34,462 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-03T17:57:34,952 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 2026-04-03T17:57:34,975 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-03T17:57:36,789 Collecting setuptools>=60 2026-04-03T17:57:36,890 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-03T17:57:37,269 Collecting setuptools-scm>=8.0 2026-04-03T17:57:37,284 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-10.0.5-py3-none-any.whl (21 kB) 2026-04-03T17:57:37,366 Collecting vcs-versioning>=1.0.0.dev0 2026-04-03T17:57:37,382 Using cached https://www.piwheels.org/simple/vcs-versioning/vcs_versioning-1.1.1-py3-none-any.whl (79 kB) 2026-04-03T17:57:37,566 Collecting packaging>=20 2026-04-03T17:57:37,582 Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB) 2026-04-03T17:57:40,592 Installing collected packages: setuptools, packaging, vcs-versioning, setuptools-scm 2026-04-03T17:57:44,190 Creating /tmp/pip-build-env-kvaupzjl/overlay/local/bin 2026-04-03T17:57:44,192 changing mode of /tmp/pip-build-env-kvaupzjl/overlay/local/bin/vcs-versioning to 755 2026-04-03T17:57:44,305 changing mode of /tmp/pip-build-env-kvaupzjl/overlay/local/bin/setuptools-scm to 755 2026-04-03T17:57:44,332 Successfully installed packaging-26.0 setuptools-82.0.1 setuptools-scm-10.0.5 vcs-versioning-1.1.1 2026-04-03T17:57:44,618 Installing build dependencies: finished with status 'done' 2026-04-03T17:57:44,637 Getting requirements to build wheel: started 2026-04-03T17:57:44,638 Running command Getting requirements to build wheel 2026-04-03T17:57:45,324 toml section missing PosixPath('pyproject.toml') does not contain any of the tool sections: ['setuptools_scm', 'vcs-versioning'] 2026-04-03T17:57:45,442 /tmp/pip-build-env-kvaupzjl/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-03T17:57:45,442 !! 2026-04-03T17:57:45,443 ******************************************************************************** 2026-04-03T17:57:45,444 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-03T17:57:45,445 License :: OSI Approved :: Apache Software License 2026-04-03T17:57:45,446 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-03T17:57:45,446 ******************************************************************************** 2026-04-03T17:57:45,447 !! 2026-04-03T17:57:45,448 dist._finalize_license_expression() 2026-04-03T17:57:45,448 /tmp/pip-build-env-kvaupzjl/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-03T17:57:45,449 !! 2026-04-03T17:57:45,450 ******************************************************************************** 2026-04-03T17:57:45,450 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-03T17:57:45,451 License :: OSI Approved :: Apache Software License 2026-04-03T17:57:45,452 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-03T17:57:45,453 ******************************************************************************** 2026-04-03T17:57:45,454 !! 2026-04-03T17:57:45,455 self._finalize_license_expression() 2026-04-03T17:57:45,456 running egg_info 2026-04-03T17:57:45,462 writing pirlygenes.egg-info/PKG-INFO 2026-04-03T17:57:45,466 writing dependency_links to pirlygenes.egg-info/dependency_links.txt 2026-04-03T17:57:45,468 writing entry points to pirlygenes.egg-info/entry_points.txt 2026-04-03T17:57:45,470 writing requirements to pirlygenes.egg-info/requires.txt 2026-04-03T17:57:45,471 writing top-level names to pirlygenes.egg-info/top_level.txt 2026-04-03T17:57:45,512 /tmp/pip-build-env-kvaupzjl/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. 2026-04-03T17:57:45,512 return get_active_overrides().subprocess_timeout 2026-04-03T17:57:45,520 listing git files failed - pretending there aren't any 2026-04-03T17:57:45,529 reading manifest file 'pirlygenes.egg-info/SOURCES.txt' 2026-04-03T17:57:45,537 adding license file 'LICENSE' 2026-04-03T17:57:45,542 writing manifest file 'pirlygenes.egg-info/SOURCES.txt' 2026-04-03T17:57:45,647 Getting requirements to build wheel: finished with status 'done' 2026-04-03T17:57:45,651 Created temporary directory: /tmp/pip-modern-metadata-0sa1aoja 2026-04-03T17:57:45,653 Preparing metadata (pyproject.toml): started 2026-04-03T17:57:45,654 Running command Preparing metadata (pyproject.toml) 2026-04-03T17:57:46,289 toml section missing PosixPath('pyproject.toml') does not contain any of the tool sections: ['setuptools_scm', 'vcs-versioning'] 2026-04-03T17:57:46,404 /tmp/pip-build-env-kvaupzjl/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-03T17:57:46,405 !! 2026-04-03T17:57:46,406 ******************************************************************************** 2026-04-03T17:57:46,407 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-03T17:57:46,408 License :: OSI Approved :: Apache Software License 2026-04-03T17:57:46,409 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-03T17:57:46,410 ******************************************************************************** 2026-04-03T17:57:46,411 !! 2026-04-03T17:57:46,411 dist._finalize_license_expression() 2026-04-03T17:57:46,412 /tmp/pip-build-env-kvaupzjl/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-03T17:57:46,412 !! 2026-04-03T17:57:46,413 ******************************************************************************** 2026-04-03T17:57:46,414 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-03T17:57:46,415 License :: OSI Approved :: Apache Software License 2026-04-03T17:57:46,416 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-03T17:57:46,416 ******************************************************************************** 2026-04-03T17:57:46,417 !! 2026-04-03T17:57:46,418 self._finalize_license_expression() 2026-04-03T17:57:46,422 running dist_info 2026-04-03T17:57:46,436 creating /tmp/pip-modern-metadata-0sa1aoja/pirlygenes.egg-info 2026-04-03T17:57:46,437 writing /tmp/pip-modern-metadata-0sa1aoja/pirlygenes.egg-info/PKG-INFO 2026-04-03T17:57:46,441 writing dependency_links to /tmp/pip-modern-metadata-0sa1aoja/pirlygenes.egg-info/dependency_links.txt 2026-04-03T17:57:46,443 writing entry points to /tmp/pip-modern-metadata-0sa1aoja/pirlygenes.egg-info/entry_points.txt 2026-04-03T17:57:46,445 writing requirements to /tmp/pip-modern-metadata-0sa1aoja/pirlygenes.egg-info/requires.txt 2026-04-03T17:57:46,446 writing top-level names to /tmp/pip-modern-metadata-0sa1aoja/pirlygenes.egg-info/top_level.txt 2026-04-03T17:57:46,448 writing manifest file '/tmp/pip-modern-metadata-0sa1aoja/pirlygenes.egg-info/SOURCES.txt' 2026-04-03T17:57:46,487 /tmp/pip-build-env-kvaupzjl/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. 2026-04-03T17:57:46,488 return get_active_overrides().subprocess_timeout 2026-04-03T17:57:46,494 listing git files failed - pretending there aren't any 2026-04-03T17:57:46,502 reading manifest file '/tmp/pip-modern-metadata-0sa1aoja/pirlygenes.egg-info/SOURCES.txt' 2026-04-03T17:57:46,504 adding license file 'LICENSE' 2026-04-03T17:57:46,508 writing manifest file '/tmp/pip-modern-metadata-0sa1aoja/pirlygenes.egg-info/SOURCES.txt' 2026-04-03T17:57:46,509 creating '/tmp/pip-modern-metadata-0sa1aoja/pirlygenes-1.9.0.dist-info' 2026-04-03T17:57:46,647 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-03T17:57:46,652 Source in /tmp/pip-wheel-_e1de1ik/pirlygenes_469223c6d026426089175d64a62805b3 has version 1.9.0, which satisfies requirement pirlygenes==1.9.0 from https://files.pythonhosted.org/packages/00/21/33762d0e1497cb8f52920f8804591991b077145275a9bb472d54cb34bd3b/pirlygenes-1.9.0.tar.gz 2026-04-03T17:57:46,653 Removed pirlygenes==1.9.0 from https://files.pythonhosted.org/packages/00/21/33762d0e1497cb8f52920f8804591991b077145275a9bb472d54cb34bd3b/pirlygenes-1.9.0.tar.gz from build tracker '/tmp/pip-build-tracker-dc295aqe' 2026-04-03T17:57:46,660 Created temporary directory: /tmp/pip-unpack-xp9je11f 2026-04-03T17:57:46,660 Building wheels for collected packages: pirlygenes 2026-04-03T17:57:46,665 Created temporary directory: /tmp/pip-wheel-cpvm9ijx 2026-04-03T17:57:46,665 Destination directory: /tmp/pip-wheel-cpvm9ijx 2026-04-03T17:57:46,668 Building wheel for pirlygenes (pyproject.toml): started 2026-04-03T17:57:46,670 Running command Building wheel for pirlygenes (pyproject.toml) 2026-04-03T17:57:47,302 toml section missing PosixPath('pyproject.toml') does not contain any of the tool sections: ['setuptools_scm', 'vcs-versioning'] 2026-04-03T17:57:47,406 /tmp/pip-build-env-kvaupzjl/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-03T17:57:47,407 !! 2026-04-03T17:57:47,408 ******************************************************************************** 2026-04-03T17:57:47,408 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-03T17:57:47,409 License :: OSI Approved :: Apache Software License 2026-04-03T17:57:47,410 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-03T17:57:47,410 ******************************************************************************** 2026-04-03T17:57:47,411 !! 2026-04-03T17:57:47,412 dist._finalize_license_expression() 2026-04-03T17:57:47,412 /tmp/pip-build-env-kvaupzjl/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-04-03T17:57:47,413 !! 2026-04-03T17:57:47,414 ******************************************************************************** 2026-04-03T17:57:47,414 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-04-03T17:57:47,415 License :: OSI Approved :: Apache Software License 2026-04-03T17:57:47,416 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-03T17:57:47,416 ******************************************************************************** 2026-04-03T17:57:47,417 !! 2026-04-03T17:57:47,418 self._finalize_license_expression() 2026-04-03T17:57:47,419 running bdist_wheel 2026-04-03T17:57:47,440 running build 2026-04-03T17:57:47,440 running build_py 2026-04-03T17:57:47,442 creating build/lib/pirlygenes 2026-04-03T17:57:47,444 copying pirlygenes/version.py -> build/lib/pirlygenes 2026-04-03T17:57:47,446 copying pirlygenes/plot_data_helpers.py -> build/lib/pirlygenes 2026-04-03T17:57:47,448 copying pirlygenes/aggregate_gene_expression.py -> build/lib/pirlygenes 2026-04-03T17:57:47,451 copying pirlygenes/cli.py -> build/lib/pirlygenes 2026-04-03T17:57:47,453 copying pirlygenes/gene_sets_old.py -> build/lib/pirlygenes 2026-04-03T17:57:47,455 copying pirlygenes/plot.py -> build/lib/pirlygenes 2026-04-03T17:57:47,457 copying pirlygenes/gene_names.py -> build/lib/pirlygenes 2026-04-03T17:57:47,459 copying pirlygenes/gene_sets_cancer.py -> build/lib/pirlygenes 2026-04-03T17:57:47,461 copying pirlygenes/gene_ids.py -> build/lib/pirlygenes 2026-04-03T17:57:47,464 copying pirlygenes/common.py -> build/lib/pirlygenes 2026-04-03T17:57:47,465 copying pirlygenes/__init__.py -> build/lib/pirlygenes 2026-04-03T17:57:47,467 copying pirlygenes/load_dataset.py -> build/lib/pirlygenes 2026-04-03T17:57:47,469 copying pirlygenes/load_expression.py -> build/lib/pirlygenes 2026-04-03T17:57:47,471 copying pirlygenes/transcript_to_gene.py -> build/lib/pirlygenes 2026-04-03T17:57:47,473 running egg_info 2026-04-03T17:57:47,488 writing pirlygenes.egg-info/PKG-INFO 2026-04-03T17:57:47,491 writing dependency_links to pirlygenes.egg-info/dependency_links.txt 2026-04-03T17:57:47,493 writing entry points to pirlygenes.egg-info/entry_points.txt 2026-04-03T17:57:47,494 writing requirements to pirlygenes.egg-info/requires.txt 2026-04-03T17:57:47,495 writing top-level names to pirlygenes.egg-info/top_level.txt 2026-04-03T17:57:47,524 /tmp/pip-build-env-kvaupzjl/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. 2026-04-03T17:57:47,525 return get_active_overrides().subprocess_timeout 2026-04-03T17:57:47,531 listing git files failed - pretending there aren't any 2026-04-03T17:57:47,539 reading manifest file 'pirlygenes.egg-info/SOURCES.txt' 2026-04-03T17:57:47,544 adding license file 'LICENSE' 2026-04-03T17:57:47,548 writing manifest file 'pirlygenes.egg-info/SOURCES.txt' 2026-04-03T17:57:47,551 /tmp/pip-build-env-kvaupzjl/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pirlygenes.data' is absent from the `packages` configuration. 2026-04-03T17:57:47,551 !! 2026-04-03T17:57:47,552 ******************************************************************************** 2026-04-03T17:57:47,553 ############################ 2026-04-03T17:57:47,553 # Package would be ignored # 2026-04-03T17:57:47,553 ############################ 2026-04-03T17:57:47,554 Python recognizes 'pirlygenes.data' as an importable package[^1], 2026-04-03T17:57:47,554 but it is absent from setuptools' `packages` configuration. 2026-04-03T17:57:47,555 This leads to an ambiguous overall configuration. If you want to distribute this 2026-04-03T17:57:47,555 package, please make sure that 'pirlygenes.data' is explicitly added 2026-04-03T17:57:47,556 to the `packages` configuration field. 2026-04-03T17:57:47,557 Alternatively, you can also rely on setuptools' discovery methods 2026-04-03T17:57:47,557 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2026-04-03T17:57:47,558 instead of `find_packages(...)`/`find:`). 2026-04-03T17:57:47,559 You can read more about "package discovery" on setuptools documentation page: 2026-04-03T17:57:47,560 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2026-04-03T17:57:47,561 If you don't want 'pirlygenes.data' to be distributed and are 2026-04-03T17:57:47,561 already explicitly excluding 'pirlygenes.data' via 2026-04-03T17:57:47,562 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2026-04-03T17:57:47,562 you can try to use `exclude_package_data`, or `include-package-data=False` in 2026-04-03T17:57:47,563 combination with a more fine grained `package-data` configuration. 2026-04-03T17:57:47,564 You can read more about "package data files" on setuptools documentation page: 2026-04-03T17:57:47,566 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2026-04-03T17:57:47,567 [^1]: For Python, any directory (with suitable naming) can be imported, 2026-04-03T17:57:47,568 even if it does not contain any `.py` files. 2026-04-03T17:57:47,568 On the other hand, currently there is no concept of package data 2026-04-03T17:57:47,569 directory, all directories are treated like packages. 2026-04-03T17:57:47,569 ******************************************************************************** 2026-04-03T17:57:47,571 !! 2026-04-03T17:57:47,571 check.warn(importable) 2026-04-03T17:57:47,572 copying pirlygenes/PLAN-1.4.0-radioligand.md -> build/lib/pirlygenes 2026-04-03T17:57:47,573 creating build/lib/pirlygenes/data 2026-04-03T17:57:47,573 copying pirlygenes/data/ADC-approved.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,574 copying pirlygenes/data/ADC-trials.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,574 copying pirlygenes/data/ADC-withdrawn.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,575 copying pirlygenes/data/CAR-T-approved.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,575 copying pirlygenes/data/TCR-T-trials.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,576 copying pirlygenes/data/bispecific-antibodies-approved.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,577 copying pirlygenes/data/cancer-driver-genes.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,580 copying pirlygenes/data/cancer-driver-variants.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,583 copying pirlygenes/data/cancer-testis-antigens.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,587 copying pirlygenes/data/class1-mhc-presentation-pathway.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,589 copying pirlygenes/data/interferon-response.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,591 copying pirlygenes/data/multispecific-tcell-engager-trials.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,594 copying pirlygenes/data/radioligand-targets.csv -> build/lib/pirlygenes/data 2026-04-03T17:57:47,610 installing to build/bdist.linux-armv7l/wheel 2026-04-03T17:57:47,610 running install 2026-04-03T17:57:47,633 running install_lib 2026-04-03T17:57:47,641 creating build/bdist.linux-armv7l/wheel 2026-04-03T17:57:47,643 creating build/bdist.linux-armv7l/wheel/pirlygenes 2026-04-03T17:57:47,644 copying build/lib/pirlygenes/version.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,646 copying build/lib/pirlygenes/plot_data_helpers.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,649 copying build/lib/pirlygenes/aggregate_gene_expression.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,651 copying build/lib/pirlygenes/cli.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,653 copying build/lib/pirlygenes/PLAN-1.4.0-radioligand.md -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,656 creating build/bdist.linux-armv7l/wheel/pirlygenes/data 2026-04-03T17:57:47,657 copying build/lib/pirlygenes/data/ADC-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,659 copying build/lib/pirlygenes/data/class1-mhc-presentation-pathway.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,661 copying build/lib/pirlygenes/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,664 copying build/lib/pirlygenes/data/TCR-T-trials.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,666 copying build/lib/pirlygenes/data/interferon-response.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,668 copying build/lib/pirlygenes/data/CAR-T-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,670 copying build/lib/pirlygenes/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,674 copying build/lib/pirlygenes/data/ADC-withdrawn.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,676 copying build/lib/pirlygenes/data/ADC-trials.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,679 copying build/lib/pirlygenes/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,682 copying build/lib/pirlygenes/data/radioligand-targets.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,683 copying build/lib/pirlygenes/data/bispecific-antibodies-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,685 copying build/lib/pirlygenes/data/multispecific-tcell-engager-trials.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data 2026-04-03T17:57:47,687 copying build/lib/pirlygenes/gene_sets_old.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,689 copying build/lib/pirlygenes/plot.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,691 copying build/lib/pirlygenes/gene_names.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,693 copying build/lib/pirlygenes/gene_sets_cancer.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,695 copying build/lib/pirlygenes/gene_ids.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,698 copying build/lib/pirlygenes/common.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,699 copying build/lib/pirlygenes/__init__.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,701 copying build/lib/pirlygenes/load_dataset.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,703 copying build/lib/pirlygenes/load_expression.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,705 copying build/lib/pirlygenes/transcript_to_gene.py -> build/bdist.linux-armv7l/wheel/./pirlygenes 2026-04-03T17:57:47,707 running install_egg_info 2026-04-03T17:57:47,714 Copying pirlygenes.egg-info to build/bdist.linux-armv7l/wheel/./pirlygenes-1.9.0-py3.11.egg-info 2026-04-03T17:57:47,726 running install_scripts 2026-04-03T17:57:47,737 creating build/bdist.linux-armv7l/wheel/pirlygenes-1.9.0.dist-info/WHEEL 2026-04-03T17:57:47,740 creating '/tmp/pip-wheel-cpvm9ijx/.tmp-jjqkzdnf/pirlygenes-1.9.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-03T17:57:47,743 adding 'pirlygenes/PLAN-1.4.0-radioligand.md' 2026-04-03T17:57:47,744 adding 'pirlygenes/__init__.py' 2026-04-03T17:57:47,746 adding 'pirlygenes/aggregate_gene_expression.py' 2026-04-03T17:57:47,747 adding 'pirlygenes/cli.py' 2026-04-03T17:57:47,748 adding 'pirlygenes/common.py' 2026-04-03T17:57:47,750 adding 'pirlygenes/gene_ids.py' 2026-04-03T17:57:47,752 adding 'pirlygenes/gene_names.py' 2026-04-03T17:57:47,754 adding 'pirlygenes/gene_sets_cancer.py' 2026-04-03T17:57:47,755 adding 'pirlygenes/gene_sets_old.py' 2026-04-03T17:57:47,757 adding 'pirlygenes/load_dataset.py' 2026-04-03T17:57:47,758 adding 'pirlygenes/load_expression.py' 2026-04-03T17:57:47,760 adding 'pirlygenes/plot.py' 2026-04-03T17:57:47,762 adding 'pirlygenes/plot_data_helpers.py' 2026-04-03T17:57:47,764 adding 'pirlygenes/transcript_to_gene.py' 2026-04-03T17:57:47,765 adding 'pirlygenes/version.py' 2026-04-03T17:57:47,767 adding 'pirlygenes/data/ADC-approved.csv' 2026-04-03T17:57:47,771 adding 'pirlygenes/data/ADC-trials.csv' 2026-04-03T17:57:47,772 adding 'pirlygenes/data/ADC-withdrawn.csv' 2026-04-03T17:57:47,774 adding 'pirlygenes/data/CAR-T-approved.csv' 2026-04-03T17:57:47,777 adding 'pirlygenes/data/TCR-T-trials.csv' 2026-04-03T17:57:47,778 adding 'pirlygenes/data/bispecific-antibodies-approved.csv' 2026-04-03T17:57:47,784 adding 'pirlygenes/data/cancer-driver-genes.csv' 2026-04-03T17:57:47,786 adding 'pirlygenes/data/cancer-driver-variants.csv' 2026-04-03T17:57:47,792 adding 'pirlygenes/data/cancer-testis-antigens.csv' 2026-04-03T17:57:47,794 adding 'pirlygenes/data/class1-mhc-presentation-pathway.csv' 2026-04-03T17:57:47,795 adding 'pirlygenes/data/interferon-response.csv' 2026-04-03T17:57:47,797 adding 'pirlygenes/data/multispecific-tcell-engager-trials.csv' 2026-04-03T17:57:47,798 adding 'pirlygenes/data/radioligand-targets.csv' 2026-04-03T17:57:47,802 adding 'pirlygenes-1.9.0.dist-info/licenses/LICENSE' 2026-04-03T17:57:47,804 adding 'pirlygenes-1.9.0.dist-info/METADATA' 2026-04-03T17:57:47,805 adding 'pirlygenes-1.9.0.dist-info/WHEEL' 2026-04-03T17:57:47,806 adding 'pirlygenes-1.9.0.dist-info/entry_points.txt' 2026-04-03T17:57:47,807 adding 'pirlygenes-1.9.0.dist-info/top_level.txt' 2026-04-03T17:57:47,808 adding 'pirlygenes-1.9.0.dist-info/RECORD' 2026-04-03T17:57:47,810 removing build/bdist.linux-armv7l/wheel 2026-04-03T17:57:47,925 Building wheel for pirlygenes (pyproject.toml): finished with status 'done' 2026-04-03T17:57:47,931 Created wheel for pirlygenes: filename=pirlygenes-1.9.0-py3-none-any.whl size=89197 sha256=3be90370a11cc9b33de80e02b84f99700133addc5994e35bcb8b80b76f09f8ae 2026-04-03T17:57:47,933 Stored in directory: /tmp/pip-ephem-wheel-cache-4rh9xg73/wheels/4d/f5/d1/a3bc7d337928c76c31054e6477372277d36482df74bb53ad3f 2026-04-03T17:57:47,946 Successfully built pirlygenes 2026-04-03T17:57:47,952 Removed build tracker: '/tmp/pip-build-tracker-dc295aqe'