2025-12-06T17:50:03,508 Created temporary directory: /tmp/pip-ephem-wheel-cache-dprd9341 2025-12-06T17:50:03,510 Created temporary directory: /tmp/pip-build-tracker-dfogejci 2025-12-06T17:50:03,510 Initialized build tracking at /tmp/pip-build-tracker-dfogejci 2025-12-06T17:50:03,511 Created build tracker: /tmp/pip-build-tracker-dfogejci 2025-12-06T17:50:03,511 Entered build tracker: /tmp/pip-build-tracker-dfogejci 2025-12-06T17:50:03,512 Created temporary directory: /tmp/pip-wheel-h_fomyvf 2025-12-06T17:50:03,515 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 2025-12-06T17:50:03,517 Created temporary directory: /tmp/pip-ephem-wheel-cache-36yzhwm7 2025-12-06T17:50:03,541 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-12-06T17:50:03,545 2 location(s) to search for versions of homi-pipeline: 2025-12-06T17:50:03,545 * https://pypi.org/simple/homi-pipeline/ 2025-12-06T17:50:03,545 * https://www.piwheels.org/simple/homi-pipeline/ 2025-12-06T17:50:03,546 Fetching project page and analyzing links: https://pypi.org/simple/homi-pipeline/ 2025-12-06T17:50:03,546 Getting page https://pypi.org/simple/homi-pipeline/ 2025-12-06T17:50:03,548 Found index url https://pypi.org/simple 2025-12-06T17:50:03,757 Fetched page https://pypi.org/simple/homi-pipeline/ as application/vnd.pypi.simple.v1+json 2025-12-06T17:50:03,762 Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/2b/2f/d7f737bbbcf5acdb21caad36381ddf833f3ae20a98eb9f38a60d630f8b19/HoMi_pipeline-1.0.4-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,763 Found link https://files.pythonhosted.org/packages/56/81/2de14d31804045b5b7a0c582de19188c01a8de5ad3f953841f01aef86419/homi_pipeline-1.0.4.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.4 2025-12-06T17:50:03,764 Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/14/73/530144aadf2b945ecb5d635e333dfc6038a5ce1a1ea03a1d54f1cf4a40a5/HoMi_pipeline-1.0.5-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,765 Found link https://files.pythonhosted.org/packages/81/4c/0bfa30002f2c33ff1bb90392ccdf509e1f38a472e5807bc4238fb1842d7c/homi_pipeline-1.0.5.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.5 2025-12-06T17:50:03,766 Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/1e/5f/eaa4752e3474d13c00c1e7a1e6e797c898bb925f2b3bcb39fd57474bbf72/HoMi_pipeline-1.0.6-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,767 Found link https://files.pythonhosted.org/packages/96/1c/d8cf18b86b78600bbd4b771fd8c2c1965c2397e162575c65e4e1d081a12e/homi_pipeline-1.0.6.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.6 2025-12-06T17:50:03,768 Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/e7/82/b5cf93b605bb58cf43d5086e05573f7b960410768cfd10c9212c884356fe/HoMi_pipeline-1.0.7-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,768 Found link https://files.pythonhosted.org/packages/8c/ce/d1098487cb2f77ab95dab26bd6fdb548572494e84034a9ce6deb2f986b0b/homi_pipeline-1.0.7.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.7 2025-12-06T17:50:03,769 Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/67/28/51f5cc23bbf4b5db0b1afb91dc058649b690bf64beaea710305f5014b2c1/HoMi_pipeline-1.0.8-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,770 Found link https://files.pythonhosted.org/packages/58/bf/fa627d33c0c8a77ef1f2bf3ad69560a790a8b2c8cce78041b3723fa24a8d/homi_pipeline-1.0.8.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.8 2025-12-06T17:50:03,771 Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/b3/f4/88f0f43ae830bcde620a8013bf0385035eb78e6ae8dd5ef66e9499e417cd/homi_pipeline-1.0.9-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,772 Found link https://files.pythonhosted.org/packages/5e/66/35b815aa9f646b0adaa5a6b98ead6067515c76903ca272eb913d78f2c379/homi_pipeline-1.0.9.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.9 2025-12-06T17:50:03,772 Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/31/eb/3763821c57a80520685fcc7c95c3665d5b1060a84b505f7ebadad54a3b7c/homi_pipeline-1.0.10-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,773 Found link https://files.pythonhosted.org/packages/d1/5f/828957918f33fbed6588f625aaf9384a9d7569e21606e2f7560f1249b70e/homi_pipeline-1.0.10.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.10 2025-12-06T17:50:03,774 Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/ee/b7/5c8fd935b67baff8e1c27b43911a490ffe7310e210e95e541acb66663f2d/homi_pipeline-1.0.11-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,774 Found link https://files.pythonhosted.org/packages/77/41/ca735a610bd9f7998c347c3d498e65bef1dabc02f42a217adad1d4cd19dd/homi_pipeline-1.0.11.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.11 2025-12-06T17:50:03,775 Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/8b/27/5f3915836722d13033a603ff16a9f608869cf1b8ce4b9bc00a29536c0b17/homi_pipeline-1.0.12-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,776 Found link https://files.pythonhosted.org/packages/6b/5a/bcf2cb296114b08c23319bac9bf748c0978f63d2e24dd0e7c66305192ec8/homi_pipeline-1.0.12.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.12 2025-12-06T17:50:03,776 Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/74/9a/d2da42129c7899a7593cee2f9e2ef373989b1f8e2367d2b2cdb5ac6a7574/homi_pipeline-1.0.13-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,777 Found link https://files.pythonhosted.org/packages/03/a7/3a980dec3d3b7aad9fe7cd4086816f8d842a96ec3a3f243b8b4e92965ef5/homi_pipeline-1.0.13.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.13 2025-12-06T17:50:03,778 Fetching project page and analyzing links: https://www.piwheels.org/simple/homi-pipeline/ 2025-12-06T17:50:03,779 Getting page https://www.piwheels.org/simple/homi-pipeline/ 2025-12-06T17:50:03,780 Found index url https://www.piwheels.org/simple 2025-12-06T17:50:03,930 Fetched page https://www.piwheels.org/simple/homi-pipeline/ as text/html 2025-12-06T17:50:03,934 Skipping link: No binaries permitted for homi-pipeline: https://archive1.piwheels.org/simple/homi-pipeline/homi_pipeline-1.0.12-py3-none-any.whl#sha256=9e996678bebe3b97072ad16e50c5b8953a6fb84c7e7ec6311e6fb27d3e5fade7 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,934 Skipping link: No binaries permitted for homi-pipeline: https://archive1.piwheels.org/simple/homi-pipeline/homi_pipeline-1.0.11-py3-none-any.whl#sha256=f38d6f322e26b94c4b6d87ace732c953b2d93a6a5f5004b6cd68d53aeff65eb6 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,935 Skipping link: No binaries permitted for homi-pipeline: https://archive1.piwheels.org/simple/homi-pipeline/homi_pipeline-1.0.10-py3-none-any.whl#sha256=47782d893da5b163f47b447ce6624f07704ace41e7e743841962d5c074b4e366 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,936 Skipping link: No binaries permitted for homi-pipeline: https://archive1.piwheels.org/simple/homi-pipeline/homi_pipeline-1.0.9-py3-none-any.whl#sha256=7e6216111167f6a7190da3e0cde77f73360b79a8177fb09035bd1ae650c1e507 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,937 Skipping link: No binaries permitted for homi-pipeline: https://archive1.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.8-py3-none-any.whl#sha256=51b4b72a1a7278e9e56e84f3c6747b186a3e4745ad6ab68800b30a50bc914f86 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,937 Skipping link: No binaries permitted for homi-pipeline: https://archive1.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.7-py3-none-any.whl#sha256=f0dc342ef3431deb1fe0119908dfaf6639c2172a72f2e024cd0ed49f2835183a (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,937 Skipping link: No binaries permitted for homi-pipeline: https://archive1.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.6-py3-none-any.whl#sha256=db11d135158a25a6e0c26125df20efe6c4215670508e11b243dc26bde8fa475d (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,938 Skipping link: No binaries permitted for homi-pipeline: https://archive1.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.5-py3-none-any.whl#sha256=e3d12dbe9433bef87e816014c345a09af2f99a91d543497606b0105bf3c73421 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,938 Skipping link: No binaries permitted for homi-pipeline: https://archive1.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.4-py3-none-any.whl#sha256=a28da3efa0ab27e400f13a9e67038b54c72121a15fcebb90b87e2520fb85756f (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0) 2025-12-06T17:50:03,939 Skipping link: not a file: https://www.piwheels.org/simple/homi-pipeline/ 2025-12-06T17:50:03,940 Skipping link: not a file: https://pypi.org/simple/homi-pipeline/ 2025-12-06T17:50:03,964 Given no hashes to check 1 links for project 'homi-pipeline': discarding no candidates 2025-12-06T17:50:03,990 Collecting homi-pipeline==1.0.13 2025-12-06T17:50:03,994 Created temporary directory: /tmp/pip-unpack-g7ng2tp6 2025-12-06T17:50:04,145 Downloading homi_pipeline-1.0.13.tar.gz (50 kB) 2025-12-06T17:50:04,515 Added homi-pipeline==1.0.13 from https://files.pythonhosted.org/packages/03/a7/3a980dec3d3b7aad9fe7cd4086816f8d842a96ec3a3f243b8b4e92965ef5/homi_pipeline-1.0.13.tar.gz to build tracker '/tmp/pip-build-tracker-dfogejci' 2025-12-06T17:50:04,517 Running setup.py (path:/tmp/pip-wheel-h_fomyvf/homi-pipeline_b74f7552cfa34d038e8aa00e7a38ff53/setup.py) egg_info for package homi-pipeline 2025-12-06T17:50:04,518 Created temporary directory: /tmp/pip-pip-egg-info-am7okfwn 2025-12-06T17:50:04,519 Preparing metadata (setup.py): started 2025-12-06T17:50:04,520 Running command python setup.py egg_info 2025-12-06T17:50:05,098 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-12-06T17:50:05,099 !! 2025-12-06T17:50:05,100 ******************************************************************************** 2025-12-06T17:50:05,101 Requirements should be satisfied by a PEP 517 installer. 2025-12-06T17:50:05,101 If you are using pip, you can try `pip install --use-pep517`. 2025-12-06T17:50:05,102 This deprecation is overdue, please update your project and remove deprecated 2025-12-06T17:50:05,103 calls to avoid build errors in the future. 2025-12-06T17:50:05,104 ******************************************************************************** 2025-12-06T17:50:05,105 !! 2025-12-06T17:50:05,105 dist.fetch_build_eggs(dist.setup_requires) 2025-12-06T17:50:07,968 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-12-06T17:50:07,969 warnings.warn(msg) 2025-12-06T17:50:08,058 running egg_info 2025-12-06T17:50:08,087 creating /tmp/pip-pip-egg-info-am7okfwn/homi_pipeline.egg-info 2025-12-06T17:50:08,088 writing /tmp/pip-pip-egg-info-am7okfwn/homi_pipeline.egg-info/PKG-INFO 2025-12-06T17:50:08,092 writing dependency_links to /tmp/pip-pip-egg-info-am7okfwn/homi_pipeline.egg-info/dependency_links.txt 2025-12-06T17:50:08,093 writing requirements to /tmp/pip-pip-egg-info-am7okfwn/homi_pipeline.egg-info/requires.txt 2025-12-06T17:50:08,094 writing top-level names to /tmp/pip-pip-egg-info-am7okfwn/homi_pipeline.egg-info/top_level.txt 2025-12-06T17:50:08,096 writing manifest file '/tmp/pip-pip-egg-info-am7okfwn/homi_pipeline.egg-info/SOURCES.txt' 2025-12-06T17:50:08,227 reading manifest file '/tmp/pip-pip-egg-info-am7okfwn/homi_pipeline.egg-info/SOURCES.txt' 2025-12-06T17:50:08,228 adding license file 'LICENSE' 2025-12-06T17:50:08,232 writing manifest file '/tmp/pip-pip-egg-info-am7okfwn/homi_pipeline.egg-info/SOURCES.txt' 2025-12-06T17:50:08,344 Preparing metadata (setup.py): finished with status 'done' 2025-12-06T17:50:08,348 Source in /tmp/pip-wheel-h_fomyvf/homi-pipeline_b74f7552cfa34d038e8aa00e7a38ff53 has version 1.0.13, which satisfies requirement homi-pipeline==1.0.13 from https://files.pythonhosted.org/packages/03/a7/3a980dec3d3b7aad9fe7cd4086816f8d842a96ec3a3f243b8b4e92965ef5/homi_pipeline-1.0.13.tar.gz 2025-12-06T17:50:08,349 Removed homi-pipeline==1.0.13 from https://files.pythonhosted.org/packages/03/a7/3a980dec3d3b7aad9fe7cd4086816f8d842a96ec3a3f243b8b4e92965ef5/homi_pipeline-1.0.13.tar.gz from build tracker '/tmp/pip-build-tracker-dfogejci' 2025-12-06T17:50:08,355 Created temporary directory: /tmp/pip-unpack-j5_vbqf5 2025-12-06T17:50:08,355 Building wheels for collected packages: homi-pipeline 2025-12-06T17:50:08,360 Created temporary directory: /tmp/pip-wheel-fm68voq8 2025-12-06T17:50:08,361 Building wheel for homi-pipeline (setup.py): started 2025-12-06T17:50:08,362 Destination directory: /tmp/pip-wheel-fm68voq8 2025-12-06T17:50:08,362 Running command python setup.py bdist_wheel 2025-12-06T17:50:08,889 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-12-06T17:50:08,890 !! 2025-12-06T17:50:08,891 ******************************************************************************** 2025-12-06T17:50:08,891 Requirements should be satisfied by a PEP 517 installer. 2025-12-06T17:50:08,892 If you are using pip, you can try `pip install --use-pep517`. 2025-12-06T17:50:08,893 This deprecation is overdue, please update your project and remove deprecated 2025-12-06T17:50:08,893 calls to avoid build errors in the future. 2025-12-06T17:50:08,894 ******************************************************************************** 2025-12-06T17:50:08,895 !! 2025-12-06T17:50:08,895 dist.fetch_build_eggs(dist.setup_requires) 2025-12-06T17:50:09,123 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-12-06T17:50:09,123 warnings.warn(msg) 2025-12-06T17:50:09,415 running bdist_wheel 2025-12-06T17:50:09,556 running build 2025-12-06T17:50:09,556 running build_py 2025-12-06T17:50:09,591 creating build/lib/homi_pipeline 2025-12-06T17:50:09,593 copying src/homi_pipeline/HoMi_cleanup.py -> build/lib/homi_pipeline 2025-12-06T17:50:09,595 copying src/homi_pipeline/profile_setup.py -> build/lib/homi_pipeline 2025-12-06T17:50:09,598 copying src/homi_pipeline/__init__.py -> build/lib/homi_pipeline 2025-12-06T17:50:09,600 copying src/homi_pipeline/HoMi.py -> build/lib/homi_pipeline 2025-12-06T17:50:09,602 copying src/homi_pipeline/check_config.py -> build/lib/homi_pipeline 2025-12-06T17:50:09,605 copying src/homi_pipeline/snake_utils.py -> build/lib/homi_pipeline 2025-12-06T17:50:09,607 running egg_info 2025-12-06T17:50:09,636 writing src/homi_pipeline.egg-info/PKG-INFO 2025-12-06T17:50:09,640 writing dependency_links to src/homi_pipeline.egg-info/dependency_links.txt 2025-12-06T17:50:09,643 writing requirements to src/homi_pipeline.egg-info/requires.txt 2025-12-06T17:50:09,645 writing top-level names to src/homi_pipeline.egg-info/top_level.txt 2025-12-06T17:50:09,681 reading manifest file 'src/homi_pipeline.egg-info/SOURCES.txt' 2025-12-06T17:50:09,685 adding license file 'LICENSE' 2025-12-06T17:50:09,689 writing manifest file 'src/homi_pipeline.egg-info/SOURCES.txt' 2025-12-06T17:50:09,692 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'homi_pipeline.conda_envs' is absent from the `packages` configuration. 2025-12-06T17:50:09,692 !! 2025-12-06T17:50:09,693 ******************************************************************************** 2025-12-06T17:50:09,694 ############################ 2025-12-06T17:50:09,694 # Package would be ignored # 2025-12-06T17:50:09,695 ############################ 2025-12-06T17:50:09,695 Python recognizes 'homi_pipeline.conda_envs' as an importable package[^1], 2025-12-06T17:50:09,696 but it is absent from setuptools' `packages` configuration. 2025-12-06T17:50:09,697 This leads to an ambiguous overall configuration. If you want to distribute this 2025-12-06T17:50:09,697 package, please make sure that 'homi_pipeline.conda_envs' is explicitly added 2025-12-06T17:50:09,698 to the `packages` configuration field. 2025-12-06T17:50:09,699 Alternatively, you can also rely on setuptools' discovery methods 2025-12-06T17:50:09,700 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-12-06T17:50:09,701 instead of `find_packages(...)`/`find:`). 2025-12-06T17:50:09,703 You can read more about "package discovery" on setuptools documentation page: 2025-12-06T17:50:09,704 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-12-06T17:50:09,705 If you don't want 'homi_pipeline.conda_envs' to be distributed and are 2025-12-06T17:50:09,706 already explicitly excluding 'homi_pipeline.conda_envs' via 2025-12-06T17:50:09,706 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-12-06T17:50:09,707 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-12-06T17:50:09,707 combination with a more fine grained `package-data` configuration. 2025-12-06T17:50:09,708 You can read more about "package data files" on setuptools documentation page: 2025-12-06T17:50:09,709 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-12-06T17:50:09,711 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-12-06T17:50:09,712 even if it does not contain any `.py` files. 2025-12-06T17:50:09,712 On the other hand, currently there is no concept of package data 2025-12-06T17:50:09,713 directory, all directories are treated like packages. 2025-12-06T17:50:09,713 ******************************************************************************** 2025-12-06T17:50:09,714 !! 2025-12-06T17:50:09,715 check.warn(importable) 2025-12-06T17:50:09,716 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'homi_pipeline.data' is absent from the `packages` configuration. 2025-12-06T17:50:09,716 !! 2025-12-06T17:50:09,717 ******************************************************************************** 2025-12-06T17:50:09,718 ############################ 2025-12-06T17:50:09,718 # Package would be ignored # 2025-12-06T17:50:09,718 ############################ 2025-12-06T17:50:09,719 Python recognizes 'homi_pipeline.data' as an importable package[^1], 2025-12-06T17:50:09,719 but it is absent from setuptools' `packages` configuration. 2025-12-06T17:50:09,720 This leads to an ambiguous overall configuration. If you want to distribute this 2025-12-06T17:50:09,720 package, please make sure that 'homi_pipeline.data' is explicitly added 2025-12-06T17:50:09,721 to the `packages` configuration field. 2025-12-06T17:50:09,722 Alternatively, you can also rely on setuptools' discovery methods 2025-12-06T17:50:09,722 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-12-06T17:50:09,723 instead of `find_packages(...)`/`find:`). 2025-12-06T17:50:09,724 You can read more about "package discovery" on setuptools documentation page: 2025-12-06T17:50:09,724 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-12-06T17:50:09,725 If you don't want 'homi_pipeline.data' to be distributed and are 2025-12-06T17:50:09,726 already explicitly excluding 'homi_pipeline.data' via 2025-12-06T17:50:09,726 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-12-06T17:50:09,727 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-12-06T17:50:09,727 combination with a more fine grained `package-data` configuration. 2025-12-06T17:50:09,728 You can read more about "package data files" on setuptools documentation page: 2025-12-06T17:50:09,729 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-12-06T17:50:09,730 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-12-06T17:50:09,731 even if it does not contain any `.py` files. 2025-12-06T17:50:09,731 On the other hand, currently there is no concept of package data 2025-12-06T17:50:09,732 directory, all directories are treated like packages. 2025-12-06T17:50:09,732 ******************************************************************************** 2025-12-06T17:50:09,733 !! 2025-12-06T17:50:09,734 check.warn(importable) 2025-12-06T17:50:09,734 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'homi_pipeline.rule_utils' is absent from the `packages` configuration. 2025-12-06T17:50:09,735 !! 2025-12-06T17:50:09,736 ******************************************************************************** 2025-12-06T17:50:09,736 ############################ 2025-12-06T17:50:09,737 # Package would be ignored # 2025-12-06T17:50:09,737 ############################ 2025-12-06T17:50:09,738 Python recognizes 'homi_pipeline.rule_utils' as an importable package[^1], 2025-12-06T17:50:09,738 but it is absent from setuptools' `packages` configuration. 2025-12-06T17:50:09,739 This leads to an ambiguous overall configuration. If you want to distribute this 2025-12-06T17:50:09,740 package, please make sure that 'homi_pipeline.rule_utils' is explicitly added 2025-12-06T17:50:09,740 to the `packages` configuration field. 2025-12-06T17:50:09,741 Alternatively, you can also rely on setuptools' discovery methods 2025-12-06T17:50:09,742 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-12-06T17:50:09,742 instead of `find_packages(...)`/`find:`). 2025-12-06T17:50:09,743 You can read more about "package discovery" on setuptools documentation page: 2025-12-06T17:50:09,744 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-12-06T17:50:09,746 If you don't want 'homi_pipeline.rule_utils' to be distributed and are 2025-12-06T17:50:09,747 already explicitly excluding 'homi_pipeline.rule_utils' via 2025-12-06T17:50:09,748 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-12-06T17:50:09,748 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-12-06T17:50:09,749 combination with a more fine grained `package-data` configuration. 2025-12-06T17:50:09,750 You can read more about "package data files" on setuptools documentation page: 2025-12-06T17:50:09,751 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-12-06T17:50:09,753 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-12-06T17:50:09,754 even if it does not contain any `.py` files. 2025-12-06T17:50:09,754 On the other hand, currently there is no concept of package data 2025-12-06T17:50:09,755 directory, all directories are treated like packages. 2025-12-06T17:50:09,756 ******************************************************************************** 2025-12-06T17:50:09,757 !! 2025-12-06T17:50:09,757 check.warn(importable) 2025-12-06T17:50:09,758 copying src/homi_pipeline/snakefile -> build/lib/homi_pipeline 2025-12-06T17:50:09,758 creating build/lib/homi_pipeline/conda_envs 2025-12-06T17:50:09,759 copying src/homi_pipeline/conda_envs/bbmap.yaml -> build/lib/homi_pipeline/conda_envs 2025-12-06T17:50:09,759 copying src/homi_pipeline/conda_envs/fastqc.yaml -> build/lib/homi_pipeline/conda_envs 2025-12-06T17:50:09,760 copying src/homi_pipeline/conda_envs/featureCounts.yaml -> build/lib/homi_pipeline/conda_envs 2025-12-06T17:50:09,760 copying src/homi_pipeline/conda_envs/hisat2.yaml -> build/lib/homi_pipeline/conda_envs 2025-12-06T17:50:09,761 copying src/homi_pipeline/conda_envs/hostile.yaml -> build/lib/homi_pipeline/conda_envs 2025-12-06T17:50:09,761 copying src/homi_pipeline/conda_envs/humann.yaml -> build/lib/homi_pipeline/conda_envs 2025-12-06T17:50:09,762 copying src/homi_pipeline/conda_envs/kraken.yaml -> build/lib/homi_pipeline/conda_envs 2025-12-06T17:50:09,762 copying src/homi_pipeline/conda_envs/nonpareil.yaml -> build/lib/homi_pipeline/conda_envs 2025-12-06T17:50:09,763 copying src/homi_pipeline/conda_envs/r_env.yaml -> build/lib/homi_pipeline/conda_envs 2025-12-06T17:50:09,763 copying src/homi_pipeline/conda_envs/seqtk.yaml -> build/lib/homi_pipeline/conda_envs 2025-12-06T17:50:09,764 copying src/homi_pipeline/conda_envs/trimmomatic.yaml -> build/lib/homi_pipeline/conda_envs 2025-12-06T17:50:09,764 creating build/lib/homi_pipeline/data 2025-12-06T17:50:09,765 copying src/homi_pipeline/data/adapters.fa -> build/lib/homi_pipeline/data 2025-12-06T17:50:09,765 creating build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,766 copying src/homi_pipeline/rule_utils/Gut_metabolic_modules.Rmd -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,766 copying src/homi_pipeline/rule_utils/HUMAnN_microshades.Rmd -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,767 copying src/homi_pipeline/rule_utils/HUMAnN_to_phyloseq_helper.R -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,767 copying src/homi_pipeline/rule_utils/Kraken_microshades.Rmd -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,768 copying src/homi_pipeline/rule_utils/Metaphlan_microshades.Rmd -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,768 copying src/homi_pipeline/rule_utils/R_packages.R -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,769 copying src/homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,769 copying src/homi_pipeline/rule_utils/bracken_to_phyloseq_helper.R -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,770 copying src/homi_pipeline/rule_utils/combine_kreports.py -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,772 copying src/homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,775 copying src/homi_pipeline/rule_utils/counts_to_tpm.py -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,777 copying src/homi_pipeline/rule_utils/metaphlan_to_phyloseq_helper.R -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,779 copying src/homi_pipeline/rule_utils/nonpareil_curves.Rmd -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,782 copying src/homi_pipeline/rule_utils/read_reports.py -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,785 copying src/homi_pipeline/rule_utils/sam2bam.sh -> build/lib/homi_pipeline/rule_utils 2025-12-06T17:50:09,787 running build_scripts 2025-12-06T17:50:09,788 creating build/scripts-3.11 2025-12-06T17:50:09,789 copying and adjusting src/homi_pipeline/HoMi.py -> build/scripts-3.11 2025-12-06T17:50:09,792 copying src/homi_pipeline/snake_utils.py -> build/scripts-3.11 2025-12-06T17:50:09,794 copying and adjusting src/homi_pipeline/HoMi_cleanup.py -> build/scripts-3.11 2025-12-06T17:50:09,796 copying and adjusting src/homi_pipeline/profile_setup.py -> build/scripts-3.11 2025-12-06T17:50:09,799 copying and adjusting src/homi_pipeline/check_config.py -> build/scripts-3.11 2025-12-06T17:50:09,802 copying and adjusting src/homi_pipeline/rule_utils/combine_kreports.py -> build/scripts-3.11 2025-12-06T17:50:09,805 copying and adjusting src/homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py -> build/scripts-3.11 2025-12-06T17:50:09,808 copying and adjusting src/homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py -> build/scripts-3.11 2025-12-06T17:50:09,810 copying and adjusting src/homi_pipeline/rule_utils/counts_to_tpm.py -> build/scripts-3.11 2025-12-06T17:50:09,811 copying and adjusting src/homi_pipeline/rule_utils/read_reports.py -> build/scripts-3.11 2025-12-06T17:50:09,813 changing mode of build/scripts-3.11/HoMi.py from 644 to 755 2025-12-06T17:50:09,813 changing mode of build/scripts-3.11/snake_utils.py from 644 to 755 2025-12-06T17:50:09,814 changing mode of build/scripts-3.11/HoMi_cleanup.py from 644 to 755 2025-12-06T17:50:09,814 changing mode of build/scripts-3.11/profile_setup.py from 644 to 755 2025-12-06T17:50:09,815 changing mode of build/scripts-3.11/check_config.py from 644 to 755 2025-12-06T17:50:09,815 changing mode of build/scripts-3.11/combine_kreports.py from 644 to 755 2025-12-06T17:50:09,816 changing mode of build/scripts-3.11/aggregate_metaphlan_bugslists.py from 644 to 755 2025-12-06T17:50:09,816 changing mode of build/scripts-3.11/convert_mphlan_v4_to_v3.py from 644 to 755 2025-12-06T17:50:09,817 changing mode of build/scripts-3.11/counts_to_tpm.py from 644 to 755 2025-12-06T17:50:09,817 changing mode of build/scripts-3.11/read_reports.py from 644 to 755 2025-12-06T17:50:09,846 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-12-06T17:50:09,846 !! 2025-12-06T17:50:09,848 ******************************************************************************** 2025-12-06T17:50:09,848 Please avoid running ``setup.py`` directly. 2025-12-06T17:50:09,849 Instead, use pypa/build, pypa/installer or other 2025-12-06T17:50:09,850 standards-based tools. 2025-12-06T17:50:09,851 This deprecation is overdue, please update your project and remove deprecated 2025-12-06T17:50:09,852 calls to avoid build errors in the future. 2025-12-06T17:50:09,853 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-12-06T17:50:09,854 ******************************************************************************** 2025-12-06T17:50:09,855 !! 2025-12-06T17:50:09,856 self.initialize_options() 2025-12-06T17:50:09,878 installing to build/bdist.linux-armv7l/wheel 2025-12-06T17:50:09,879 running install 2025-12-06T17:50:09,904 running install_lib 2025-12-06T17:50:09,934 creating build/bdist.linux-armv7l/wheel 2025-12-06T17:50:09,936 creating build/bdist.linux-armv7l/wheel/homi_pipeline 2025-12-06T17:50:09,937 copying build/lib/homi_pipeline/HoMi_cleanup.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline 2025-12-06T17:50:09,939 copying build/lib/homi_pipeline/profile_setup.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline 2025-12-06T17:50:09,942 copying build/lib/homi_pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline 2025-12-06T17:50:09,945 copying build/lib/homi_pipeline/HoMi.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline 2025-12-06T17:50:09,949 creating build/bdist.linux-armv7l/wheel/homi_pipeline/conda_envs 2025-12-06T17:50:09,951 copying build/lib/homi_pipeline/conda_envs/nonpareil.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs 2025-12-06T17:50:09,954 copying build/lib/homi_pipeline/conda_envs/humann.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs 2025-12-06T17:50:09,958 copying build/lib/homi_pipeline/conda_envs/fastqc.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs 2025-12-06T17:50:09,960 copying build/lib/homi_pipeline/conda_envs/bbmap.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs 2025-12-06T17:50:09,962 copying build/lib/homi_pipeline/conda_envs/hostile.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs 2025-12-06T17:50:09,964 copying build/lib/homi_pipeline/conda_envs/trimmomatic.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs 2025-12-06T17:50:09,966 copying build/lib/homi_pipeline/conda_envs/kraken.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs 2025-12-06T17:50:09,967 copying build/lib/homi_pipeline/conda_envs/r_env.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs 2025-12-06T17:50:09,969 copying build/lib/homi_pipeline/conda_envs/seqtk.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs 2025-12-06T17:50:09,971 copying build/lib/homi_pipeline/conda_envs/hisat2.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs 2025-12-06T17:50:09,973 copying build/lib/homi_pipeline/conda_envs/featureCounts.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs 2025-12-06T17:50:09,975 copying build/lib/homi_pipeline/check_config.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline 2025-12-06T17:50:09,977 copying build/lib/homi_pipeline/snakefile -> build/bdist.linux-armv7l/wheel/./homi_pipeline 2025-12-06T17:50:09,980 copying build/lib/homi_pipeline/snake_utils.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline 2025-12-06T17:50:09,983 creating build/bdist.linux-armv7l/wheel/homi_pipeline/data 2025-12-06T17:50:09,984 copying build/lib/homi_pipeline/data/adapters.fa -> build/bdist.linux-armv7l/wheel/./homi_pipeline/data 2025-12-06T17:50:09,987 creating build/bdist.linux-armv7l/wheel/homi_pipeline/rule_utils 2025-12-06T17:50:09,988 copying build/lib/homi_pipeline/rule_utils/nonpareil_curves.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:09,990 copying build/lib/homi_pipeline/rule_utils/HUMAnN_to_phyloseq_helper.R -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:09,992 copying build/lib/homi_pipeline/rule_utils/Gut_metabolic_modules.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:09,995 copying build/lib/homi_pipeline/rule_utils/read_reports.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:09,998 copying build/lib/homi_pipeline/rule_utils/counts_to_tpm.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:10,001 copying build/lib/homi_pipeline/rule_utils/bracken_to_phyloseq_helper.R -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:10,004 copying build/lib/homi_pipeline/rule_utils/Kraken_microshades.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:10,008 copying build/lib/homi_pipeline/rule_utils/metaphlan_to_phyloseq_helper.R -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:10,010 copying build/lib/homi_pipeline/rule_utils/sam2bam.sh -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:10,012 copying build/lib/homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:10,013 copying build/lib/homi_pipeline/rule_utils/R_packages.R -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:10,015 copying build/lib/homi_pipeline/rule_utils/Metaphlan_microshades.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:10,017 copying build/lib/homi_pipeline/rule_utils/combine_kreports.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:10,020 copying build/lib/homi_pipeline/rule_utils/HUMAnN_microshades.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:10,023 copying build/lib/homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils 2025-12-06T17:50:10,025 running install_egg_info 2025-12-06T17:50:10,057 Copying src/homi_pipeline.egg-info to build/bdist.linux-armv7l/wheel/./homi_pipeline-1.0.13-py3.11.egg-info 2025-12-06T17:50:10,067 running install_scripts 2025-12-06T17:50:10,068 creating build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts 2025-12-06T17:50:10,070 copying build/scripts-3.11/HoMi_cleanup.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts 2025-12-06T17:50:10,072 copying build/scripts-3.11/read_reports.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts 2025-12-06T17:50:10,075 copying build/scripts-3.11/profile_setup.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts 2025-12-06T17:50:10,077 copying build/scripts-3.11/counts_to_tpm.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts 2025-12-06T17:50:10,080 copying build/scripts-3.11/HoMi.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts 2025-12-06T17:50:10,082 copying build/scripts-3.11/convert_mphlan_v4_to_v3.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts 2025-12-06T17:50:10,084 copying build/scripts-3.11/combine_kreports.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts 2025-12-06T17:50:10,087 copying build/scripts-3.11/check_config.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts 2025-12-06T17:50:10,089 copying build/scripts-3.11/snake_utils.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts 2025-12-06T17:50:10,091 copying build/scripts-3.11/aggregate_metaphlan_bugslists.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts 2025-12-06T17:50:10,093 changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts/HoMi_cleanup.py to 755 2025-12-06T17:50:10,093 changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts/read_reports.py to 755 2025-12-06T17:50:10,094 changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts/profile_setup.py to 755 2025-12-06T17:50:10,094 changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts/counts_to_tpm.py to 755 2025-12-06T17:50:10,095 changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts/HoMi.py to 755 2025-12-06T17:50:10,095 changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts/convert_mphlan_v4_to_v3.py to 755 2025-12-06T17:50:10,096 changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts/combine_kreports.py to 755 2025-12-06T17:50:10,096 changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts/check_config.py to 755 2025-12-06T17:50:10,097 changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts/snake_utils.py to 755 2025-12-06T17:50:10,097 changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.data/scripts/aggregate_metaphlan_bugslists.py to 755 2025-12-06T17:50:10,111 creating build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.13.dist-info/WHEEL 2025-12-06T17:50:10,113 creating '/tmp/pip-wheel-fm68voq8/homi_pipeline-1.0.13-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-12-06T17:50:10,116 adding 'homi_pipeline/HoMi.py' 2025-12-06T17:50:10,117 adding 'homi_pipeline/HoMi_cleanup.py' 2025-12-06T17:50:10,118 adding 'homi_pipeline/__init__.py' 2025-12-06T17:50:10,120 adding 'homi_pipeline/check_config.py' 2025-12-06T17:50:10,121 adding 'homi_pipeline/profile_setup.py' 2025-12-06T17:50:10,123 adding 'homi_pipeline/snake_utils.py' 2025-12-06T17:50:10,128 adding 'homi_pipeline/snakefile' 2025-12-06T17:50:10,130 adding 'homi_pipeline/conda_envs/bbmap.yaml' 2025-12-06T17:50:10,131 adding 'homi_pipeline/conda_envs/fastqc.yaml' 2025-12-06T17:50:10,132 adding 'homi_pipeline/conda_envs/featureCounts.yaml' 2025-12-06T17:50:10,133 adding 'homi_pipeline/conda_envs/hisat2.yaml' 2025-12-06T17:50:10,134 adding 'homi_pipeline/conda_envs/hostile.yaml' 2025-12-06T17:50:10,135 adding 'homi_pipeline/conda_envs/humann.yaml' 2025-12-06T17:50:10,137 adding 'homi_pipeline/conda_envs/kraken.yaml' 2025-12-06T17:50:10,138 adding 'homi_pipeline/conda_envs/nonpareil.yaml' 2025-12-06T17:50:10,139 adding 'homi_pipeline/conda_envs/r_env.yaml' 2025-12-06T17:50:10,140 adding 'homi_pipeline/conda_envs/seqtk.yaml' 2025-12-06T17:50:10,141 adding 'homi_pipeline/conda_envs/trimmomatic.yaml' 2025-12-06T17:50:10,143 adding 'homi_pipeline/data/adapters.fa' 2025-12-06T17:50:10,145 adding 'homi_pipeline/rule_utils/Gut_metabolic_modules.Rmd' 2025-12-06T17:50:10,147 adding 'homi_pipeline/rule_utils/HUMAnN_microshades.Rmd' 2025-12-06T17:50:10,148 adding 'homi_pipeline/rule_utils/HUMAnN_to_phyloseq_helper.R' 2025-12-06T17:50:10,150 adding 'homi_pipeline/rule_utils/Kraken_microshades.Rmd' 2025-12-06T17:50:10,152 adding 'homi_pipeline/rule_utils/Metaphlan_microshades.Rmd' 2025-12-06T17:50:10,153 adding 'homi_pipeline/rule_utils/R_packages.R' 2025-12-06T17:50:10,154 adding 'homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py' 2025-12-06T17:50:10,156 adding 'homi_pipeline/rule_utils/bracken_to_phyloseq_helper.R' 2025-12-06T17:50:10,158 adding 'homi_pipeline/rule_utils/combine_kreports.py' 2025-12-06T17:50:10,159 adding 'homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py' 2025-12-06T17:50:10,160 adding 'homi_pipeline/rule_utils/counts_to_tpm.py' 2025-12-06T17:50:10,162 adding 'homi_pipeline/rule_utils/metaphlan_to_phyloseq_helper.R' 2025-12-06T17:50:10,163 adding 'homi_pipeline/rule_utils/nonpareil_curves.Rmd' 2025-12-06T17:50:10,164 adding 'homi_pipeline/rule_utils/read_reports.py' 2025-12-06T17:50:10,165 adding 'homi_pipeline/rule_utils/sam2bam.sh' 2025-12-06T17:50:10,168 adding 'homi_pipeline-1.0.13.data/scripts/HoMi.py' 2025-12-06T17:50:10,169 adding 'homi_pipeline-1.0.13.data/scripts/HoMi_cleanup.py' 2025-12-06T17:50:10,171 adding 'homi_pipeline-1.0.13.data/scripts/aggregate_metaphlan_bugslists.py' 2025-12-06T17:50:10,172 adding 'homi_pipeline-1.0.13.data/scripts/check_config.py' 2025-12-06T17:50:10,174 adding 'homi_pipeline-1.0.13.data/scripts/combine_kreports.py' 2025-12-06T17:50:10,175 adding 'homi_pipeline-1.0.13.data/scripts/convert_mphlan_v4_to_v3.py' 2025-12-06T17:50:10,177 adding 'homi_pipeline-1.0.13.data/scripts/counts_to_tpm.py' 2025-12-06T17:50:10,178 adding 'homi_pipeline-1.0.13.data/scripts/profile_setup.py' 2025-12-06T17:50:10,180 adding 'homi_pipeline-1.0.13.data/scripts/read_reports.py' 2025-12-06T17:50:10,181 adding 'homi_pipeline-1.0.13.data/scripts/snake_utils.py' 2025-12-06T17:50:10,185 adding 'homi_pipeline-1.0.13.dist-info/licenses/LICENSE' 2025-12-06T17:50:10,187 adding 'homi_pipeline-1.0.13.dist-info/METADATA' 2025-12-06T17:50:10,188 adding 'homi_pipeline-1.0.13.dist-info/WHEEL' 2025-12-06T17:50:10,189 adding 'homi_pipeline-1.0.13.dist-info/top_level.txt' 2025-12-06T17:50:10,190 adding 'homi_pipeline-1.0.13.dist-info/RECORD' 2025-12-06T17:50:10,193 removing build/bdist.linux-armv7l/wheel 2025-12-06T17:50:10,319 Building wheel for homi-pipeline (setup.py): finished with status 'done' 2025-12-06T17:50:10,323 Created wheel for homi-pipeline: filename=homi_pipeline-1.0.13-py3-none-any.whl size=72997 sha256=f4f3f0efc19bc6dec22571e5038dbf4aa09bc085a707d57751c9d1415f1f5480 2025-12-06T17:50:10,324 Stored in directory: /tmp/pip-ephem-wheel-cache-36yzhwm7/wheels/b2/fe/70/dd3a95094e539e8ecfd7aeb2ff88a9834348f1f515003f3d8a 2025-12-06T17:50:10,336 Successfully built homi-pipeline 2025-12-06T17:50:10,341 Removed build tracker: '/tmp/pip-build-tracker-dfogejci'