2025-06-11T20:53:47,038 Created temporary directory: /tmp/pip-build-tracker-zdfey1ad 2025-06-11T20:53:47,039 Initialized build tracking at /tmp/pip-build-tracker-zdfey1ad 2025-06-11T20:53:47,040 Created build tracker: /tmp/pip-build-tracker-zdfey1ad 2025-06-11T20:53:47,040 Entered build tracker: /tmp/pip-build-tracker-zdfey1ad 2025-06-11T20:53:47,041 Created temporary directory: /tmp/pip-wheel-d0w_7wwq 2025-06-11T20:53:47,045 Created temporary directory: /tmp/pip-ephem-wheel-cache-926hs9t4 2025-06-11T20:53:47,098 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-11T20:53:47,100 2 location(s) to search for versions of pymlst: 2025-06-11T20:53:47,100 * https://pypi.org/simple/pymlst/ 2025-06-11T20:53:47,100 * https://www.piwheels.org/simple/pymlst/ 2025-06-11T20:53:47,101 Fetching project page and analyzing links: https://pypi.org/simple/pymlst/ 2025-06-11T20:53:47,102 Getting page https://pypi.org/simple/pymlst/ 2025-06-11T20:53:47,104 Found index url https://pypi.org/simple/ 2025-06-11T20:53:47,337 Fetched page https://pypi.org/simple/pymlst/ as application/vnd.pypi.simple.v1+json 2025-06-11T20:53:47,340 Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/c9/58/b20aff870603ed350a23e651f3051764f84411f47dce6a04fb7005da52a4/PyMLST-2.0.1-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0) 2025-06-11T20:53:47,341 Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/ee/ae/cb1ae640761c8bd7001800973a72b475552793dd99b8caa5e078f29a0faa/PyMLST-2.1.0-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0) 2025-06-11T20:53:47,341 Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/46/2d/d32aed32e3a77ae21226a144f0ca31b040907cfa65c6b0de4c95a49768bf/PyMLST-2.1.1-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0) 2025-06-11T20:53:47,342 Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/a1/ac/76b9312b65e1f7f7638b6eb46cecb9341c7d55a34a9796b96ce22366522f/PyMLST-2.1.2-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0) 2025-06-11T20:53:47,343 Found link https://files.pythonhosted.org/packages/b8/96/cca409adee7a3c61adc124ac12da584545819427f10487a01d84eadc71c5/PyMLST-2.1.2.tar.gz (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0), version: 2.1.2 2025-06-11T20:53:47,344 Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/79/fa/b291f5dbc74c78c7ff6f0e4225d1199d10d3e750c4273935f83327fbfedd/PyMLST-2.1.3-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0) 2025-06-11T20:53:47,345 Found link https://files.pythonhosted.org/packages/f1/ee/77f0663a2221d7e44b07a14f74c6d3279c19640338e84f2c39ed984bb166/PyMLST-2.1.3.tar.gz (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0), version: 2.1.3 2025-06-11T20:53:47,345 Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/58/2c/9087cc4a524d0ebf9a2104e229422266299f5e37d01d09f75d10288d7162/PyMLST-2.1.4-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0) 2025-06-11T20:53:47,346 Found link https://files.pythonhosted.org/packages/58/54/4ddd2e96629a17bf60e728e48e53e47f0720710db9b1416b3d34716f9824/PyMLST-2.1.4.tar.gz (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0), version: 2.1.4 2025-06-11T20:53:47,347 Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/10/24/f5fe2d09f56d6e608f0807a60f2734c2919a594bfeaee597af31dfc74324/PyMLST-2.1.5-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0) 2025-06-11T20:53:47,348 Found link https://files.pythonhosted.org/packages/e4/b0/96c1a8c9399e5bb594048bf3c9cbedb1f1708d2bd251cd540460dfb343eb/PyMLST-2.1.5.tar.gz (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0), version: 2.1.5 2025-06-11T20:53:47,348 Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/dd/50/964d6216670084035fbd5eba552322f6899802ac8603b8ba68e5806d64b8/PyMLST-2.1.6-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0) 2025-06-11T20:53:47,349 Found link https://files.pythonhosted.org/packages/d9/20/714bafa3d1d2d2ec7bbed2ada2109fa23c00432f7b4c31892b216b5bc3b4/PyMLST-2.1.6.tar.gz (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0), version: 2.1.6 2025-06-11T20:53:47,350 Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/9b/66/70a19f60f1d2f8acea2ed6bdc84acd5b71e947404392cd39c6bfd7729b67/pymlst-2.2.0-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0) 2025-06-11T20:53:47,351 Found link https://files.pythonhosted.org/packages/f9/ab/7603a73eb36681c9b81757f2626058a3f816e91803f32bca22404e3be926/pymlst-2.2.0.tar.gz (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0), version: 2.2.0 2025-06-11T20:53:47,351 Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/30/f7/bd5fbf3bbc63e3314e8fedd0e29848c446743e9d53d3260044466d2e25b1/pymlst-2.2.1-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0) 2025-06-11T20:53:47,352 Found link https://files.pythonhosted.org/packages/e6/ab/4c8c0da60a0102a3fc0b148e26989f6f32b3fe592cb9c1477b42dc316995/pymlst-2.2.1.tar.gz (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0), version: 2.2.1 2025-06-11T20:53:47,352 Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/b7/05/ef24fdf0d4930cd6c5ed697ede3a2b6567b58a5dcdc49f64bf9704ce27cd/pymlst-2.2.2-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0) 2025-06-11T20:53:47,353 Found link https://files.pythonhosted.org/packages/a9/2e/5097659fd066abe21291e0c5986e858f08dbd6ab17f13a0f1c7b09420ba7/pymlst-2.2.2.tar.gz (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0), version: 2.2.2 2025-06-11T20:53:47,354 Fetching project page and analyzing links: https://www.piwheels.org/simple/pymlst/ 2025-06-11T20:53:47,355 Getting page https://www.piwheels.org/simple/pymlst/ 2025-06-11T20:53:47,356 Found index url https://www.piwheels.org/simple/ 2025-06-11T20:53:47,516 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pymlst/ 2025-06-11T20:53:48,177 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pymlst/ 2025-06-11T20:53:49,341 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pymlst/ 2025-06-11T20:53:51,505 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pymlst/ 2025-06-11T20:53:55,666 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pymlst/ 2025-06-11T20:53:55,827 Could not fetch URL https://www.piwheels.org/simple/pymlst/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/pymlst/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping 2025-06-11T20:53:55,828 Skipping link: not a file: https://www.piwheels.org/simple/pymlst/ 2025-06-11T20:53:55,829 Skipping link: not a file: https://pypi.org/simple/pymlst/ 2025-06-11T20:53:55,848 Given no hashes to check 1 links for project 'pymlst': discarding no candidates 2025-06-11T20:53:55,849 Collecting pymlst==2.2.2 2025-06-11T20:53:55,852 Created temporary directory: /tmp/pip-unpack-d33gvng1 2025-06-11T20:53:56,079 Downloading pymlst-2.2.2.tar.gz (54 kB) 2025-06-11T20:53:56,277 Added pymlst==2.2.2 from https://files.pythonhosted.org/packages/a9/2e/5097659fd066abe21291e0c5986e858f08dbd6ab17f13a0f1c7b09420ba7/pymlst-2.2.2.tar.gz to build tracker '/tmp/pip-build-tracker-zdfey1ad' 2025-06-11T20:53:56,279 Running setup.py (path:/tmp/pip-wheel-d0w_7wwq/pymlst_06b0ab58aec8467eb252b36ef28824e7/setup.py) egg_info for package pymlst 2025-06-11T20:53:56,280 Created temporary directory: /tmp/pip-pip-egg-info-m4wt9kos 2025-06-11T20:53:56,281 Preparing metadata (setup.py): started 2025-06-11T20:53:56,282 Running command python setup.py egg_info 2025-06-11T20:53:56,834 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. 2025-06-11T20:53:56,835 !! 2025-06-11T20:53:56,836 ******************************************************************************** 2025-06-11T20:53:56,836 Usage of dash-separated 'description-file' will not be supported in future 2025-06-11T20:53:56,837 versions. Please use the underscore name 'description_file' instead. 2025-06-11T20:53:56,838 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-06-11T20:53:56,839 or your builds will no longer be supported. 2025-06-11T20:53:56,840 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-06-11T20:53:56,840 ******************************************************************************** 2025-06-11T20:53:56,842 !! 2025-06-11T20:53:56,843 opt = self._enforce_underscore(opt, section) 2025-06-11T20:53:56,866 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-06-11T20:53:56,867 !! 2025-06-11T20:53:56,868 ******************************************************************************** 2025-06-11T20:53:56,869 Requirements should be satisfied by a PEP 517 installer. 2025-06-11T20:53:56,869 If you are using pip, you can try `pip install --use-pep517`. 2025-06-11T20:53:56,871 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-11T20:53:56,871 or your builds will no longer be supported. 2025-06-11T20:53:56,872 ******************************************************************************** 2025-06-11T20:53:56,873 !! 2025-06-11T20:53:56,873 dist.fetch_build_eggs(dist.setup_requires) 2025-06-11T20:53:57,290 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. 2025-06-11T20:53:57,291 !! 2025-06-11T20:53:57,292 ******************************************************************************** 2025-06-11T20:53:57,293 Usage of dash-separated 'description-file' will not be supported in future 2025-06-11T20:53:57,294 versions. Please use the underscore name 'description_file' instead. 2025-06-11T20:53:57,294 (Affected: PyMLST). 2025-06-11T20:53:57,295 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-06-11T20:53:57,296 or your builds will no longer be supported. 2025-06-11T20:53:57,297 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-06-11T20:53:57,298 ******************************************************************************** 2025-06-11T20:53:57,300 !! 2025-06-11T20:53:57,301 opt = self._enforce_underscore(opt, section) 2025-06-11T20:53:57,301 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-11T20:53:57,302 !! 2025-06-11T20:53:57,303 ******************************************************************************** 2025-06-11T20:53:57,303 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-11T20:53:57,304 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-06-11T20:53:57,305 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-11T20:53:57,305 ******************************************************************************** 2025-06-11T20:53:57,306 !! 2025-06-11T20:53:57,307 self._finalize_license_expression() 2025-06-11T20:53:57,324 running egg_info 2025-06-11T20:53:57,353 creating /tmp/pip-pip-egg-info-m4wt9kos/PyMLST.egg-info 2025-06-11T20:53:57,354 writing /tmp/pip-pip-egg-info-m4wt9kos/PyMLST.egg-info/PKG-INFO 2025-06-11T20:53:57,358 writing dependency_links to /tmp/pip-pip-egg-info-m4wt9kos/PyMLST.egg-info/dependency_links.txt 2025-06-11T20:53:57,359 writing entry points to /tmp/pip-pip-egg-info-m4wt9kos/PyMLST.egg-info/entry_points.txt 2025-06-11T20:53:57,361 writing requirements to /tmp/pip-pip-egg-info-m4wt9kos/PyMLST.egg-info/requires.txt 2025-06-11T20:53:57,362 writing top-level names to /tmp/pip-pip-egg-info-m4wt9kos/PyMLST.egg-info/top_level.txt 2025-06-11T20:53:57,364 writing manifest file '/tmp/pip-pip-egg-info-m4wt9kos/PyMLST.egg-info/SOURCES.txt' 2025-06-11T20:53:57,466 reading manifest file '/tmp/pip-pip-egg-info-m4wt9kos/PyMLST.egg-info/SOURCES.txt' 2025-06-11T20:53:57,467 reading manifest template 'MANIFEST.in' 2025-06-11T20:53:57,473 adding license file 'LICENSE' 2025-06-11T20:53:57,477 writing manifest file '/tmp/pip-pip-egg-info-m4wt9kos/PyMLST.egg-info/SOURCES.txt' 2025-06-11T20:53:57,592 Preparing metadata (setup.py): finished with status 'done' 2025-06-11T20:53:57,597 Source in /tmp/pip-wheel-d0w_7wwq/pymlst_06b0ab58aec8467eb252b36ef28824e7 has version 2.2.2, which satisfies requirement pymlst==2.2.2 from https://files.pythonhosted.org/packages/a9/2e/5097659fd066abe21291e0c5986e858f08dbd6ab17f13a0f1c7b09420ba7/pymlst-2.2.2.tar.gz 2025-06-11T20:53:57,598 Removed pymlst==2.2.2 from https://files.pythonhosted.org/packages/a9/2e/5097659fd066abe21291e0c5986e858f08dbd6ab17f13a0f1c7b09420ba7/pymlst-2.2.2.tar.gz from build tracker '/tmp/pip-build-tracker-zdfey1ad' 2025-06-11T20:53:57,608 Created temporary directory: /tmp/pip-unpack-lj8nfzp7 2025-06-11T20:53:57,609 Created temporary directory: /tmp/pip-unpack-ampcyk6d 2025-06-11T20:53:57,610 Building wheels for collected packages: pymlst 2025-06-11T20:53:57,615 Created temporary directory: /tmp/pip-wheel-qjoojgnu 2025-06-11T20:53:57,615 DEPRECATION: Building 'pymlst' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pymlst'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-06-11T20:53:57,617 Building wheel for pymlst (setup.py): started 2025-06-11T20:53:57,618 Destination directory: /tmp/pip-wheel-qjoojgnu 2025-06-11T20:53:57,619 Running command python setup.py bdist_wheel 2025-06-11T20:53:58,393 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. 2025-06-11T20:53:58,393 !! 2025-06-11T20:53:58,394 ******************************************************************************** 2025-06-11T20:53:58,395 Usage of dash-separated 'description-file' will not be supported in future 2025-06-11T20:53:58,395 versions. Please use the underscore name 'description_file' instead. 2025-06-11T20:53:58,396 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-06-11T20:53:58,396 or your builds will no longer be supported. 2025-06-11T20:53:58,397 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-06-11T20:53:58,398 ******************************************************************************** 2025-06-11T20:53:58,399 !! 2025-06-11T20:53:58,399 opt = self._enforce_underscore(opt, section) 2025-06-11T20:53:58,421 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-06-11T20:53:58,421 !! 2025-06-11T20:53:58,422 ******************************************************************************** 2025-06-11T20:53:58,423 Requirements should be satisfied by a PEP 517 installer. 2025-06-11T20:53:58,423 If you are using pip, you can try `pip install --use-pep517`. 2025-06-11T20:53:58,424 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-11T20:53:58,425 or your builds will no longer be supported. 2025-06-11T20:53:58,425 ******************************************************************************** 2025-06-11T20:53:58,426 !! 2025-06-11T20:53:58,427 dist.fetch_build_eggs(dist.setup_requires) 2025-06-11T20:53:58,853 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. 2025-06-11T20:53:58,854 !! 2025-06-11T20:53:58,855 ******************************************************************************** 2025-06-11T20:53:58,856 Usage of dash-separated 'description-file' will not be supported in future 2025-06-11T20:53:58,856 versions. Please use the underscore name 'description_file' instead. 2025-06-11T20:53:58,857 (Affected: PyMLST). 2025-06-11T20:53:58,859 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-06-11T20:53:58,859 or your builds will no longer be supported. 2025-06-11T20:53:58,861 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-06-11T20:53:58,862 ******************************************************************************** 2025-06-11T20:53:58,864 !! 2025-06-11T20:53:58,865 opt = self._enforce_underscore(opt, section) 2025-06-11T20:53:58,867 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-11T20:53:58,868 !! 2025-06-11T20:53:58,871 ******************************************************************************** 2025-06-11T20:53:58,872 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-11T20:53:58,875 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-06-11T20:53:58,878 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-11T20:53:58,880 ******************************************************************************** 2025-06-11T20:53:58,883 !! 2025-06-11T20:53:58,884 self._finalize_license_expression() 2025-06-11T20:53:58,886 running bdist_wheel 2025-06-11T20:53:59,463 running build 2025-06-11T20:53:59,464 running build_py 2025-06-11T20:53:59,495 creating build/lib/pymlst 2025-06-11T20:53:59,497 copying pymlst/config.py -> build/lib/pymlst 2025-06-11T20:53:59,500 copying pymlst/version.py -> build/lib/pymlst 2025-06-11T20:53:59,501 copying pymlst/__init__.py -> build/lib/pymlst 2025-06-11T20:53:59,503 copying pymlst/cmd.py -> build/lib/pymlst 2025-06-11T20:53:59,506 creating build/lib/pymlst/common 2025-06-11T20:53:59,507 copying pymlst/common/web.py -> build/lib/pymlst/common 2025-06-11T20:53:59,510 copying pymlst/common/kma.py -> build/lib/pymlst/common 2025-06-11T20:53:59,512 copying pymlst/common/__init__.py -> build/lib/pymlst/common 2025-06-11T20:53:59,514 copying pymlst/common/blat.py -> build/lib/pymlst/common 2025-06-11T20:53:59,516 copying pymlst/common/flag.py -> build/lib/pymlst/common 2025-06-11T20:53:59,517 copying pymlst/common/psl.py -> build/lib/pymlst/common 2025-06-11T20:53:59,520 copying pymlst/common/utils.py -> build/lib/pymlst/common 2025-06-11T20:53:59,522 copying pymlst/common/mafft.py -> build/lib/pymlst/common 2025-06-11T20:53:59,524 copying pymlst/common/exceptions.py -> build/lib/pymlst/common 2025-06-11T20:53:59,526 creating build/lib/pymlst/wg 2025-06-11T20:53:59,527 copying pymlst/wg/__init__.py -> build/lib/pymlst/wg 2025-06-11T20:53:59,529 copying pymlst/wg/core.py -> build/lib/pymlst/wg 2025-06-11T20:53:59,532 copying pymlst/wg/extractors.py -> build/lib/pymlst/wg 2025-06-11T20:53:59,534 copying pymlst/wg/model.py -> build/lib/pymlst/wg 2025-06-11T20:53:59,537 creating build/lib/pymlst/pytyper 2025-06-11T20:53:59,539 copying pymlst/pytyper/__init__.py -> build/lib/pymlst/pytyper 2025-06-11T20:53:59,541 copying pymlst/pytyper/core.py -> build/lib/pymlst/pytyper 2025-06-11T20:53:59,545 copying pymlst/pytyper/url.py -> build/lib/pymlst/pytyper 2025-06-11T20:53:59,546 copying pymlst/pytyper/method.py -> build/lib/pymlst/pytyper 2025-06-11T20:53:59,548 copying pymlst/pytyper/model.py -> build/lib/pymlst/pytyper 2025-06-11T20:53:59,550 creating build/lib/pymlst/cla 2025-06-11T20:53:59,551 copying pymlst/cla/__init__.py -> build/lib/pymlst/cla 2025-06-11T20:53:59,553 copying pymlst/cla/core.py -> build/lib/pymlst/cla 2025-06-11T20:53:59,556 copying pymlst/cla/model.py -> build/lib/pymlst/cla 2025-06-11T20:53:59,558 creating build/lib/pymlst/common/commands 2025-06-11T20:53:59,559 copying pymlst/common/commands/__init__.py -> build/lib/pymlst/common/commands 2025-06-11T20:53:59,561 copying pymlst/common/commands/configure.py -> build/lib/pymlst/common/commands 2025-06-11T20:53:59,564 creating build/lib/pymlst/wg/commands 2025-06-11T20:53:59,565 copying pymlst/wg/commands/add.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,567 copying pymlst/wg/commands/add2.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,568 copying pymlst/wg/commands/__init__.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,570 copying pymlst/wg/commands/msa.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,572 copying pymlst/wg/commands/mlst.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,574 copying pymlst/wg/commands/recombination.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,575 copying pymlst/wg/commands/sequence.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,577 copying pymlst/wg/commands/import.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,580 copying pymlst/wg/commands/create.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,582 copying pymlst/wg/commands/gene.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,583 copying pymlst/wg/commands/strain.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,585 copying pymlst/wg/commands/distance.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,587 copying pymlst/wg/commands/subgraph.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,589 copying pymlst/wg/commands/remove.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,591 copying pymlst/wg/commands/stats.py -> build/lib/pymlst/wg/commands 2025-06-11T20:53:59,594 creating build/lib/pymlst/pytyper/commands 2025-06-11T20:53:59,595 copying pymlst/pytyper/commands/__init__.py -> build/lib/pymlst/pytyper/commands 2025-06-11T20:53:59,597 copying pymlst/pytyper/commands/search.py -> build/lib/pymlst/pytyper/commands 2025-06-11T20:53:59,599 creating build/lib/pymlst/cla/commands 2025-06-11T20:53:59,600 copying pymlst/cla/commands/__init__.py -> build/lib/pymlst/cla/commands 2025-06-11T20:53:59,602 copying pymlst/cla/commands/search.py -> build/lib/pymlst/cla/commands 2025-06-11T20:53:59,604 copying pymlst/cla/commands/info.py -> build/lib/pymlst/cla/commands 2025-06-11T20:53:59,605 copying pymlst/cla/commands/import.py -> build/lib/pymlst/cla/commands 2025-06-11T20:53:59,607 copying pymlst/cla/commands/create.py -> build/lib/pymlst/cla/commands 2025-06-11T20:53:59,609 copying pymlst/cla/commands/search2.py -> build/lib/pymlst/cla/commands 2025-06-11T20:53:59,611 copying pymlst/cla/commands/remove.py -> build/lib/pymlst/cla/commands 2025-06-11T20:53:59,612 running egg_info 2025-06-11T20:53:59,642 writing PyMLST.egg-info/PKG-INFO 2025-06-11T20:53:59,645 writing dependency_links to PyMLST.egg-info/dependency_links.txt 2025-06-11T20:53:59,647 writing entry points to PyMLST.egg-info/entry_points.txt 2025-06-11T20:53:59,649 writing requirements to PyMLST.egg-info/requires.txt 2025-06-11T20:53:59,650 writing top-level names to PyMLST.egg-info/top_level.txt 2025-06-11T20:53:59,689 reading manifest file 'PyMLST.egg-info/SOURCES.txt' 2025-06-11T20:53:59,696 reading manifest template 'MANIFEST.in' 2025-06-11T20:53:59,701 adding license file 'LICENSE' 2025-06-11T20:53:59,706 writing manifest file 'PyMLST.egg-info/SOURCES.txt' 2025-06-11T20:53:59,708 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pymlst.data.alembic' is absent from the `packages` configuration. 2025-06-11T20:53:59,709 !! 2025-06-11T20:53:59,710 ******************************************************************************** 2025-06-11T20:53:59,711 ############################ 2025-06-11T20:53:59,711 # Package would be ignored # 2025-06-11T20:53:59,712 ############################ 2025-06-11T20:53:59,713 Python recognizes 'pymlst.data.alembic' as an importable package[^1], 2025-06-11T20:53:59,713 but it is absent from setuptools' `packages` configuration. 2025-06-11T20:53:59,715 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T20:53:59,715 package, please make sure that 'pymlst.data.alembic' is explicitly added 2025-06-11T20:53:59,716 to the `packages` configuration field. 2025-06-11T20:53:59,717 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T20:53:59,717 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T20:53:59,718 instead of `find_packages(...)`/`find:`). 2025-06-11T20:53:59,719 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T20:53:59,720 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T20:53:59,722 If you don't want 'pymlst.data.alembic' to be distributed and are 2025-06-11T20:53:59,722 already explicitly excluding 'pymlst.data.alembic' via 2025-06-11T20:53:59,723 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T20:53:59,723 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T20:53:59,724 combination with a more fine grained `package-data` configuration. 2025-06-11T20:53:59,725 You can read more about "package data files" on setuptools documentation page: 2025-06-11T20:53:59,726 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T20:53:59,728 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T20:53:59,729 even if it does not contain any `.py` files. 2025-06-11T20:53:59,729 On the other hand, currently there is no concept of package data 2025-06-11T20:53:59,730 directory, all directories are treated like packages. 2025-06-11T20:53:59,731 ******************************************************************************** 2025-06-11T20:53:59,732 !! 2025-06-11T20:53:59,732 check.warn(importable) 2025-06-11T20:53:59,733 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pymlst.data.alembic.cla' is absent from the `packages` configuration. 2025-06-11T20:53:59,733 !! 2025-06-11T20:53:59,734 ******************************************************************************** 2025-06-11T20:53:59,735 ############################ 2025-06-11T20:53:59,735 # Package would be ignored # 2025-06-11T20:53:59,736 ############################ 2025-06-11T20:53:59,736 Python recognizes 'pymlst.data.alembic.cla' as an importable package[^1], 2025-06-11T20:53:59,737 but it is absent from setuptools' `packages` configuration. 2025-06-11T20:53:59,738 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T20:53:59,738 package, please make sure that 'pymlst.data.alembic.cla' is explicitly added 2025-06-11T20:53:59,739 to the `packages` configuration field. 2025-06-11T20:53:59,740 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T20:53:59,740 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T20:53:59,741 instead of `find_packages(...)`/`find:`). 2025-06-11T20:53:59,742 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T20:53:59,743 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T20:53:59,744 If you don't want 'pymlst.data.alembic.cla' to be distributed and are 2025-06-11T20:53:59,744 already explicitly excluding 'pymlst.data.alembic.cla' via 2025-06-11T20:53:59,745 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T20:53:59,745 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T20:53:59,746 combination with a more fine grained `package-data` configuration. 2025-06-11T20:53:59,747 You can read more about "package data files" on setuptools documentation page: 2025-06-11T20:53:59,748 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T20:53:59,750 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T20:53:59,751 even if it does not contain any `.py` files. 2025-06-11T20:53:59,751 On the other hand, currently there is no concept of package data 2025-06-11T20:53:59,752 directory, all directories are treated like packages. 2025-06-11T20:53:59,752 ******************************************************************************** 2025-06-11T20:53:59,753 !! 2025-06-11T20:53:59,754 check.warn(importable) 2025-06-11T20:53:59,754 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pymlst.data.alembic.cla.versions' is absent from the `packages` configuration. 2025-06-11T20:53:59,755 !! 2025-06-11T20:53:59,756 ******************************************************************************** 2025-06-11T20:53:59,757 ############################ 2025-06-11T20:53:59,757 # Package would be ignored # 2025-06-11T20:53:59,758 ############################ 2025-06-11T20:53:59,758 Python recognizes 'pymlst.data.alembic.cla.versions' as an importable package[^1], 2025-06-11T20:53:59,759 but it is absent from setuptools' `packages` configuration. 2025-06-11T20:53:59,760 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T20:53:59,761 package, please make sure that 'pymlst.data.alembic.cla.versions' is explicitly added 2025-06-11T20:53:59,761 to the `packages` configuration field. 2025-06-11T20:53:59,762 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T20:53:59,763 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T20:53:59,763 instead of `find_packages(...)`/`find:`). 2025-06-11T20:53:59,765 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T20:53:59,765 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T20:53:59,766 If you don't want 'pymlst.data.alembic.cla.versions' to be distributed and are 2025-06-11T20:53:59,767 already explicitly excluding 'pymlst.data.alembic.cla.versions' via 2025-06-11T20:53:59,767 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T20:53:59,768 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T20:53:59,768 combination with a more fine grained `package-data` configuration. 2025-06-11T20:53:59,769 You can read more about "package data files" on setuptools documentation page: 2025-06-11T20:53:59,770 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T20:53:59,772 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T20:53:59,772 even if it does not contain any `.py` files. 2025-06-11T20:53:59,773 On the other hand, currently there is no concept of package data 2025-06-11T20:53:59,773 directory, all directories are treated like packages. 2025-06-11T20:53:59,774 ******************************************************************************** 2025-06-11T20:53:59,775 !! 2025-06-11T20:53:59,776 check.warn(importable) 2025-06-11T20:53:59,776 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pymlst.data.alembic.pytyper' is absent from the `packages` configuration. 2025-06-11T20:53:59,777 !! 2025-06-11T20:53:59,779 ******************************************************************************** 2025-06-11T20:53:59,779 ############################ 2025-06-11T20:53:59,780 # Package would be ignored # 2025-06-11T20:53:59,780 ############################ 2025-06-11T20:53:59,781 Python recognizes 'pymlst.data.alembic.pytyper' as an importable package[^1], 2025-06-11T20:53:59,782 but it is absent from setuptools' `packages` configuration. 2025-06-11T20:53:59,783 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T20:53:59,784 package, please make sure that 'pymlst.data.alembic.pytyper' is explicitly added 2025-06-11T20:53:59,784 to the `packages` configuration field. 2025-06-11T20:53:59,786 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T20:53:59,787 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T20:53:59,787 instead of `find_packages(...)`/`find:`). 2025-06-11T20:53:59,789 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T20:53:59,790 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T20:53:59,791 If you don't want 'pymlst.data.alembic.pytyper' to be distributed and are 2025-06-11T20:53:59,792 already explicitly excluding 'pymlst.data.alembic.pytyper' via 2025-06-11T20:53:59,793 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T20:53:59,793 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T20:53:59,794 combination with a more fine grained `package-data` configuration. 2025-06-11T20:53:59,796 You can read more about "package data files" on setuptools documentation page: 2025-06-11T20:53:59,797 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T20:53:59,798 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T20:53:59,799 even if it does not contain any `.py` files. 2025-06-11T20:53:59,799 On the other hand, currently there is no concept of package data 2025-06-11T20:53:59,800 directory, all directories are treated like packages. 2025-06-11T20:53:59,800 ******************************************************************************** 2025-06-11T20:53:59,801 !! 2025-06-11T20:53:59,801 check.warn(importable) 2025-06-11T20:53:59,802 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pymlst.data.alembic.pytyper.versions' is absent from the `packages` configuration. 2025-06-11T20:53:59,802 !! 2025-06-11T20:53:59,803 ******************************************************************************** 2025-06-11T20:53:59,804 ############################ 2025-06-11T20:53:59,804 # Package would be ignored # 2025-06-11T20:53:59,805 ############################ 2025-06-11T20:53:59,805 Python recognizes 'pymlst.data.alembic.pytyper.versions' as an importable package[^1], 2025-06-11T20:53:59,806 but it is absent from setuptools' `packages` configuration. 2025-06-11T20:53:59,807 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T20:53:59,807 package, please make sure that 'pymlst.data.alembic.pytyper.versions' is explicitly added 2025-06-11T20:53:59,808 to the `packages` configuration field. 2025-06-11T20:53:59,809 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T20:53:59,810 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T20:53:59,810 instead of `find_packages(...)`/`find:`). 2025-06-11T20:53:59,812 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T20:53:59,813 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T20:53:59,814 If you don't want 'pymlst.data.alembic.pytyper.versions' to be distributed and are 2025-06-11T20:53:59,815 already explicitly excluding 'pymlst.data.alembic.pytyper.versions' via 2025-06-11T20:53:59,816 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T20:53:59,816 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T20:53:59,817 combination with a more fine grained `package-data` configuration. 2025-06-11T20:53:59,818 You can read more about "package data files" on setuptools documentation page: 2025-06-11T20:53:59,819 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T20:53:59,821 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T20:53:59,822 even if it does not contain any `.py` files. 2025-06-11T20:53:59,822 On the other hand, currently there is no concept of package data 2025-06-11T20:53:59,823 directory, all directories are treated like packages. 2025-06-11T20:53:59,824 ******************************************************************************** 2025-06-11T20:53:59,825 !! 2025-06-11T20:53:59,825 check.warn(importable) 2025-06-11T20:53:59,826 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pymlst.data.alembic.wg' is absent from the `packages` configuration. 2025-06-11T20:53:59,827 !! 2025-06-11T20:53:59,828 ******************************************************************************** 2025-06-11T20:53:59,829 ############################ 2025-06-11T20:53:59,830 # Package would be ignored # 2025-06-11T20:53:59,830 ############################ 2025-06-11T20:53:59,831 Python recognizes 'pymlst.data.alembic.wg' as an importable package[^1], 2025-06-11T20:53:59,831 but it is absent from setuptools' `packages` configuration. 2025-06-11T20:53:59,832 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T20:53:59,832 package, please make sure that 'pymlst.data.alembic.wg' is explicitly added 2025-06-11T20:53:59,833 to the `packages` configuration field. 2025-06-11T20:53:59,834 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T20:53:59,834 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T20:53:59,835 instead of `find_packages(...)`/`find:`). 2025-06-11T20:53:59,836 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T20:53:59,837 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T20:53:59,838 If you don't want 'pymlst.data.alembic.wg' to be distributed and are 2025-06-11T20:53:59,838 already explicitly excluding 'pymlst.data.alembic.wg' via 2025-06-11T20:53:59,839 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T20:53:59,839 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T20:53:59,840 combination with a more fine grained `package-data` configuration. 2025-06-11T20:53:59,841 You can read more about "package data files" on setuptools documentation page: 2025-06-11T20:53:59,842 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T20:53:59,844 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T20:53:59,845 even if it does not contain any `.py` files. 2025-06-11T20:53:59,846 On the other hand, currently there is no concept of package data 2025-06-11T20:53:59,846 directory, all directories are treated like packages. 2025-06-11T20:53:59,847 ******************************************************************************** 2025-06-11T20:53:59,848 !! 2025-06-11T20:53:59,849 check.warn(importable) 2025-06-11T20:53:59,849 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pymlst.data.alembic.wg.versions' is absent from the `packages` configuration. 2025-06-11T20:53:59,850 !! 2025-06-11T20:53:59,851 ******************************************************************************** 2025-06-11T20:53:59,852 ############################ 2025-06-11T20:53:59,853 # Package would be ignored # 2025-06-11T20:53:59,853 ############################ 2025-06-11T20:53:59,854 Python recognizes 'pymlst.data.alembic.wg.versions' as an importable package[^1], 2025-06-11T20:53:59,854 but it is absent from setuptools' `packages` configuration. 2025-06-11T20:53:59,855 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T20:53:59,856 package, please make sure that 'pymlst.data.alembic.wg.versions' is explicitly added 2025-06-11T20:53:59,856 to the `packages` configuration field. 2025-06-11T20:53:59,858 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T20:53:59,858 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T20:53:59,859 instead of `find_packages(...)`/`find:`). 2025-06-11T20:53:59,860 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T20:53:59,862 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T20:53:59,863 If you don't want 'pymlst.data.alembic.wg.versions' to be distributed and are 2025-06-11T20:53:59,864 already explicitly excluding 'pymlst.data.alembic.wg.versions' via 2025-06-11T20:53:59,865 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T20:53:59,865 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T20:53:59,866 combination with a more fine grained `package-data` configuration. 2025-06-11T20:53:59,867 You can read more about "package data files" on setuptools documentation page: 2025-06-11T20:53:59,868 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T20:53:59,869 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T20:53:59,870 even if it does not contain any `.py` files. 2025-06-11T20:53:59,870 On the other hand, currently there is no concept of package data 2025-06-11T20:53:59,871 directory, all directories are treated like packages. 2025-06-11T20:53:59,871 ******************************************************************************** 2025-06-11T20:53:59,872 !! 2025-06-11T20:53:59,873 check.warn(importable) 2025-06-11T20:53:59,873 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pymlst.data.pytyper' is absent from the `packages` configuration. 2025-06-11T20:53:59,874 !! 2025-06-11T20:53:59,875 ******************************************************************************** 2025-06-11T20:53:59,875 ############################ 2025-06-11T20:53:59,876 # Package would be ignored # 2025-06-11T20:53:59,876 ############################ 2025-06-11T20:53:59,877 Python recognizes 'pymlst.data.pytyper' as an importable package[^1], 2025-06-11T20:53:59,877 but it is absent from setuptools' `packages` configuration. 2025-06-11T20:53:59,879 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T20:53:59,879 package, please make sure that 'pymlst.data.pytyper' is explicitly added 2025-06-11T20:53:59,880 to the `packages` configuration field. 2025-06-11T20:53:59,881 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T20:53:59,882 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T20:53:59,883 instead of `find_packages(...)`/`find:`). 2025-06-11T20:53:59,885 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T20:53:59,887 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T20:53:59,888 If you don't want 'pymlst.data.pytyper' to be distributed and are 2025-06-11T20:53:59,889 already explicitly excluding 'pymlst.data.pytyper' via 2025-06-11T20:53:59,890 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T20:53:59,891 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T20:53:59,892 combination with a more fine grained `package-data` configuration. 2025-06-11T20:53:59,893 You can read more about "package data files" on setuptools documentation page: 2025-06-11T20:53:59,895 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T20:53:59,896 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T20:53:59,897 even if it does not contain any `.py` files. 2025-06-11T20:53:59,897 On the other hand, currently there is no concept of package data 2025-06-11T20:53:59,898 directory, all directories are treated like packages. 2025-06-11T20:53:59,899 ******************************************************************************** 2025-06-11T20:53:59,900 !! 2025-06-11T20:53:59,901 check.warn(importable) 2025-06-11T20:53:59,901 creating build/lib/pymlst/data/alembic 2025-06-11T20:53:59,902 copying pymlst/data/alembic/alembic.ini -> build/lib/pymlst/data/alembic 2025-06-11T20:53:59,903 creating build/lib/pymlst/data/alembic/cla 2025-06-11T20:53:59,903 copying pymlst/data/alembic/cla/env.py -> build/lib/pymlst/data/alembic/cla 2025-06-11T20:53:59,904 copying pymlst/data/alembic/cla/script.py.mako -> build/lib/pymlst/data/alembic/cla 2025-06-11T20:53:59,904 creating build/lib/pymlst/data/alembic/cla/versions 2025-06-11T20:53:59,905 copying pymlst/data/alembic/cla/versions/21efe503d07d_initial.py -> build/lib/pymlst/data/alembic/cla/versions 2025-06-11T20:53:59,905 copying pymlst/data/alembic/cla/versions/c0f871a99d96_add_database_infos.py -> build/lib/pymlst/data/alembic/cla/versions 2025-06-11T20:53:59,906 creating build/lib/pymlst/data/alembic/pytyper 2025-06-11T20:53:59,906 copying pymlst/data/alembic/pytyper/env.py -> build/lib/pymlst/data/alembic/pytyper 2025-06-11T20:53:59,907 copying pymlst/data/alembic/pytyper/script.py.mako -> build/lib/pymlst/data/alembic/pytyper 2025-06-11T20:53:59,907 creating build/lib/pymlst/data/alembic/pytyper/versions 2025-06-11T20:53:59,908 copying pymlst/data/alembic/pytyper/versions/1f96d027f4aa_initial.py -> build/lib/pymlst/data/alembic/pytyper/versions 2025-06-11T20:53:59,908 creating build/lib/pymlst/data/alembic/wg 2025-06-11T20:53:59,909 copying pymlst/data/alembic/wg/env.py -> build/lib/pymlst/data/alembic/wg 2025-06-11T20:53:59,909 copying pymlst/data/alembic/wg/script.py.mako -> build/lib/pymlst/data/alembic/wg 2025-06-11T20:53:59,910 creating build/lib/pymlst/data/alembic/wg/versions 2025-06-11T20:53:59,910 copying pymlst/data/alembic/wg/versions/52ae99cb5f33_initial.py -> build/lib/pymlst/data/alembic/wg/versions 2025-06-11T20:53:59,911 copying pymlst/data/alembic/wg/versions/a793f8f3fd83_add_database_infos.py -> build/lib/pymlst/data/alembic/wg/versions 2025-06-11T20:53:59,912 creating build/lib/pymlst/data/pytyper 2025-06-11T20:53:59,912 copying pymlst/data/pytyper/clmt.fna -> build/lib/pymlst/data/pytyper 2025-06-11T20:53:59,913 copying pymlst/data/pytyper/clmt.txt -> build/lib/pymlst/data/pytyper 2025-06-11T20:53:59,913 copying pymlst/data/pytyper/fimh.fna -> build/lib/pymlst/data/pytyper 2025-06-11T20:53:59,914 copying pymlst/data/pytyper/spa.fna -> build/lib/pymlst/data/pytyper 2025-06-11T20:53:59,914 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-11T20:53:59,915 !! 2025-06-11T20:53:59,916 ******************************************************************************** 2025-06-11T20:53:59,917 Please avoid running ``setup.py`` directly. 2025-06-11T20:53:59,917 Instead, use pypa/build, pypa/installer or other 2025-06-11T20:53:59,918 standards-based tools. 2025-06-11T20:53:59,919 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-11T20:53:59,920 or your builds will no longer be supported. 2025-06-11T20:53:59,921 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-11T20:53:59,921 ******************************************************************************** 2025-06-11T20:53:59,923 !! 2025-06-11T20:53:59,923 self.initialize_options() 2025-06-11T20:53:59,924 installing to build/bdist.linux-armv7l/wheel 2025-06-11T20:53:59,924 running install 2025-06-11T20:53:59,925 running install_lib 2025-06-11T20:53:59,925 creating build/bdist.linux-armv7l/wheel 2025-06-11T20:53:59,926 creating build/bdist.linux-armv7l/wheel/pymlst 2025-06-11T20:53:59,927 copying build/lib/pymlst/config.py -> build/bdist.linux-armv7l/wheel/./pymlst 2025-06-11T20:53:59,927 copying build/lib/pymlst/version.py -> build/bdist.linux-armv7l/wheel/./pymlst 2025-06-11T20:53:59,928 copying build/lib/pymlst/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst 2025-06-11T20:53:59,928 creating build/bdist.linux-armv7l/wheel/pymlst/common 2025-06-11T20:53:59,929 copying build/lib/pymlst/common/web.py -> build/bdist.linux-armv7l/wheel/./pymlst/common 2025-06-11T20:53:59,930 copying build/lib/pymlst/common/kma.py -> build/bdist.linux-armv7l/wheel/./pymlst/common 2025-06-11T20:53:59,930 copying build/lib/pymlst/common/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/common 2025-06-11T20:53:59,931 copying build/lib/pymlst/common/blat.py -> build/bdist.linux-armv7l/wheel/./pymlst/common 2025-06-11T20:53:59,931 copying build/lib/pymlst/common/flag.py -> build/bdist.linux-armv7l/wheel/./pymlst/common 2025-06-11T20:53:59,932 copying build/lib/pymlst/common/psl.py -> build/bdist.linux-armv7l/wheel/./pymlst/common 2025-06-11T20:53:59,932 copying build/lib/pymlst/common/utils.py -> build/bdist.linux-armv7l/wheel/./pymlst/common 2025-06-11T20:53:59,933 copying build/lib/pymlst/common/mafft.py -> build/bdist.linux-armv7l/wheel/./pymlst/common 2025-06-11T20:53:59,934 copying build/lib/pymlst/common/exceptions.py -> build/bdist.linux-armv7l/wheel/./pymlst/common 2025-06-11T20:53:59,936 creating build/bdist.linux-armv7l/wheel/pymlst/common/commands 2025-06-11T20:53:59,937 copying build/lib/pymlst/common/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/common/commands 2025-06-11T20:53:59,939 copying build/lib/pymlst/common/commands/configure.py -> build/bdist.linux-armv7l/wheel/./pymlst/common/commands 2025-06-11T20:53:59,941 copying build/lib/pymlst/cmd.py -> build/bdist.linux-armv7l/wheel/./pymlst 2025-06-11T20:53:59,943 creating build/bdist.linux-armv7l/wheel/pymlst/wg 2025-06-11T20:53:59,944 copying build/lib/pymlst/wg/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg 2025-06-11T20:53:59,946 copying build/lib/pymlst/wg/core.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg 2025-06-11T20:53:59,949 copying build/lib/pymlst/wg/extractors.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg 2025-06-11T20:53:59,951 copying build/lib/pymlst/wg/model.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg 2025-06-11T20:53:59,953 creating build/bdist.linux-armv7l/wheel/pymlst/wg/commands 2025-06-11T20:53:59,954 copying build/lib/pymlst/wg/commands/add.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,956 copying build/lib/pymlst/wg/commands/add2.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,958 copying build/lib/pymlst/wg/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,960 copying build/lib/pymlst/wg/commands/msa.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,962 copying build/lib/pymlst/wg/commands/mlst.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,964 copying build/lib/pymlst/wg/commands/recombination.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,966 copying build/lib/pymlst/wg/commands/sequence.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,968 copying build/lib/pymlst/wg/commands/import.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,970 copying build/lib/pymlst/wg/commands/create.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,973 copying build/lib/pymlst/wg/commands/gene.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,975 copying build/lib/pymlst/wg/commands/strain.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,977 copying build/lib/pymlst/wg/commands/distance.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,979 copying build/lib/pymlst/wg/commands/subgraph.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,982 copying build/lib/pymlst/wg/commands/remove.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,985 copying build/lib/pymlst/wg/commands/stats.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands 2025-06-11T20:53:59,989 creating build/bdist.linux-armv7l/wheel/pymlst/pytyper 2025-06-11T20:53:59,991 copying build/lib/pymlst/pytyper/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper 2025-06-11T20:53:59,994 copying build/lib/pymlst/pytyper/core.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper 2025-06-11T20:53:59,997 copying build/lib/pymlst/pytyper/url.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper 2025-06-11T20:53:59,999 copying build/lib/pymlst/pytyper/method.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper 2025-06-11T20:54:00,000 copying build/lib/pymlst/pytyper/model.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper 2025-06-11T20:54:00,002 creating build/bdist.linux-armv7l/wheel/pymlst/pytyper/commands 2025-06-11T20:54:00,003 copying build/lib/pymlst/pytyper/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper/commands 2025-06-11T20:54:00,005 copying build/lib/pymlst/pytyper/commands/search.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper/commands 2025-06-11T20:54:00,008 creating build/bdist.linux-armv7l/wheel/pymlst/data 2025-06-11T20:54:00,009 creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic 2025-06-11T20:54:00,010 copying build/lib/pymlst/data/alembic/alembic.ini -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic 2025-06-11T20:54:00,013 creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/wg 2025-06-11T20:54:00,015 creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/wg/versions 2025-06-11T20:54:00,016 copying build/lib/pymlst/data/alembic/wg/versions/52ae99cb5f33_initial.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/wg/versions 2025-06-11T20:54:00,018 copying build/lib/pymlst/data/alembic/wg/versions/a793f8f3fd83_add_database_infos.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/wg/versions 2025-06-11T20:54:00,020 copying build/lib/pymlst/data/alembic/wg/env.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/wg 2025-06-11T20:54:00,022 copying build/lib/pymlst/data/alembic/wg/script.py.mako -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/wg 2025-06-11T20:54:00,024 creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/pytyper 2025-06-11T20:54:00,026 creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/pytyper/versions 2025-06-11T20:54:00,027 copying build/lib/pymlst/data/alembic/pytyper/versions/1f96d027f4aa_initial.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/pytyper/versions 2025-06-11T20:54:00,029 copying build/lib/pymlst/data/alembic/pytyper/env.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/pytyper 2025-06-11T20:54:00,031 copying build/lib/pymlst/data/alembic/pytyper/script.py.mako -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/pytyper 2025-06-11T20:54:00,033 creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/cla 2025-06-11T20:54:00,035 creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/cla/versions 2025-06-11T20:54:00,036 copying build/lib/pymlst/data/alembic/cla/versions/c0f871a99d96_add_database_infos.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/cla/versions 2025-06-11T20:54:00,038 copying build/lib/pymlst/data/alembic/cla/versions/21efe503d07d_initial.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/cla/versions 2025-06-11T20:54:00,040 copying build/lib/pymlst/data/alembic/cla/env.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/cla 2025-06-11T20:54:00,042 copying build/lib/pymlst/data/alembic/cla/script.py.mako -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/cla 2025-06-11T20:54:00,044 creating build/bdist.linux-armv7l/wheel/pymlst/data/pytyper 2025-06-11T20:54:00,045 copying build/lib/pymlst/data/pytyper/spa.fna -> build/bdist.linux-armv7l/wheel/./pymlst/data/pytyper 2025-06-11T20:54:00,047 copying build/lib/pymlst/data/pytyper/fimh.fna -> build/bdist.linux-armv7l/wheel/./pymlst/data/pytyper 2025-06-11T20:54:00,049 copying build/lib/pymlst/data/pytyper/clmt.txt -> build/bdist.linux-armv7l/wheel/./pymlst/data/pytyper 2025-06-11T20:54:00,051 copying build/lib/pymlst/data/pytyper/clmt.fna -> build/bdist.linux-armv7l/wheel/./pymlst/data/pytyper 2025-06-11T20:54:00,054 creating build/bdist.linux-armv7l/wheel/pymlst/cla 2025-06-11T20:54:00,055 copying build/lib/pymlst/cla/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla 2025-06-11T20:54:00,057 copying build/lib/pymlst/cla/core.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla 2025-06-11T20:54:00,059 copying build/lib/pymlst/cla/model.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla 2025-06-11T20:54:00,062 creating build/bdist.linux-armv7l/wheel/pymlst/cla/commands 2025-06-11T20:54:00,063 copying build/lib/pymlst/cla/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands 2025-06-11T20:54:00,064 copying build/lib/pymlst/cla/commands/search.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands 2025-06-11T20:54:00,066 copying build/lib/pymlst/cla/commands/info.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands 2025-06-11T20:54:00,068 copying build/lib/pymlst/cla/commands/import.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands 2025-06-11T20:54:00,070 copying build/lib/pymlst/cla/commands/create.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands 2025-06-11T20:54:00,071 copying build/lib/pymlst/cla/commands/search2.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands 2025-06-11T20:54:00,073 copying build/lib/pymlst/cla/commands/remove.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands 2025-06-11T20:54:00,075 running install_egg_info 2025-06-11T20:54:00,110 Copying PyMLST.egg-info to build/bdist.linux-armv7l/wheel/./PyMLST-2.2.2-py3.11.egg-info 2025-06-11T20:54:00,121 running install_scripts 2025-06-11T20:54:00,134 creating build/bdist.linux-armv7l/wheel/pymlst-2.2.2.dist-info/WHEEL 2025-06-11T20:54:00,137 creating '/tmp/pip-wheel-qjoojgnu/pymlst-2.2.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-11T20:54:00,140 adding 'pymlst/__init__.py' 2025-06-11T20:54:00,141 adding 'pymlst/cmd.py' 2025-06-11T20:54:00,143 adding 'pymlst/config.py' 2025-06-11T20:54:00,145 adding 'pymlst/version.py' 2025-06-11T20:54:00,147 adding 'pymlst/cla/__init__.py' 2025-06-11T20:54:00,151 adding 'pymlst/cla/core.py' 2025-06-11T20:54:00,152 adding 'pymlst/cla/model.py' 2025-06-11T20:54:00,154 adding 'pymlst/cla/commands/__init__.py' 2025-06-11T20:54:00,155 adding 'pymlst/cla/commands/create.py' 2025-06-11T20:54:00,157 adding 'pymlst/cla/commands/import.py' 2025-06-11T20:54:00,158 adding 'pymlst/cla/commands/info.py' 2025-06-11T20:54:00,159 adding 'pymlst/cla/commands/remove.py' 2025-06-11T20:54:00,161 adding 'pymlst/cla/commands/search.py' 2025-06-11T20:54:00,162 adding 'pymlst/cla/commands/search2.py' 2025-06-11T20:54:00,164 adding 'pymlst/common/__init__.py' 2025-06-11T20:54:00,165 adding 'pymlst/common/blat.py' 2025-06-11T20:54:00,166 adding 'pymlst/common/exceptions.py' 2025-06-11T20:54:00,168 adding 'pymlst/common/flag.py' 2025-06-11T20:54:00,169 adding 'pymlst/common/kma.py' 2025-06-11T20:54:00,171 adding 'pymlst/common/mafft.py' 2025-06-11T20:54:00,172 adding 'pymlst/common/psl.py' 2025-06-11T20:54:00,174 adding 'pymlst/common/utils.py' 2025-06-11T20:54:00,176 adding 'pymlst/common/web.py' 2025-06-11T20:54:00,178 adding 'pymlst/common/commands/__init__.py' 2025-06-11T20:54:00,179 adding 'pymlst/common/commands/configure.py' 2025-06-11T20:54:00,182 adding 'pymlst/data/alembic/alembic.ini' 2025-06-11T20:54:00,185 adding 'pymlst/data/alembic/cla/env.py' 2025-06-11T20:54:00,186 adding 'pymlst/data/alembic/cla/script.py.mako' 2025-06-11T20:54:00,189 adding 'pymlst/data/alembic/cla/versions/21efe503d07d_initial.py' 2025-06-11T20:54:00,191 adding 'pymlst/data/alembic/cla/versions/c0f871a99d96_add_database_infos.py' 2025-06-11T20:54:00,193 adding 'pymlst/data/alembic/pytyper/env.py' 2025-06-11T20:54:00,195 adding 'pymlst/data/alembic/pytyper/script.py.mako' 2025-06-11T20:54:00,198 adding 'pymlst/data/alembic/pytyper/versions/1f96d027f4aa_initial.py' 2025-06-11T20:54:00,201 adding 'pymlst/data/alembic/wg/env.py' 2025-06-11T20:54:00,202 adding 'pymlst/data/alembic/wg/script.py.mako' 2025-06-11T20:54:00,205 adding 'pymlst/data/alembic/wg/versions/52ae99cb5f33_initial.py' 2025-06-11T20:54:00,206 adding 'pymlst/data/alembic/wg/versions/a793f8f3fd83_add_database_infos.py' 2025-06-11T20:54:00,210 adding 'pymlst/data/pytyper/clmt.fna' 2025-06-11T20:54:00,211 adding 'pymlst/data/pytyper/clmt.txt' 2025-06-11T20:54:00,213 adding 'pymlst/data/pytyper/fimh.fna' 2025-06-11T20:54:00,214 adding 'pymlst/data/pytyper/spa.fna' 2025-06-11T20:54:00,217 adding 'pymlst/pytyper/__init__.py' 2025-06-11T20:54:00,220 adding 'pymlst/pytyper/core.py' 2025-06-11T20:54:00,221 adding 'pymlst/pytyper/method.py' 2025-06-11T20:54:00,222 adding 'pymlst/pytyper/model.py' 2025-06-11T20:54:00,223 adding 'pymlst/pytyper/url.py' 2025-06-11T20:54:00,225 adding 'pymlst/pytyper/commands/__init__.py' 2025-06-11T20:54:00,226 adding 'pymlst/pytyper/commands/search.py' 2025-06-11T20:54:00,228 adding 'pymlst/wg/__init__.py' 2025-06-11T20:54:00,233 adding 'pymlst/wg/core.py' 2025-06-11T20:54:00,235 adding 'pymlst/wg/extractors.py' 2025-06-11T20:54:00,236 adding 'pymlst/wg/model.py' 2025-06-11T20:54:00,238 adding 'pymlst/wg/commands/__init__.py' 2025-06-11T20:54:00,239 adding 'pymlst/wg/commands/add.py' 2025-06-11T20:54:00,241 adding 'pymlst/wg/commands/add2.py' 2025-06-11T20:54:00,242 adding 'pymlst/wg/commands/create.py' 2025-06-11T20:54:00,243 adding 'pymlst/wg/commands/distance.py' 2025-06-11T20:54:00,244 adding 'pymlst/wg/commands/gene.py' 2025-06-11T20:54:00,246 adding 'pymlst/wg/commands/import.py' 2025-06-11T20:54:00,247 adding 'pymlst/wg/commands/mlst.py' 2025-06-11T20:54:00,249 adding 'pymlst/wg/commands/msa.py' 2025-06-11T20:54:00,250 adding 'pymlst/wg/commands/recombination.py' 2025-06-11T20:54:00,252 adding 'pymlst/wg/commands/remove.py' 2025-06-11T20:54:00,253 adding 'pymlst/wg/commands/sequence.py' 2025-06-11T20:54:00,254 adding 'pymlst/wg/commands/stats.py' 2025-06-11T20:54:00,256 adding 'pymlst/wg/commands/strain.py' 2025-06-11T20:54:00,257 adding 'pymlst/wg/commands/subgraph.py' 2025-06-11T20:54:00,263 adding 'pymlst-2.2.2.dist-info/licenses/LICENSE' 2025-06-11T20:54:00,264 adding 'pymlst-2.2.2.dist-info/METADATA' 2025-06-11T20:54:00,265 adding 'pymlst-2.2.2.dist-info/WHEEL' 2025-06-11T20:54:00,266 adding 'pymlst-2.2.2.dist-info/entry_points.txt' 2025-06-11T20:54:00,267 adding 'pymlst-2.2.2.dist-info/top_level.txt' 2025-06-11T20:54:00,269 adding 'pymlst-2.2.2.dist-info/RECORD' 2025-06-11T20:54:00,272 removing build/bdist.linux-armv7l/wheel 2025-06-11T20:54:00,410 Building wheel for pymlst (setup.py): finished with status 'done' 2025-06-11T20:54:00,413 Created wheel for pymlst: filename=pymlst-2.2.2-py3-none-any.whl size=72641 sha256=6c9e4d4b80c2e436e6a7092724a2af1af0a5a882bbf47e4c5764762fd07bb525 2025-06-11T20:54:00,415 Stored in directory: /tmp/pip-ephem-wheel-cache-926hs9t4/wheels/39/df/4e/142879c563bca8090647d3738c99ef825fca532ede74238ef7 2025-06-11T20:54:00,430 Successfully built pymlst 2025-06-11T20:54:00,436 Removed build tracker: '/tmp/pip-build-tracker-zdfey1ad'