2026-06-17T07:57:45,579 Created temporary directory: /tmp/pip-ephem-wheel-cache-vwlrb0mb
2026-06-17T07:57:45,581 Created temporary directory: /tmp/pip-build-tracker-513_fti0
2026-06-17T07:57:45,582 Initialized build tracking at /tmp/pip-build-tracker-513_fti0
2026-06-17T07:57:45,582 Created build tracker: /tmp/pip-build-tracker-513_fti0
2026-06-17T07:57:45,583 Entered build tracker: /tmp/pip-build-tracker-513_fti0
2026-06-17T07:57:45,583 Created temporary directory: /tmp/pip-wheel-54xkr7le
2026-06-17T07:57:45,586 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2026-06-17T07:57:45,589 Created temporary directory: /tmp/pip-ephem-wheel-cache-ufiuwnx8
2026-06-17T07:57:45,610 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-06-17T07:57:45,614 2 location(s) to search for versions of pymlst:
2026-06-17T07:57:45,614 * https://pypi.org/simple/pymlst/
2026-06-17T07:57:45,614 * https://www.piwheels.org/simple/pymlst/
2026-06-17T07:57:45,615 Fetching project page and analyzing links: https://pypi.org/simple/pymlst/
2026-06-17T07:57:45,615 Getting page https://pypi.org/simple/pymlst/
2026-06-17T07:57:45,617 Found index url https://pypi.org/simple
2026-06-17T07:57:45,769 Fetched page https://pypi.org/simple/pymlst/ as application/vnd.pypi.simple.v1+json
2026-06-17T07:57:45,774   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)
2026-06-17T07:57:45,774   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)
2026-06-17T07:57:45,775   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)
2026-06-17T07:57:45,775   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)
2026-06-17T07:57:45,777   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
2026-06-17T07:57:45,777   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)
2026-06-17T07:57:45,778   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
2026-06-17T07:57:45,779   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)
2026-06-17T07:57:45,780   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
2026-06-17T07:57:45,781   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)
2026-06-17T07:57:45,782   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
2026-06-17T07:57:45,783   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)
2026-06-17T07:57:45,784   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
2026-06-17T07:57:45,784   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)
2026-06-17T07:57:45,785   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
2026-06-17T07:57:45,786   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)
2026-06-17T07:57:45,787   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
2026-06-17T07:57:45,787   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)
2026-06-17T07:57:45,788   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
2026-06-17T07:57:45,789   Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/96/73/4d52c3ed3479bf01807b464b2d1f571f58270b73f9d15ed2bee562215822/pymlst-2.3.1-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0)
2026-06-17T07:57:45,790   Found link https://files.pythonhosted.org/packages/4e/7f/27a646e359f5e3afec03de071db7e58fda2dffa85982ff99c794188517b6/pymlst-2.3.1.tar.gz (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0), version: 2.3.1
2026-06-17T07:57:45,791   Skipping link: No binaries permitted for pymlst: https://files.pythonhosted.org/packages/1e/ab/677340bd948de34d8420bf8eb8fb07a3a24ab94895cd141b3f23c5659163/pymlst-2.3.2-py3-none-any.whl (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0)
2026-06-17T07:57:45,792   Found link https://files.pythonhosted.org/packages/29/6e/9fcaabf8b88fca876eac3be2b94623e8ec021f652f1b5481a1dc688c14f3/pymlst-2.3.2.tar.gz (from https://pypi.org/simple/pymlst/) (requires-python:>=3.7.0), version: 2.3.2
2026-06-17T07:57:45,793 Fetching project page and analyzing links: https://www.piwheels.org/simple/pymlst/
2026-06-17T07:57:45,794 Getting page https://www.piwheels.org/simple/pymlst/
2026-06-17T07:57:45,795 Found index url https://www.piwheels.org/simple
2026-06-17T07:57:45,964 Fetched page https://www.piwheels.org/simple/pymlst/ as text/html
2026-06-17T07:57:45,968   Skipping link: No binaries permitted for pymlst: https://archive1.piwheels.org/simple/pymlst/pymlst-2.3.1-py3-none-any.whl#sha256=7432971b857b67f93e0685de572141e2c28f0cb0a9d43af9d1ce0cdfacaa6992 (from https://www.piwheels.org/simple/pymlst/) (requires-python:>=3.7.0)
2026-06-17T07:57:45,969   Skipping link: No binaries permitted for pymlst: https://archive1.piwheels.org/simple/pymlst/pymlst-2.2.2-py3-none-any.whl#sha256=6c9e4d4b80c2e436e6a7092724a2af1af0a5a882bbf47e4c5764762fd07bb525 (from https://www.piwheels.org/simple/pymlst/) (requires-python:>=3.7.0)
2026-06-17T07:57:45,971   Skipping link: No binaries permitted for pymlst: https://archive1.piwheels.org/simple/pymlst/PyMLST-2.2.1-py3-none-any.whl#sha256=bb4e9bee8716053e3cc3fff0551aec157b0b594e887ead0bad2b102dd5343f12 (from https://www.piwheels.org/simple/pymlst/) (requires-python:>=3.7.0)
2026-06-17T07:57:45,972   Skipping link: No binaries permitted for pymlst: https://archive1.piwheels.org/simple/pymlst/PyMLST-2.2.0-py3-none-any.whl#sha256=c915538feda73b6751ef6a6b9741f62f25c84c0dd636d498a34ffc1b97bb6a97 (from https://www.piwheels.org/simple/pymlst/) (requires-python:>=3.7.0)
2026-06-17T07:57:45,972   Skipping link: No binaries permitted for pymlst: https://archive1.piwheels.org/simple/pymlst/PyMLST-2.1.6-py3-none-any.whl#sha256=ece835bc63448a03352c031050db6b7df4b52e97b6937f9ec14af3dc2c362727 (from https://www.piwheels.org/simple/pymlst/) (requires-python:>=3.7.0)
2026-06-17T07:57:45,973   Skipping link: No binaries permitted for pymlst: https://archive1.piwheels.org/simple/pymlst/PyMLST-2.1.5-py3-none-any.whl#sha256=e38b9c1963b2c716d732ab1dc563d6f74b98e4ccef1a40ae039525256743bd7a (from https://www.piwheels.org/simple/pymlst/) (requires-python:>=3.7.0)
2026-06-17T07:57:45,974   Skipping link: No binaries permitted for pymlst: https://archive1.piwheels.org/simple/pymlst/PyMLST-2.1.4-py3-none-any.whl#sha256=1ef8f7966d09ce4aaf7cb04b9eb249944571ae0ea90baf0208af43def98b40aa (from https://www.piwheels.org/simple/pymlst/) (requires-python:>=3.7.0)
2026-06-17T07:57:45,974   Skipping link: No binaries permitted for pymlst: https://archive1.piwheels.org/simple/pymlst/PyMLST-2.1.3-py3-none-any.whl#sha256=f2069f50ecc8c8b203e9257f5c011010e50959605a806e70142dfde35d0e77eb (from https://www.piwheels.org/simple/pymlst/) (requires-python:>=3.7.0)
2026-06-17T07:57:45,975   Skipping link: No binaries permitted for pymlst: https://archive1.piwheels.org/simple/pymlst/PyMLST-2.1.2-py3-none-any.whl#sha256=23fec25be78d92f9683e799227d86c9a19ca909d5f9ecae088c1d70ef372395b (from https://www.piwheels.org/simple/pymlst/) (requires-python:>=3.7.0)
2026-06-17T07:57:45,975 Skipping link: not a file: https://www.piwheels.org/simple/pymlst/
2026-06-17T07:57:45,976 Skipping link: not a file: https://pypi.org/simple/pymlst/
2026-06-17T07:57:45,997 Given no hashes to check 1 links for project 'pymlst': discarding no candidates
2026-06-17T07:57:46,016 Collecting pymlst==2.3.2
2026-06-17T07:57:46,019   Created temporary directory: /tmp/pip-unpack-p2ditauv
2026-06-17T07:57:46,246   Downloading pymlst-2.3.2.tar.gz (54 kB)
2026-06-17T07:57:46,452   Added pymlst==2.3.2 from https://files.pythonhosted.org/packages/29/6e/9fcaabf8b88fca876eac3be2b94623e8ec021f652f1b5481a1dc688c14f3/pymlst-2.3.2.tar.gz to build tracker '/tmp/pip-build-tracker-513_fti0'
2026-06-17T07:57:46,455   Running setup.py (path:/tmp/pip-wheel-54xkr7le/pymlst_141034e6584240b7928929a49ea8e164/setup.py) egg_info for package pymlst
2026-06-17T07:57:46,456   Created temporary directory: /tmp/pip-pip-egg-info-m4f45woo
2026-06-17T07:57:46,457   Preparing metadata (setup.py): started
2026-06-17T07:57:46,458   Running command python setup.py egg_info
2026-06-17T07:57:47,140   /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.
2026-06-17T07:57:47,140   !!

2026-06-17T07:57:47,141           ********************************************************************************
2026-06-17T07:57:47,142           Usage of dash-separated 'description-file' will not be supported in future
2026-06-17T07:57:47,142           versions. Please use the underscore name 'description_file' instead.


2026-06-17T07:57:47,144           Available configuration options are listed in:
2026-06-17T07:57:47,145           https://setuptools.pypa.io/en/latest/userguide/declarative_config.html

2026-06-17T07:57:47,146           This deprecation is overdue, please update your project and remove deprecated
2026-06-17T07:57:47,146           calls to avoid build errors in the future.

2026-06-17T07:57:47,147           See https://github.com/pypa/setuptools/discussions/5011 for details.
2026-06-17T07:57:47,148           ********************************************************************************

2026-06-17T07:57:47,149   !!
2026-06-17T07:57:47,149     opt = self._enforce_underscore(opt, section)
2026-06-17T07:57:47,185   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2026-06-17T07:57:47,186   !!

2026-06-17T07:57:47,187           ********************************************************************************
2026-06-17T07:57:47,187           Requirements should be satisfied by a PEP 517 installer.
2026-06-17T07:57:47,188           If you are using pip, you can try `pip install --use-pep517`.

2026-06-17T07:57:47,189           This deprecation is overdue, please update your project and remove deprecated
2026-06-17T07:57:47,189           calls to avoid build errors in the future.
2026-06-17T07:57:47,190           ********************************************************************************

2026-06-17T07:57:47,191   !!
2026-06-17T07:57:47,191     dist.fetch_build_eggs(dist.setup_requires)
2026-06-17T07:57:47,677   /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.
2026-06-17T07:57:47,677   !!

2026-06-17T07:57:47,679           ********************************************************************************
2026-06-17T07:57:47,679           Usage of dash-separated 'description-file' will not be supported in future
2026-06-17T07:57:47,680           versions. Please use the underscore name 'description_file' instead.
2026-06-17T07:57:47,680           (Affected: PyMLST).

2026-06-17T07:57:47,682           Available configuration options are listed in:
2026-06-17T07:57:47,682           https://setuptools.pypa.io/en/latest/userguide/declarative_config.html

2026-06-17T07:57:47,683           This deprecation is overdue, please update your project and remove deprecated
2026-06-17T07:57:47,684           calls to avoid build errors in the future.

2026-06-17T07:57:47,685           See https://github.com/pypa/setuptools/discussions/5011 for details.
2026-06-17T07:57:47,686           ********************************************************************************

2026-06-17T07:57:47,687   !!
2026-06-17T07:57:47,688     opt = self._enforce_underscore(opt, section)
2026-06-17T07:57:47,688   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-06-17T07:57:47,689   !!

2026-06-17T07:57:47,690           ********************************************************************************
2026-06-17T07:57:47,691           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-06-17T07:57:47,692           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2026-06-17T07:57:47,693           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-06-17T07:57:47,694           ********************************************************************************

2026-06-17T07:57:47,695   !!
2026-06-17T07:57:47,696     self._finalize_license_expression()
2026-06-17T07:57:47,713   running egg_info
2026-06-17T07:57:47,740   creating /tmp/pip-pip-egg-info-m4f45woo/PyMLST.egg-info
2026-06-17T07:57:47,741   writing /tmp/pip-pip-egg-info-m4f45woo/PyMLST.egg-info/PKG-INFO
2026-06-17T07:57:47,745   writing dependency_links to /tmp/pip-pip-egg-info-m4f45woo/PyMLST.egg-info/dependency_links.txt
2026-06-17T07:57:47,746   writing entry points to /tmp/pip-pip-egg-info-m4f45woo/PyMLST.egg-info/entry_points.txt
2026-06-17T07:57:47,748   writing requirements to /tmp/pip-pip-egg-info-m4f45woo/PyMLST.egg-info/requires.txt
2026-06-17T07:57:47,749   writing top-level names to /tmp/pip-pip-egg-info-m4f45woo/PyMLST.egg-info/top_level.txt
2026-06-17T07:57:47,751   writing manifest file '/tmp/pip-pip-egg-info-m4f45woo/PyMLST.egg-info/SOURCES.txt'
2026-06-17T07:57:47,851   reading manifest file '/tmp/pip-pip-egg-info-m4f45woo/PyMLST.egg-info/SOURCES.txt'
2026-06-17T07:57:47,853   reading manifest template 'MANIFEST.in'
2026-06-17T07:57:47,858   adding license file 'LICENSE'
2026-06-17T07:57:47,863   writing manifest file '/tmp/pip-pip-egg-info-m4f45woo/PyMLST.egg-info/SOURCES.txt'
2026-06-17T07:57:47,975   Preparing metadata (setup.py): finished with status 'done'
2026-06-17T07:57:47,980   Source in /tmp/pip-wheel-54xkr7le/pymlst_141034e6584240b7928929a49ea8e164 has version 2.3.2, which satisfies requirement pymlst==2.3.2 from https://files.pythonhosted.org/packages/29/6e/9fcaabf8b88fca876eac3be2b94623e8ec021f652f1b5481a1dc688c14f3/pymlst-2.3.2.tar.gz
2026-06-17T07:57:47,980   Removed pymlst==2.3.2 from https://files.pythonhosted.org/packages/29/6e/9fcaabf8b88fca876eac3be2b94623e8ec021f652f1b5481a1dc688c14f3/pymlst-2.3.2.tar.gz from build tracker '/tmp/pip-build-tracker-513_fti0'
2026-06-17T07:57:47,987 Created temporary directory: /tmp/pip-unpack-6gy9m82x
2026-06-17T07:57:47,987 Building wheels for collected packages: pymlst
2026-06-17T07:57:47,992   Created temporary directory: /tmp/pip-wheel-_905vfn8
2026-06-17T07:57:47,992   Building wheel for pymlst (setup.py): started
2026-06-17T07:57:47,993   Destination directory: /tmp/pip-wheel-_905vfn8
2026-06-17T07:57:47,994   Running command python setup.py bdist_wheel
2026-06-17T07:57:48,537   /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.
2026-06-17T07:57:48,537   !!

2026-06-17T07:57:48,538           ********************************************************************************
2026-06-17T07:57:48,539           Usage of dash-separated 'description-file' will not be supported in future
2026-06-17T07:57:48,540           versions. Please use the underscore name 'description_file' instead.


2026-06-17T07:57:48,541           Available configuration options are listed in:
2026-06-17T07:57:48,542           https://setuptools.pypa.io/en/latest/userguide/declarative_config.html

2026-06-17T07:57:48,543           This deprecation is overdue, please update your project and remove deprecated
2026-06-17T07:57:48,544           calls to avoid build errors in the future.

2026-06-17T07:57:48,545           See https://github.com/pypa/setuptools/discussions/5011 for details.
2026-06-17T07:57:48,546           ********************************************************************************

2026-06-17T07:57:48,547   !!
2026-06-17T07:57:48,548     opt = self._enforce_underscore(opt, section)
2026-06-17T07:57:48,564   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2026-06-17T07:57:48,565   !!

2026-06-17T07:57:48,566           ********************************************************************************
2026-06-17T07:57:48,567           Requirements should be satisfied by a PEP 517 installer.
2026-06-17T07:57:48,567           If you are using pip, you can try `pip install --use-pep517`.

2026-06-17T07:57:48,569           This deprecation is overdue, please update your project and remove deprecated
2026-06-17T07:57:48,569           calls to avoid build errors in the future.
2026-06-17T07:57:48,570           ********************************************************************************

2026-06-17T07:57:48,571   !!
2026-06-17T07:57:48,572     dist.fetch_build_eggs(dist.setup_requires)
2026-06-17T07:57:48,941   /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.
2026-06-17T07:57:48,941   !!

2026-06-17T07:57:48,942           ********************************************************************************
2026-06-17T07:57:48,943           Usage of dash-separated 'description-file' will not be supported in future
2026-06-17T07:57:48,943           versions. Please use the underscore name 'description_file' instead.
2026-06-17T07:57:48,944           (Affected: PyMLST).

2026-06-17T07:57:48,945           Available configuration options are listed in:
2026-06-17T07:57:48,945           https://setuptools.pypa.io/en/latest/userguide/declarative_config.html

2026-06-17T07:57:48,946           This deprecation is overdue, please update your project and remove deprecated
2026-06-17T07:57:48,947           calls to avoid build errors in the future.

2026-06-17T07:57:48,948           See https://github.com/pypa/setuptools/discussions/5011 for details.
2026-06-17T07:57:48,948           ********************************************************************************

2026-06-17T07:57:48,949   !!
2026-06-17T07:57:48,949     opt = self._enforce_underscore(opt, section)
2026-06-17T07:57:48,950   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-06-17T07:57:48,950   !!

2026-06-17T07:57:48,952           ********************************************************************************
2026-06-17T07:57:48,952           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-06-17T07:57:48,953           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2026-06-17T07:57:48,954           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-06-17T07:57:48,955           ********************************************************************************

2026-06-17T07:57:48,956   !!
2026-06-17T07:57:48,956     self._finalize_license_expression()
2026-06-17T07:57:48,957   running bdist_wheel
2026-06-17T07:57:49,082   running build
2026-06-17T07:57:49,082   running build_py
2026-06-17T07:57:49,112   creating build/lib/pymlst
2026-06-17T07:57:49,114   copying pymlst/__init__.py -> build/lib/pymlst
2026-06-17T07:57:49,116   copying pymlst/config.py -> build/lib/pymlst
2026-06-17T07:57:49,118   copying pymlst/cmd.py -> build/lib/pymlst
2026-06-17T07:57:49,120   copying pymlst/version.py -> build/lib/pymlst
2026-06-17T07:57:49,122   creating build/lib/pymlst/wg
2026-06-17T07:57:49,123   copying pymlst/wg/__init__.py -> build/lib/pymlst/wg
2026-06-17T07:57:49,125   copying pymlst/wg/model.py -> build/lib/pymlst/wg
2026-06-17T07:57:49,127   copying pymlst/wg/extractors.py -> build/lib/pymlst/wg
2026-06-17T07:57:49,129   copying pymlst/wg/core.py -> build/lib/pymlst/wg
2026-06-17T07:57:49,132   creating build/lib/pymlst/pytyper
2026-06-17T07:57:49,133   copying pymlst/pytyper/method.py -> build/lib/pymlst/pytyper
2026-06-17T07:57:49,135   copying pymlst/pytyper/__init__.py -> build/lib/pymlst/pytyper
2026-06-17T07:57:49,137   copying pymlst/pytyper/model.py -> build/lib/pymlst/pytyper
2026-06-17T07:57:49,139   copying pymlst/pytyper/url.py -> build/lib/pymlst/pytyper
2026-06-17T07:57:49,140   copying pymlst/pytyper/core.py -> build/lib/pymlst/pytyper
2026-06-17T07:57:49,143   creating build/lib/pymlst/common
2026-06-17T07:57:49,144   copying pymlst/common/__init__.py -> build/lib/pymlst/common
2026-06-17T07:57:49,146   copying pymlst/common/exceptions.py -> build/lib/pymlst/common
2026-06-17T07:57:49,148   copying pymlst/common/kma.py -> build/lib/pymlst/common
2026-06-17T07:57:49,150   copying pymlst/common/mafft.py -> build/lib/pymlst/common
2026-06-17T07:57:49,152   copying pymlst/common/web.py -> build/lib/pymlst/common
2026-06-17T07:57:49,154   copying pymlst/common/blat.py -> build/lib/pymlst/common
2026-06-17T07:57:49,156   copying pymlst/common/flag.py -> build/lib/pymlst/common
2026-06-17T07:57:49,158   copying pymlst/common/utils.py -> build/lib/pymlst/common
2026-06-17T07:57:49,160   copying pymlst/common/psl.py -> build/lib/pymlst/common
2026-06-17T07:57:49,162   creating build/lib/pymlst/cla
2026-06-17T07:57:49,163   copying pymlst/cla/__init__.py -> build/lib/pymlst/cla
2026-06-17T07:57:49,165   copying pymlst/cla/model.py -> build/lib/pymlst/cla
2026-06-17T07:57:49,168   copying pymlst/cla/core.py -> build/lib/pymlst/cla
2026-06-17T07:57:49,175   creating build/lib/pymlst/wg/commands
2026-06-17T07:57:49,178   copying pymlst/wg/commands/recombination.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,183   copying pymlst/wg/commands/__init__.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,184   copying pymlst/wg/commands/subgraph.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,186   copying pymlst/wg/commands/create.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,188   copying pymlst/wg/commands/remove.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,190   copying pymlst/wg/commands/sequence.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,191   copying pymlst/wg/commands/distance.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,193   copying pymlst/wg/commands/strain.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,195   copying pymlst/wg/commands/gene.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,197   copying pymlst/wg/commands/stats.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,199   copying pymlst/wg/commands/msa.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,200   copying pymlst/wg/commands/mlst.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,202   copying pymlst/wg/commands/add2.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,204   copying pymlst/wg/commands/add.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,206   copying pymlst/wg/commands/import.py -> build/lib/pymlst/wg/commands
2026-06-17T07:57:49,208   creating build/lib/pymlst/pytyper/commands
2026-06-17T07:57:49,209   copying pymlst/pytyper/commands/__init__.py -> build/lib/pymlst/pytyper/commands
2026-06-17T07:57:49,211   copying pymlst/pytyper/commands/search.py -> build/lib/pymlst/pytyper/commands
2026-06-17T07:57:49,213   creating build/lib/pymlst/common/commands
2026-06-17T07:57:49,214   copying pymlst/common/commands/__init__.py -> build/lib/pymlst/common/commands
2026-06-17T07:57:49,216   copying pymlst/common/commands/configure.py -> build/lib/pymlst/common/commands
2026-06-17T07:57:49,218   creating build/lib/pymlst/cla/commands
2026-06-17T07:57:49,220   copying pymlst/cla/commands/__init__.py -> build/lib/pymlst/cla/commands
2026-06-17T07:57:49,221   copying pymlst/cla/commands/create.py -> build/lib/pymlst/cla/commands
2026-06-17T07:57:49,223   copying pymlst/cla/commands/remove.py -> build/lib/pymlst/cla/commands
2026-06-17T07:57:49,225   copying pymlst/cla/commands/info.py -> build/lib/pymlst/cla/commands
2026-06-17T07:57:49,227   copying pymlst/cla/commands/search.py -> build/lib/pymlst/cla/commands
2026-06-17T07:57:49,229   copying pymlst/cla/commands/search2.py -> build/lib/pymlst/cla/commands
2026-06-17T07:57:49,231   copying pymlst/cla/commands/import.py -> build/lib/pymlst/cla/commands
2026-06-17T07:57:49,233   running egg_info
2026-06-17T07:57:49,260   writing PyMLST.egg-info/PKG-INFO
2026-06-17T07:57:49,264   writing dependency_links to PyMLST.egg-info/dependency_links.txt
2026-06-17T07:57:49,265   writing entry points to PyMLST.egg-info/entry_points.txt
2026-06-17T07:57:49,267   writing requirements to PyMLST.egg-info/requires.txt
2026-06-17T07:57:49,268   writing top-level names to PyMLST.egg-info/top_level.txt
2026-06-17T07:57:49,306   reading manifest file 'PyMLST.egg-info/SOURCES.txt'
2026-06-17T07:57:49,312   reading manifest template 'MANIFEST.in'
2026-06-17T07:57:49,316   adding license file 'LICENSE'
2026-06-17T07:57:49,321   writing manifest file 'PyMLST.egg-info/SOURCES.txt'
2026-06-17T07:57:49,325   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pymlst.data.alembic' is absent from the `packages` configuration.
2026-06-17T07:57:49,325   !!

2026-06-17T07:57:49,326           ********************************************************************************
2026-06-17T07:57:49,327           ############################
2026-06-17T07:57:49,327           # Package would be ignored #
2026-06-17T07:57:49,328           ############################
2026-06-17T07:57:49,328           Python recognizes 'pymlst.data.alembic' as an importable package[^1],
2026-06-17T07:57:49,329           but it is absent from setuptools' `packages` configuration.

2026-06-17T07:57:49,330           This leads to an ambiguous overall configuration. If you want to distribute this
2026-06-17T07:57:49,330           package, please make sure that 'pymlst.data.alembic' is explicitly added
2026-06-17T07:57:49,331           to the `packages` configuration field.

2026-06-17T07:57:49,332           Alternatively, you can also rely on setuptools' discovery methods
2026-06-17T07:57:49,332           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-06-17T07:57:49,333           instead of `find_packages(...)`/`find:`).

2026-06-17T07:57:49,334           You can read more about "package discovery" on setuptools documentation page:

2026-06-17T07:57:49,335           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-06-17T07:57:49,336           If you don't want 'pymlst.data.alembic' to be distributed and are
2026-06-17T07:57:49,336           already explicitly excluding 'pymlst.data.alembic' via
2026-06-17T07:57:49,337           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-06-17T07:57:49,338           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-06-17T07:57:49,338           combination with a more fine grained `package-data` configuration.

2026-06-17T07:57:49,339           You can read more about "package data files" on setuptools documentation page:

2026-06-17T07:57:49,340           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-06-17T07:57:49,342           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-06-17T07:57:49,343                 even if it does not contain any `.py` files.
2026-06-17T07:57:49,343                 On the other hand, currently there is no concept of package data
2026-06-17T07:57:49,344                 directory, all directories are treated like packages.
2026-06-17T07:57:49,345           ********************************************************************************

2026-06-17T07:57:49,346   !!
2026-06-17T07:57:49,346     check.warn(importable)
2026-06-17T07:57:49,347   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pymlst.data.alembic.cla' is absent from the `packages` configuration.
2026-06-17T07:57:49,347   !!

2026-06-17T07:57:49,349           ********************************************************************************
2026-06-17T07:57:49,349           ############################
2026-06-17T07:57:49,350           # Package would be ignored #
2026-06-17T07:57:49,350           ############################
2026-06-17T07:57:49,351           Python recognizes 'pymlst.data.alembic.cla' as an importable package[^1],
2026-06-17T07:57:49,351           but it is absent from setuptools' `packages` configuration.

2026-06-17T07:57:49,353           This leads to an ambiguous overall configuration. If you want to distribute this
2026-06-17T07:57:49,353           package, please make sure that 'pymlst.data.alembic.cla' is explicitly added
2026-06-17T07:57:49,354           to the `packages` configuration field.

2026-06-17T07:57:49,355           Alternatively, you can also rely on setuptools' discovery methods
2026-06-17T07:57:49,356           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-06-17T07:57:49,356           instead of `find_packages(...)`/`find:`).

2026-06-17T07:57:49,358           You can read more about "package discovery" on setuptools documentation page:

2026-06-17T07:57:49,359           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-06-17T07:57:49,360           If you don't want 'pymlst.data.alembic.cla' to be distributed and are
2026-06-17T07:57:49,360           already explicitly excluding 'pymlst.data.alembic.cla' via
2026-06-17T07:57:49,360           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-06-17T07:57:49,361           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-06-17T07:57:49,361           combination with a more fine grained `package-data` configuration.

2026-06-17T07:57:49,362           You can read more about "package data files" on setuptools documentation page:

2026-06-17T07:57:49,363           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-06-17T07:57:49,365           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-06-17T07:57:49,365                 even if it does not contain any `.py` files.
2026-06-17T07:57:49,366                 On the other hand, currently there is no concept of package data
2026-06-17T07:57:49,366                 directory, all directories are treated like packages.
2026-06-17T07:57:49,367           ********************************************************************************

2026-06-17T07:57:49,368   !!
2026-06-17T07:57:49,368     check.warn(importable)
2026-06-17T07:57:49,369   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pymlst.data.alembic.cla.versions' is absent from the `packages` configuration.
2026-06-17T07:57:49,369   !!

2026-06-17T07:57:49,371           ********************************************************************************
2026-06-17T07:57:49,371           ############################
2026-06-17T07:57:49,372           # Package would be ignored #
2026-06-17T07:57:49,372           ############################
2026-06-17T07:57:49,373           Python recognizes 'pymlst.data.alembic.cla.versions' as an importable package[^1],
2026-06-17T07:57:49,373           but it is absent from setuptools' `packages` configuration.

2026-06-17T07:57:49,374           This leads to an ambiguous overall configuration. If you want to distribute this
2026-06-17T07:57:49,375           package, please make sure that 'pymlst.data.alembic.cla.versions' is explicitly added
2026-06-17T07:57:49,376           to the `packages` configuration field.

2026-06-17T07:57:49,377           Alternatively, you can also rely on setuptools' discovery methods
2026-06-17T07:57:49,377           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-06-17T07:57:49,378           instead of `find_packages(...)`/`find:`).

2026-06-17T07:57:49,379           You can read more about "package discovery" on setuptools documentation page:

2026-06-17T07:57:49,380           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-06-17T07:57:49,381           If you don't want 'pymlst.data.alembic.cla.versions' to be distributed and are
2026-06-17T07:57:49,382           already explicitly excluding 'pymlst.data.alembic.cla.versions' via
2026-06-17T07:57:49,383           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-06-17T07:57:49,383           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-06-17T07:57:49,384           combination with a more fine grained `package-data` configuration.

2026-06-17T07:57:49,385           You can read more about "package data files" on setuptools documentation page:

2026-06-17T07:57:49,386           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-06-17T07:57:49,388           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-06-17T07:57:49,389                 even if it does not contain any `.py` files.
2026-06-17T07:57:49,389                 On the other hand, currently there is no concept of package data
2026-06-17T07:57:49,390                 directory, all directories are treated like packages.
2026-06-17T07:57:49,390           ********************************************************************************

2026-06-17T07:57:49,391   !!
2026-06-17T07:57:49,392     check.warn(importable)
2026-06-17T07:57:49,392   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pymlst.data.alembic.pytyper' is absent from the `packages` configuration.
2026-06-17T07:57:49,393   !!

2026-06-17T07:57:49,394           ********************************************************************************
2026-06-17T07:57:49,394           ############################
2026-06-17T07:57:49,395           # Package would be ignored #
2026-06-17T07:57:49,395           ############################
2026-06-17T07:57:49,396           Python recognizes 'pymlst.data.alembic.pytyper' as an importable package[^1],
2026-06-17T07:57:49,396           but it is absent from setuptools' `packages` configuration.

2026-06-17T07:57:49,397           This leads to an ambiguous overall configuration. If you want to distribute this
2026-06-17T07:57:49,397           package, please make sure that 'pymlst.data.alembic.pytyper' is explicitly added
2026-06-17T07:57:49,398           to the `packages` configuration field.

2026-06-17T07:57:49,399           Alternatively, you can also rely on setuptools' discovery methods
2026-06-17T07:57:49,399           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-06-17T07:57:49,400           instead of `find_packages(...)`/`find:`).

2026-06-17T07:57:49,401           You can read more about "package discovery" on setuptools documentation page:

2026-06-17T07:57:49,402           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-06-17T07:57:49,403           If you don't want 'pymlst.data.alembic.pytyper' to be distributed and are
2026-06-17T07:57:49,404           already explicitly excluding 'pymlst.data.alembic.pytyper' via
2026-06-17T07:57:49,404           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-06-17T07:57:49,405           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-06-17T07:57:49,406           combination with a more fine grained `package-data` configuration.

2026-06-17T07:57:49,407           You can read more about "package data files" on setuptools documentation page:

2026-06-17T07:57:49,408           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-06-17T07:57:49,410           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-06-17T07:57:49,410                 even if it does not contain any `.py` files.
2026-06-17T07:57:49,411                 On the other hand, currently there is no concept of package data
2026-06-17T07:57:49,412                 directory, all directories are treated like packages.
2026-06-17T07:57:49,412           ********************************************************************************

2026-06-17T07:57:49,413   !!
2026-06-17T07:57:49,414     check.warn(importable)
2026-06-17T07:57:49,414   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pymlst.data.alembic.pytyper.versions' is absent from the `packages` configuration.
2026-06-17T07:57:49,415   !!

2026-06-17T07:57:49,416           ********************************************************************************
2026-06-17T07:57:49,417           ############################
2026-06-17T07:57:49,417           # Package would be ignored #
2026-06-17T07:57:49,418           ############################
2026-06-17T07:57:49,419           Python recognizes 'pymlst.data.alembic.pytyper.versions' as an importable package[^1],
2026-06-17T07:57:49,419           but it is absent from setuptools' `packages` configuration.

2026-06-17T07:57:49,421           This leads to an ambiguous overall configuration. If you want to distribute this
2026-06-17T07:57:49,421           package, please make sure that 'pymlst.data.alembic.pytyper.versions' is explicitly added
2026-06-17T07:57:49,422           to the `packages` configuration field.

2026-06-17T07:57:49,423           Alternatively, you can also rely on setuptools' discovery methods
2026-06-17T07:57:49,423           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-06-17T07:57:49,423           instead of `find_packages(...)`/`find:`).

2026-06-17T07:57:49,424           You can read more about "package discovery" on setuptools documentation page:

2026-06-17T07:57:49,425           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-06-17T07:57:49,426           If you don't want 'pymlst.data.alembic.pytyper.versions' to be distributed and are
2026-06-17T07:57:49,427           already explicitly excluding 'pymlst.data.alembic.pytyper.versions' via
2026-06-17T07:57:49,427           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-06-17T07:57:49,428           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-06-17T07:57:49,428           combination with a more fine grained `package-data` configuration.

2026-06-17T07:57:49,429           You can read more about "package data files" on setuptools documentation page:

2026-06-17T07:57:49,430           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-06-17T07:57:49,431           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-06-17T07:57:49,432                 even if it does not contain any `.py` files.
2026-06-17T07:57:49,432                 On the other hand, currently there is no concept of package data
2026-06-17T07:57:49,433                 directory, all directories are treated like packages.
2026-06-17T07:57:49,433           ********************************************************************************

2026-06-17T07:57:49,434   !!
2026-06-17T07:57:49,435     check.warn(importable)
2026-06-17T07:57:49,436   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pymlst.data.alembic.wg' is absent from the `packages` configuration.
2026-06-17T07:57:49,436   !!

2026-06-17T07:57:49,437           ********************************************************************************
2026-06-17T07:57:49,438           ############################
2026-06-17T07:57:49,439           # Package would be ignored #
2026-06-17T07:57:49,439           ############################
2026-06-17T07:57:49,440           Python recognizes 'pymlst.data.alembic.wg' as an importable package[^1],
2026-06-17T07:57:49,441           but it is absent from setuptools' `packages` configuration.

2026-06-17T07:57:49,442           This leads to an ambiguous overall configuration. If you want to distribute this
2026-06-17T07:57:49,442           package, please make sure that 'pymlst.data.alembic.wg' is explicitly added
2026-06-17T07:57:49,443           to the `packages` configuration field.

2026-06-17T07:57:49,444           Alternatively, you can also rely on setuptools' discovery methods
2026-06-17T07:57:49,445           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-06-17T07:57:49,445           instead of `find_packages(...)`/`find:`).

2026-06-17T07:57:49,446           You can read more about "package discovery" on setuptools documentation page:

2026-06-17T07:57:49,447           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-06-17T07:57:49,449           If you don't want 'pymlst.data.alembic.wg' to be distributed and are
2026-06-17T07:57:49,449           already explicitly excluding 'pymlst.data.alembic.wg' via
2026-06-17T07:57:49,450           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-06-17T07:57:49,450           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-06-17T07:57:49,451           combination with a more fine grained `package-data` configuration.

2026-06-17T07:57:49,452           You can read more about "package data files" on setuptools documentation page:

2026-06-17T07:57:49,453           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-06-17T07:57:49,455           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-06-17T07:57:49,455                 even if it does not contain any `.py` files.
2026-06-17T07:57:49,456                 On the other hand, currently there is no concept of package data
2026-06-17T07:57:49,456                 directory, all directories are treated like packages.
2026-06-17T07:57:49,456           ********************************************************************************

2026-06-17T07:57:49,457   !!
2026-06-17T07:57:49,458     check.warn(importable)
2026-06-17T07:57:49,458   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pymlst.data.alembic.wg.versions' is absent from the `packages` configuration.
2026-06-17T07:57:49,459   !!

2026-06-17T07:57:49,460           ********************************************************************************
2026-06-17T07:57:49,460           ############################
2026-06-17T07:57:49,461           # Package would be ignored #
2026-06-17T07:57:49,461           ############################
2026-06-17T07:57:49,462           Python recognizes 'pymlst.data.alembic.wg.versions' as an importable package[^1],
2026-06-17T07:57:49,462           but it is absent from setuptools' `packages` configuration.

2026-06-17T07:57:49,463           This leads to an ambiguous overall configuration. If you want to distribute this
2026-06-17T07:57:49,463           package, please make sure that 'pymlst.data.alembic.wg.versions' is explicitly added
2026-06-17T07:57:49,464           to the `packages` configuration field.

2026-06-17T07:57:49,465           Alternatively, you can also rely on setuptools' discovery methods
2026-06-17T07:57:49,466           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-06-17T07:57:49,467           instead of `find_packages(...)`/`find:`).

2026-06-17T07:57:49,468           You can read more about "package discovery" on setuptools documentation page:

2026-06-17T07:57:49,469           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-06-17T07:57:49,470           If you don't want 'pymlst.data.alembic.wg.versions' to be distributed and are
2026-06-17T07:57:49,471           already explicitly excluding 'pymlst.data.alembic.wg.versions' via
2026-06-17T07:57:49,471           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-06-17T07:57:49,472           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-06-17T07:57:49,473           combination with a more fine grained `package-data` configuration.

2026-06-17T07:57:49,474           You can read more about "package data files" on setuptools documentation page:

2026-06-17T07:57:49,475           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-06-17T07:57:49,476           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-06-17T07:57:49,477                 even if it does not contain any `.py` files.
2026-06-17T07:57:49,478                 On the other hand, currently there is no concept of package data
2026-06-17T07:57:49,478                 directory, all directories are treated like packages.
2026-06-17T07:57:49,479           ********************************************************************************

2026-06-17T07:57:49,480   !!
2026-06-17T07:57:49,480     check.warn(importable)
2026-06-17T07:57:49,481   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pymlst.data.pytyper' is absent from the `packages` configuration.
2026-06-17T07:57:49,482   !!

2026-06-17T07:57:49,483           ********************************************************************************
2026-06-17T07:57:49,484           ############################
2026-06-17T07:57:49,484           # Package would be ignored #
2026-06-17T07:57:49,485           ############################
2026-06-17T07:57:49,485           Python recognizes 'pymlst.data.pytyper' as an importable package[^1],
2026-06-17T07:57:49,485           but it is absent from setuptools' `packages` configuration.

2026-06-17T07:57:49,486           This leads to an ambiguous overall configuration. If you want to distribute this
2026-06-17T07:57:49,487           package, please make sure that 'pymlst.data.pytyper' is explicitly added
2026-06-17T07:57:49,487           to the `packages` configuration field.

2026-06-17T07:57:49,488           Alternatively, you can also rely on setuptools' discovery methods
2026-06-17T07:57:49,488           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-06-17T07:57:49,488           instead of `find_packages(...)`/`find:`).

2026-06-17T07:57:49,489           You can read more about "package discovery" on setuptools documentation page:

2026-06-17T07:57:49,490           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-06-17T07:57:49,491           If you don't want 'pymlst.data.pytyper' to be distributed and are
2026-06-17T07:57:49,491           already explicitly excluding 'pymlst.data.pytyper' via
2026-06-17T07:57:49,492           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-06-17T07:57:49,492           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-06-17T07:57:49,492           combination with a more fine grained `package-data` configuration.

2026-06-17T07:57:49,494           You can read more about "package data files" on setuptools documentation page:

2026-06-17T07:57:49,495           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-06-17T07:57:49,496           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-06-17T07:57:49,497                 even if it does not contain any `.py` files.
2026-06-17T07:57:49,497                 On the other hand, currently there is no concept of package data
2026-06-17T07:57:49,498                 directory, all directories are treated like packages.
2026-06-17T07:57:49,498           ********************************************************************************

2026-06-17T07:57:49,500   !!
2026-06-17T07:57:49,500     check.warn(importable)
2026-06-17T07:57:49,501   creating build/lib/pymlst/data/alembic
2026-06-17T07:57:49,502   copying pymlst/data/alembic/alembic.ini -> build/lib/pymlst/data/alembic
2026-06-17T07:57:49,502   creating build/lib/pymlst/data/alembic/cla
2026-06-17T07:57:49,503   copying pymlst/data/alembic/cla/env.py -> build/lib/pymlst/data/alembic/cla
2026-06-17T07:57:49,503   copying pymlst/data/alembic/cla/script.py.mako -> build/lib/pymlst/data/alembic/cla
2026-06-17T07:57:49,504   creating build/lib/pymlst/data/alembic/cla/versions
2026-06-17T07:57:49,504   copying pymlst/data/alembic/cla/versions/21efe503d07d_initial.py -> build/lib/pymlst/data/alembic/cla/versions
2026-06-17T07:57:49,505   copying pymlst/data/alembic/cla/versions/c0f871a99d96_add_database_infos.py -> build/lib/pymlst/data/alembic/cla/versions
2026-06-17T07:57:49,505   creating build/lib/pymlst/data/alembic/pytyper
2026-06-17T07:57:49,506   copying pymlst/data/alembic/pytyper/env.py -> build/lib/pymlst/data/alembic/pytyper
2026-06-17T07:57:49,506   copying pymlst/data/alembic/pytyper/script.py.mako -> build/lib/pymlst/data/alembic/pytyper
2026-06-17T07:57:49,507   creating build/lib/pymlst/data/alembic/pytyper/versions
2026-06-17T07:57:49,507   copying pymlst/data/alembic/pytyper/versions/1f96d027f4aa_initial.py -> build/lib/pymlst/data/alembic/pytyper/versions
2026-06-17T07:57:49,508   creating build/lib/pymlst/data/alembic/wg
2026-06-17T07:57:49,509   copying pymlst/data/alembic/wg/env.py -> build/lib/pymlst/data/alembic/wg
2026-06-17T07:57:49,509   copying pymlst/data/alembic/wg/script.py.mako -> build/lib/pymlst/data/alembic/wg
2026-06-17T07:57:49,510   creating build/lib/pymlst/data/alembic/wg/versions
2026-06-17T07:57:49,510   copying pymlst/data/alembic/wg/versions/52ae99cb5f33_initial.py -> build/lib/pymlst/data/alembic/wg/versions
2026-06-17T07:57:49,511   copying pymlst/data/alembic/wg/versions/a793f8f3fd83_add_database_infos.py -> build/lib/pymlst/data/alembic/wg/versions
2026-06-17T07:57:49,511   creating build/lib/pymlst/data/pytyper
2026-06-17T07:57:49,512   copying pymlst/data/pytyper/clmt.fna -> build/lib/pymlst/data/pytyper
2026-06-17T07:57:49,512   copying pymlst/data/pytyper/clmt.txt -> build/lib/pymlst/data/pytyper
2026-06-17T07:57:49,513   copying pymlst/data/pytyper/fimh.fna -> build/lib/pymlst/data/pytyper
2026-06-17T07:57:49,513   copying pymlst/data/pytyper/spa.fna -> build/lib/pymlst/data/pytyper
2026-06-17T07:57:49,514   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2026-06-17T07:57:49,514   !!

2026-06-17T07:57:49,515           ********************************************************************************
2026-06-17T07:57:49,516           Please avoid running ``setup.py`` directly.
2026-06-17T07:57:49,516           Instead, use pypa/build, pypa/installer or other
2026-06-17T07:57:49,517           standards-based tools.

2026-06-17T07:57:49,518           This deprecation is overdue, please update your project and remove deprecated
2026-06-17T07:57:49,518           calls to avoid build errors in the future.

2026-06-17T07:57:49,519           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2026-06-17T07:57:49,520           ********************************************************************************

2026-06-17T07:57:49,521   !!
2026-06-17T07:57:49,521     self.initialize_options()
2026-06-17T07:57:49,522   installing to build/bdist.linux-armv7l/wheel
2026-06-17T07:57:49,522   running install
2026-06-17T07:57:49,523   running install_lib
2026-06-17T07:57:49,538   creating build/bdist.linux-armv7l/wheel
2026-06-17T07:57:49,540   creating build/bdist.linux-armv7l/wheel/pymlst
2026-06-17T07:57:49,542   creating build/bdist.linux-armv7l/wheel/pymlst/wg
2026-06-17T07:57:49,543   copying build/lib/pymlst/wg/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg
2026-06-17T07:57:49,546   creating build/bdist.linux-armv7l/wheel/pymlst/wg/commands
2026-06-17T07:57:49,547   copying build/lib/pymlst/wg/commands/recombination.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,549   copying build/lib/pymlst/wg/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,550   copying build/lib/pymlst/wg/commands/subgraph.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,552   copying build/lib/pymlst/wg/commands/create.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,554   copying build/lib/pymlst/wg/commands/remove.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,555   copying build/lib/pymlst/wg/commands/sequence.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,557   copying build/lib/pymlst/wg/commands/distance.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,559   copying build/lib/pymlst/wg/commands/strain.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,561   copying build/lib/pymlst/wg/commands/gene.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,562   copying build/lib/pymlst/wg/commands/stats.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,564   copying build/lib/pymlst/wg/commands/msa.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,566   copying build/lib/pymlst/wg/commands/mlst.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,568   copying build/lib/pymlst/wg/commands/add2.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,569   copying build/lib/pymlst/wg/commands/add.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,571   copying build/lib/pymlst/wg/commands/import.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2026-06-17T07:57:49,573   copying build/lib/pymlst/wg/model.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg
2026-06-17T07:57:49,575   copying build/lib/pymlst/wg/extractors.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg
2026-06-17T07:57:49,577   copying build/lib/pymlst/wg/core.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg
2026-06-17T07:57:49,580   copying build/lib/pymlst/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst
2026-06-17T07:57:49,581   copying build/lib/pymlst/config.py -> build/bdist.linux-armv7l/wheel/./pymlst
2026-06-17T07:57:49,583   copying build/lib/pymlst/cmd.py -> build/bdist.linux-armv7l/wheel/./pymlst
2026-06-17T07:57:49,585   creating build/bdist.linux-armv7l/wheel/pymlst/pytyper
2026-06-17T07:57:49,586   copying build/lib/pymlst/pytyper/method.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper
2026-06-17T07:57:49,588   copying build/lib/pymlst/pytyper/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper
2026-06-17T07:57:49,590   creating build/bdist.linux-armv7l/wheel/pymlst/pytyper/commands
2026-06-17T07:57:49,591   copying build/lib/pymlst/pytyper/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper/commands
2026-06-17T07:57:49,593   copying build/lib/pymlst/pytyper/commands/search.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper/commands
2026-06-17T07:57:49,594   copying build/lib/pymlst/pytyper/model.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper
2026-06-17T07:57:49,596   copying build/lib/pymlst/pytyper/url.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper
2026-06-17T07:57:49,598   copying build/lib/pymlst/pytyper/core.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper
2026-06-17T07:57:49,601   creating build/bdist.linux-armv7l/wheel/pymlst/common
2026-06-17T07:57:49,602   copying build/lib/pymlst/common/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2026-06-17T07:57:49,603   copying build/lib/pymlst/common/exceptions.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2026-06-17T07:57:49,605   copying build/lib/pymlst/common/kma.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2026-06-17T07:57:49,607   creating build/bdist.linux-armv7l/wheel/pymlst/common/commands
2026-06-17T07:57:49,608   copying build/lib/pymlst/common/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/common/commands
2026-06-17T07:57:49,610   copying build/lib/pymlst/common/commands/configure.py -> build/bdist.linux-armv7l/wheel/./pymlst/common/commands
2026-06-17T07:57:49,612   copying build/lib/pymlst/common/mafft.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2026-06-17T07:57:49,614   copying build/lib/pymlst/common/web.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2026-06-17T07:57:49,616   copying build/lib/pymlst/common/blat.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2026-06-17T07:57:49,618   copying build/lib/pymlst/common/flag.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2026-06-17T07:57:49,619   copying build/lib/pymlst/common/utils.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2026-06-17T07:57:49,622   copying build/lib/pymlst/common/psl.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2026-06-17T07:57:49,624   creating build/bdist.linux-armv7l/wheel/pymlst/cla
2026-06-17T07:57:49,625   copying build/lib/pymlst/cla/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla
2026-06-17T07:57:49,627   creating build/bdist.linux-armv7l/wheel/pymlst/cla/commands
2026-06-17T07:57:49,628   copying build/lib/pymlst/cla/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2026-06-17T07:57:49,630   copying build/lib/pymlst/cla/commands/create.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2026-06-17T07:57:49,631   copying build/lib/pymlst/cla/commands/remove.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2026-06-17T07:57:49,633   copying build/lib/pymlst/cla/commands/info.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2026-06-17T07:57:49,635   copying build/lib/pymlst/cla/commands/search.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2026-06-17T07:57:49,636   copying build/lib/pymlst/cla/commands/search2.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2026-06-17T07:57:49,638   copying build/lib/pymlst/cla/commands/import.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2026-06-17T07:57:49,640   copying build/lib/pymlst/cla/model.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla
2026-06-17T07:57:49,642   copying build/lib/pymlst/cla/core.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla
2026-06-17T07:57:49,645   creating build/bdist.linux-armv7l/wheel/pymlst/data
2026-06-17T07:57:49,646   creating build/bdist.linux-armv7l/wheel/pymlst/data/pytyper
2026-06-17T07:57:49,647   copying build/lib/pymlst/data/pytyper/clmt.txt -> build/bdist.linux-armv7l/wheel/./pymlst/data/pytyper
2026-06-17T07:57:49,649   copying build/lib/pymlst/data/pytyper/clmt.fna -> build/bdist.linux-armv7l/wheel/./pymlst/data/pytyper
2026-06-17T07:57:49,651   copying build/lib/pymlst/data/pytyper/fimh.fna -> build/bdist.linux-armv7l/wheel/./pymlst/data/pytyper
2026-06-17T07:57:49,653   copying build/lib/pymlst/data/pytyper/spa.fna -> build/bdist.linux-armv7l/wheel/./pymlst/data/pytyper
2026-06-17T07:57:49,655   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic
2026-06-17T07:57:49,657   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/wg
2026-06-17T07:57:49,658   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/wg/versions
2026-06-17T07:57:49,659   copying build/lib/pymlst/data/alembic/wg/versions/52ae99cb5f33_initial.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/wg/versions
2026-06-17T07:57:49,661   copying build/lib/pymlst/data/alembic/wg/versions/a793f8f3fd83_add_database_infos.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/wg/versions
2026-06-17T07:57:49,663   copying build/lib/pymlst/data/alembic/wg/env.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/wg
2026-06-17T07:57:49,665   copying build/lib/pymlst/data/alembic/wg/script.py.mako -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/wg
2026-06-17T07:57:49,667   copying build/lib/pymlst/data/alembic/alembic.ini -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic
2026-06-17T07:57:49,669   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/pytyper
2026-06-17T07:57:49,670   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/pytyper/versions
2026-06-17T07:57:49,671   copying build/lib/pymlst/data/alembic/pytyper/versions/1f96d027f4aa_initial.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/pytyper/versions
2026-06-17T07:57:49,673   copying build/lib/pymlst/data/alembic/pytyper/env.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/pytyper
2026-06-17T07:57:49,675   copying build/lib/pymlst/data/alembic/pytyper/script.py.mako -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/pytyper
2026-06-17T07:57:49,677   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/cla
2026-06-17T07:57:49,679   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/cla/versions
2026-06-17T07:57:49,680   copying build/lib/pymlst/data/alembic/cla/versions/c0f871a99d96_add_database_infos.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/cla/versions
2026-06-17T07:57:49,682   copying build/lib/pymlst/data/alembic/cla/versions/21efe503d07d_initial.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/cla/versions
2026-06-17T07:57:49,684   copying build/lib/pymlst/data/alembic/cla/env.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/cla
2026-06-17T07:57:49,686   copying build/lib/pymlst/data/alembic/cla/script.py.mako -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/cla
2026-06-17T07:57:49,688   copying build/lib/pymlst/version.py -> build/bdist.linux-armv7l/wheel/./pymlst
2026-06-17T07:57:49,689   running install_egg_info
2026-06-17T07:57:49,719   Copying PyMLST.egg-info to build/bdist.linux-armv7l/wheel/./PyMLST-2.3.2-py3.11.egg-info
2026-06-17T07:57:49,730   running install_scripts
2026-06-17T07:57:49,741   creating build/bdist.linux-armv7l/wheel/pymlst-2.3.2.dist-info/WHEEL
2026-06-17T07:57:49,744   creating '/tmp/pip-wheel-_905vfn8/pymlst-2.3.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-06-17T07:57:49,746   adding 'pymlst/__init__.py'
2026-06-17T07:57:49,747   adding 'pymlst/cmd.py'
2026-06-17T07:57:49,749   adding 'pymlst/config.py'
2026-06-17T07:57:49,750   adding 'pymlst/version.py'
2026-06-17T07:57:49,751   adding 'pymlst/cla/__init__.py'
2026-06-17T07:57:49,755   adding 'pymlst/cla/core.py'
2026-06-17T07:57:49,756   adding 'pymlst/cla/model.py'
2026-06-17T07:57:49,757   adding 'pymlst/cla/commands/__init__.py'
2026-06-17T07:57:49,759   adding 'pymlst/cla/commands/create.py'
2026-06-17T07:57:49,760   adding 'pymlst/cla/commands/import.py'
2026-06-17T07:57:49,761   adding 'pymlst/cla/commands/info.py'
2026-06-17T07:57:49,762   adding 'pymlst/cla/commands/remove.py'
2026-06-17T07:57:49,764   adding 'pymlst/cla/commands/search.py'
2026-06-17T07:57:49,765   adding 'pymlst/cla/commands/search2.py'
2026-06-17T07:57:49,766   adding 'pymlst/common/__init__.py'
2026-06-17T07:57:49,768   adding 'pymlst/common/blat.py'
2026-06-17T07:57:49,769   adding 'pymlst/common/exceptions.py'
2026-06-17T07:57:49,770   adding 'pymlst/common/flag.py'
2026-06-17T07:57:49,771   adding 'pymlst/common/kma.py'
2026-06-17T07:57:49,773   adding 'pymlst/common/mafft.py'
2026-06-17T07:57:49,774   adding 'pymlst/common/psl.py'
2026-06-17T07:57:49,775   adding 'pymlst/common/utils.py'
2026-06-17T07:57:49,777   adding 'pymlst/common/web.py'
2026-06-17T07:57:49,779   adding 'pymlst/common/commands/__init__.py'
2026-06-17T07:57:49,780   adding 'pymlst/common/commands/configure.py'
2026-06-17T07:57:49,783   adding 'pymlst/data/alembic/alembic.ini'
2026-06-17T07:57:49,785   adding 'pymlst/data/alembic/cla/env.py'
2026-06-17T07:57:49,786   adding 'pymlst/data/alembic/cla/script.py.mako'
2026-06-17T07:57:49,787   adding 'pymlst/data/alembic/cla/versions/21efe503d07d_initial.py'
2026-06-17T07:57:49,789   adding 'pymlst/data/alembic/cla/versions/c0f871a99d96_add_database_infos.py'
2026-06-17T07:57:49,790   adding 'pymlst/data/alembic/pytyper/env.py'
2026-06-17T07:57:49,791   adding 'pymlst/data/alembic/pytyper/script.py.mako'
2026-06-17T07:57:49,793   adding 'pymlst/data/alembic/pytyper/versions/1f96d027f4aa_initial.py'
2026-06-17T07:57:49,795   adding 'pymlst/data/alembic/wg/env.py'
2026-06-17T07:57:49,796   adding 'pymlst/data/alembic/wg/script.py.mako'
2026-06-17T07:57:49,798   adding 'pymlst/data/alembic/wg/versions/52ae99cb5f33_initial.py'
2026-06-17T07:57:49,799   adding 'pymlst/data/alembic/wg/versions/a793f8f3fd83_add_database_infos.py'
2026-06-17T07:57:49,802   adding 'pymlst/data/pytyper/clmt.fna'
2026-06-17T07:57:49,803   adding 'pymlst/data/pytyper/clmt.txt'
2026-06-17T07:57:49,804   adding 'pymlst/data/pytyper/fimh.fna'
2026-06-17T07:57:49,805   adding 'pymlst/data/pytyper/spa.fna'
2026-06-17T07:57:49,807   adding 'pymlst/pytyper/__init__.py'
2026-06-17T07:57:49,810   adding 'pymlst/pytyper/core.py'
2026-06-17T07:57:49,811   adding 'pymlst/pytyper/method.py'
2026-06-17T07:57:49,812   adding 'pymlst/pytyper/model.py'
2026-06-17T07:57:49,814   adding 'pymlst/pytyper/url.py'
2026-06-17T07:57:49,815   adding 'pymlst/pytyper/commands/__init__.py'
2026-06-17T07:57:49,817   adding 'pymlst/pytyper/commands/search.py'
2026-06-17T07:57:49,818   adding 'pymlst/wg/__init__.py'
2026-06-17T07:57:49,823   adding 'pymlst/wg/core.py'
2026-06-17T07:57:49,825   adding 'pymlst/wg/extractors.py'
2026-06-17T07:57:49,827   adding 'pymlst/wg/model.py'
2026-06-17T07:57:49,828   adding 'pymlst/wg/commands/__init__.py'
2026-06-17T07:57:49,830   adding 'pymlst/wg/commands/add.py'
2026-06-17T07:57:49,831   adding 'pymlst/wg/commands/add2.py'
2026-06-17T07:57:49,832   adding 'pymlst/wg/commands/create.py'
2026-06-17T07:57:49,834   adding 'pymlst/wg/commands/distance.py'
2026-06-17T07:57:49,835   adding 'pymlst/wg/commands/gene.py'
2026-06-17T07:57:49,836   adding 'pymlst/wg/commands/import.py'
2026-06-17T07:57:49,837   adding 'pymlst/wg/commands/mlst.py'
2026-06-17T07:57:49,838   adding 'pymlst/wg/commands/msa.py'
2026-06-17T07:57:49,840   adding 'pymlst/wg/commands/recombination.py'
2026-06-17T07:57:49,841   adding 'pymlst/wg/commands/remove.py'
2026-06-17T07:57:49,842   adding 'pymlst/wg/commands/sequence.py'
2026-06-17T07:57:49,843   adding 'pymlst/wg/commands/stats.py'
2026-06-17T07:57:49,844   adding 'pymlst/wg/commands/strain.py'
2026-06-17T07:57:49,846   adding 'pymlst/wg/commands/subgraph.py'
2026-06-17T07:57:49,848   adding 'pymlst-2.3.2.dist-info/licenses/LICENSE'
2026-06-17T07:57:49,850   adding 'pymlst-2.3.2.dist-info/METADATA'
2026-06-17T07:57:49,850   adding 'pymlst-2.3.2.dist-info/WHEEL'
2026-06-17T07:57:49,851   adding 'pymlst-2.3.2.dist-info/entry_points.txt'
2026-06-17T07:57:49,852   adding 'pymlst-2.3.2.dist-info/top_level.txt'
2026-06-17T07:57:49,854   adding 'pymlst-2.3.2.dist-info/RECORD'
2026-06-17T07:57:49,856   removing build/bdist.linux-armv7l/wheel
2026-06-17T07:57:49,993   Building wheel for pymlst (setup.py): finished with status 'done'
2026-06-17T07:57:49,997   Created wheel for pymlst: filename=pymlst-2.3.2-py3-none-any.whl size=72296 sha256=38d9976306aeb18c2b191b92065efb3debde90390b31a5d090c050427ca015cc
2026-06-17T07:57:49,998   Stored in directory: /tmp/pip-ephem-wheel-cache-ufiuwnx8/wheels/2e/c6/ad/911305c2eba4230d8bef2570fe71987c3c1906d58aba545118
2026-06-17T07:57:50,011 Successfully built pymlst
2026-06-17T07:57:50,016 Removed build tracker: '/tmp/pip-build-tracker-513_fti0'