2025-03-28T16:54:15,413 Created temporary directory: /tmp/pip-build-tracker-yjlzfow5
2025-03-28T16:54:15,414 Initialized build tracking at /tmp/pip-build-tracker-yjlzfow5
2025-03-28T16:54:15,415 Created build tracker: /tmp/pip-build-tracker-yjlzfow5
2025-03-28T16:54:15,415 Entered build tracker: /tmp/pip-build-tracker-yjlzfow5
2025-03-28T16:54:15,416 Created temporary directory: /tmp/pip-wheel-7hulwr3q
2025-03-28T16:54:15,420 Created temporary directory: /tmp/pip-ephem-wheel-cache-zo4l1e8o
2025-03-28T16:54:15,465 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-03-28T16:54:15,468 2 location(s) to search for versions of pymlst:
2025-03-28T16:54:15,468 * https://pypi.org/simple/pymlst/
2025-03-28T16:54:15,468 * https://www.piwheels.org/simple/pymlst/
2025-03-28T16:54:15,469 Fetching project page and analyzing links: https://pypi.org/simple/pymlst/
2025-03-28T16:54:15,469 Getting page https://pypi.org/simple/pymlst/
2025-03-28T16:54:15,471 Found index url https://pypi.org/simple/
2025-03-28T16:54:15,617 Fetched page https://pypi.org/simple/pymlst/ as application/vnd.pypi.simple.v1+json
2025-03-28T16:54:15,621   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)
2025-03-28T16:54:15,622   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)
2025-03-28T16:54:15,622   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)
2025-03-28T16:54:15,623   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)
2025-03-28T16:54:15,624   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
2025-03-28T16:54:15,625   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)
2025-03-28T16:54:15,626   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
2025-03-28T16:54:15,626   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)
2025-03-28T16:54:15,627   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
2025-03-28T16:54:15,628   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)
2025-03-28T16:54:15,629   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
2025-03-28T16:54:15,630   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)
2025-03-28T16:54:15,631   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
2025-03-28T16:54:15,632   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)
2025-03-28T16:54:15,633   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
2025-03-28T16:54:15,633   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)
2025-03-28T16:54:15,634   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
2025-03-28T16:54:15,635 Fetching project page and analyzing links: https://www.piwheels.org/simple/pymlst/
2025-03-28T16:54:15,636 Getting page https://www.piwheels.org/simple/pymlst/
2025-03-28T16:54:15,637 Found index url https://www.piwheels.org/simple/
2025-03-28T16:54:15,795 Fetched page https://www.piwheels.org/simple/pymlst/ as text/html
2025-03-28T16:54:15,798   Skipping link: No binaries permitted for pymlst: https://www.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)
2025-03-28T16:54:15,798   Skipping link: No binaries permitted for pymlst: https://www.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)
2025-03-28T16:54:15,799   Skipping link: No binaries permitted for pymlst: https://www.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)
2025-03-28T16:54:15,800   Skipping link: No binaries permitted for pymlst: https://www.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)
2025-03-28T16:54:15,800   Skipping link: No binaries permitted for pymlst: https://www.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)
2025-03-28T16:54:15,801   Skipping link: No binaries permitted for pymlst: https://www.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)
2025-03-28T16:54:15,802 Skipping link: not a file: https://www.piwheels.org/simple/pymlst/
2025-03-28T16:54:15,802 Skipping link: not a file: https://pypi.org/simple/pymlst/
2025-03-28T16:54:15,822 Given no hashes to check 1 links for project 'pymlst': discarding no candidates
2025-03-28T16:54:15,824 Collecting pymlst==2.2.1
2025-03-28T16:54:15,826   Created temporary directory: /tmp/pip-unpack-c3630tpu
2025-03-28T16:54:16,046   Downloading pymlst-2.2.1.tar.gz (54 kB)
2025-03-28T16:54:16,226   Added pymlst==2.2.1 from https://files.pythonhosted.org/packages/e6/ab/4c8c0da60a0102a3fc0b148e26989f6f32b3fe592cb9c1477b42dc316995/pymlst-2.2.1.tar.gz to build tracker '/tmp/pip-build-tracker-yjlzfow5'
2025-03-28T16:54:16,227   Running setup.py (path:/tmp/pip-wheel-7hulwr3q/pymlst_9e30c7a70f12458183850812d59cb2ab/setup.py) egg_info for package pymlst
2025-03-28T16:54:16,229   Created temporary directory: /tmp/pip-pip-egg-info-z7tmi0ww
2025-03-28T16:54:16,229   Preparing metadata (setup.py): started
2025-03-28T16:54:16,230   Running command python setup.py egg_info
2025-03-28T16:54:16,734   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:495: SetuptoolsDeprecationWarning: Invalid dash-separated options
2025-03-28T16:54:16,735   !!

2025-03-28T16:54:16,736           ********************************************************************************
2025-03-28T16:54:16,736           Usage of dash-separated 'description-file' will not be supported in future
2025-03-28T16:54:16,736           versions. Please use the underscore name 'description_file' instead.

2025-03-28T16:54:16,737           This deprecation is overdue, please update your project and remove deprecated
2025-03-28T16:54:16,738           calls to avoid build errors in the future.

2025-03-28T16:54:16,739           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2025-03-28T16:54:16,739           ********************************************************************************

2025-03-28T16:54:16,740   !!
2025-03-28T16:54:16,741     opt = self.warn_dash_deprecation(opt, section)
2025-03-28T16:54:16,961   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2025-03-28T16:54:16,961   !!

2025-03-28T16:54:16,963           ********************************************************************************
2025-03-28T16:54:16,963           Requirements should be satisfied by a PEP 517 installer.
2025-03-28T16:54:16,964           If you are using pip, you can try `pip install --use-pep517`.
2025-03-28T16:54:16,965           ********************************************************************************

2025-03-28T16:54:16,966   !!
2025-03-28T16:54:16,966     dist.fetch_build_eggs(dist.setup_requires)
2025-03-28T16:54:17,272   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:495: SetuptoolsDeprecationWarning: Invalid dash-separated options
2025-03-28T16:54:17,273   !!

2025-03-28T16:54:17,274           ********************************************************************************
2025-03-28T16:54:17,275           Usage of dash-separated 'description-file' will not be supported in future
2025-03-28T16:54:17,275           versions. Please use the underscore name 'description_file' instead.

2025-03-28T16:54:17,277           This deprecation is overdue, please update your project and remove deprecated
2025-03-28T16:54:17,277           calls to avoid build errors in the future.

2025-03-28T16:54:17,278           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2025-03-28T16:54:17,279           ********************************************************************************

2025-03-28T16:54:17,280   !!
2025-03-28T16:54:17,281     opt = self.warn_dash_deprecation(opt, section)
2025-03-28T16:54:17,307   running egg_info
2025-03-28T16:54:17,334   creating /tmp/pip-pip-egg-info-z7tmi0ww/PyMLST.egg-info
2025-03-28T16:54:17,335   writing /tmp/pip-pip-egg-info-z7tmi0ww/PyMLST.egg-info/PKG-INFO
2025-03-28T16:54:17,339   writing dependency_links to /tmp/pip-pip-egg-info-z7tmi0ww/PyMLST.egg-info/dependency_links.txt
2025-03-28T16:54:17,341   writing entry points to /tmp/pip-pip-egg-info-z7tmi0ww/PyMLST.egg-info/entry_points.txt
2025-03-28T16:54:17,342   writing requirements to /tmp/pip-pip-egg-info-z7tmi0ww/PyMLST.egg-info/requires.txt
2025-03-28T16:54:17,343   writing top-level names to /tmp/pip-pip-egg-info-z7tmi0ww/PyMLST.egg-info/top_level.txt
2025-03-28T16:54:17,345   writing manifest file '/tmp/pip-pip-egg-info-z7tmi0ww/PyMLST.egg-info/SOURCES.txt'
2025-03-28T16:54:17,440   reading manifest file '/tmp/pip-pip-egg-info-z7tmi0ww/PyMLST.egg-info/SOURCES.txt'
2025-03-28T16:54:17,442   reading manifest template 'MANIFEST.in'
2025-03-28T16:54:17,447   adding license file 'LICENSE'
2025-03-28T16:54:17,451   writing manifest file '/tmp/pip-pip-egg-info-z7tmi0ww/PyMLST.egg-info/SOURCES.txt'
2025-03-28T16:54:17,564   Preparing metadata (setup.py): finished with status 'done'
2025-03-28T16:54:17,568   Source in /tmp/pip-wheel-7hulwr3q/pymlst_9e30c7a70f12458183850812d59cb2ab has version 2.2.1, which satisfies requirement pymlst==2.2.1 from https://files.pythonhosted.org/packages/e6/ab/4c8c0da60a0102a3fc0b148e26989f6f32b3fe592cb9c1477b42dc316995/pymlst-2.2.1.tar.gz
2025-03-28T16:54:17,569   Removed pymlst==2.2.1 from https://files.pythonhosted.org/packages/e6/ab/4c8c0da60a0102a3fc0b148e26989f6f32b3fe592cb9c1477b42dc316995/pymlst-2.2.1.tar.gz from build tracker '/tmp/pip-build-tracker-yjlzfow5'
2025-03-28T16:54:17,577 Created temporary directory: /tmp/pip-unpack-ey65w1g4
2025-03-28T16:54:17,578 Created temporary directory: /tmp/pip-unpack-qbx3kqa9
2025-03-28T16:54:17,579 Building wheels for collected packages: pymlst
2025-03-28T16:54:17,583   Created temporary directory: /tmp/pip-wheel-xf3o7qxc
2025-03-28T16:54:17,583   Building wheel for pymlst (setup.py): started
2025-03-28T16:54:17,584   Destination directory: /tmp/pip-wheel-xf3o7qxc
2025-03-28T16:54:17,585   Running command python setup.py bdist_wheel
2025-03-28T16:54:18,093   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:495: SetuptoolsDeprecationWarning: Invalid dash-separated options
2025-03-28T16:54:18,093   !!

2025-03-28T16:54:18,094           ********************************************************************************
2025-03-28T16:54:18,095           Usage of dash-separated 'description-file' will not be supported in future
2025-03-28T16:54:18,095           versions. Please use the underscore name 'description_file' instead.

2025-03-28T16:54:18,097           This deprecation is overdue, please update your project and remove deprecated
2025-03-28T16:54:18,097           calls to avoid build errors in the future.

2025-03-28T16:54:18,098           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2025-03-28T16:54:18,099           ********************************************************************************

2025-03-28T16:54:18,100   !!
2025-03-28T16:54:18,101     opt = self.warn_dash_deprecation(opt, section)
2025-03-28T16:54:18,317   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2025-03-28T16:54:18,317   !!

2025-03-28T16:54:18,319           ********************************************************************************
2025-03-28T16:54:18,319           Requirements should be satisfied by a PEP 517 installer.
2025-03-28T16:54:18,320           If you are using pip, you can try `pip install --use-pep517`.
2025-03-28T16:54:18,320           ********************************************************************************

2025-03-28T16:54:18,322   !!
2025-03-28T16:54:18,322     dist.fetch_build_eggs(dist.setup_requires)
2025-03-28T16:54:18,626   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:495: SetuptoolsDeprecationWarning: Invalid dash-separated options
2025-03-28T16:54:18,627   !!

2025-03-28T16:54:18,628           ********************************************************************************
2025-03-28T16:54:18,629           Usage of dash-separated 'description-file' will not be supported in future
2025-03-28T16:54:18,629           versions. Please use the underscore name 'description_file' instead.

2025-03-28T16:54:18,631           This deprecation is overdue, please update your project and remove deprecated
2025-03-28T16:54:18,631           calls to avoid build errors in the future.

2025-03-28T16:54:18,633           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2025-03-28T16:54:18,633           ********************************************************************************

2025-03-28T16:54:18,634   !!
2025-03-28T16:54:18,635     opt = self.warn_dash_deprecation(opt, section)
2025-03-28T16:54:18,635   running bdist_wheel
2025-03-28T16:54:18,766   running build
2025-03-28T16:54:18,767   running build_py
2025-03-28T16:54:18,797   creating build/lib/pymlst
2025-03-28T16:54:18,800   copying pymlst/cmd.py -> build/lib/pymlst
2025-03-28T16:54:18,802   copying pymlst/__init__.py -> build/lib/pymlst
2025-03-28T16:54:18,803   copying pymlst/config.py -> build/lib/pymlst
2025-03-28T16:54:18,805   copying pymlst/version.py -> build/lib/pymlst
2025-03-28T16:54:18,807   creating build/lib/pymlst/wg
2025-03-28T16:54:18,809   copying pymlst/wg/__init__.py -> build/lib/pymlst/wg
2025-03-28T16:54:18,810   copying pymlst/wg/model.py -> build/lib/pymlst/wg
2025-03-28T16:54:18,812   copying pymlst/wg/core.py -> build/lib/pymlst/wg
2025-03-28T16:54:18,815   copying pymlst/wg/extractors.py -> build/lib/pymlst/wg
2025-03-28T16:54:18,818   creating build/lib/pymlst/pytyper
2025-03-28T16:54:18,819   copying pymlst/pytyper/__init__.py -> build/lib/pymlst/pytyper
2025-03-28T16:54:18,821   copying pymlst/pytyper/model.py -> build/lib/pymlst/pytyper
2025-03-28T16:54:18,823   copying pymlst/pytyper/method.py -> build/lib/pymlst/pytyper
2025-03-28T16:54:18,825   copying pymlst/pytyper/core.py -> build/lib/pymlst/pytyper
2025-03-28T16:54:18,827   copying pymlst/pytyper/url.py -> build/lib/pymlst/pytyper
2025-03-28T16:54:18,830   creating build/lib/pymlst/common
2025-03-28T16:54:18,831   copying pymlst/common/blat.py -> build/lib/pymlst/common
2025-03-28T16:54:18,833   copying pymlst/common/utils.py -> build/lib/pymlst/common
2025-03-28T16:54:18,835   copying pymlst/common/psl.py -> build/lib/pymlst/common
2025-03-28T16:54:18,837   copying pymlst/common/web.py -> build/lib/pymlst/common
2025-03-28T16:54:18,839   copying pymlst/common/__init__.py -> build/lib/pymlst/common
2025-03-28T16:54:18,840   copying pymlst/common/kma.py -> build/lib/pymlst/common
2025-03-28T16:54:18,842   copying pymlst/common/flag.py -> build/lib/pymlst/common
2025-03-28T16:54:18,844   copying pymlst/common/mafft.py -> build/lib/pymlst/common
2025-03-28T16:54:18,846   copying pymlst/common/exceptions.py -> build/lib/pymlst/common
2025-03-28T16:54:18,848   creating build/lib/pymlst/cla
2025-03-28T16:54:18,849   copying pymlst/cla/__init__.py -> build/lib/pymlst/cla
2025-03-28T16:54:18,851   copying pymlst/cla/model.py -> build/lib/pymlst/cla
2025-03-28T16:54:18,853   copying pymlst/cla/core.py -> build/lib/pymlst/cla
2025-03-28T16:54:18,858   creating build/lib/pymlst/wg/commands
2025-03-28T16:54:18,859   copying pymlst/wg/commands/add.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,861   copying pymlst/wg/commands/import.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,862   copying pymlst/wg/commands/add2.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,864   copying pymlst/wg/commands/remove.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,866   copying pymlst/wg/commands/recombination.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,868   copying pymlst/wg/commands/mlst.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,870   copying pymlst/wg/commands/__init__.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,871   copying pymlst/wg/commands/distance.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,873   copying pymlst/wg/commands/subgraph.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,875   copying pymlst/wg/commands/create.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,877   copying pymlst/wg/commands/strain.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,879   copying pymlst/wg/commands/sequence.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,881   copying pymlst/wg/commands/gene.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,883   copying pymlst/wg/commands/msa.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,886   copying pymlst/wg/commands/stats.py -> build/lib/pymlst/wg/commands
2025-03-28T16:54:18,888   creating build/lib/pymlst/pytyper/commands
2025-03-28T16:54:18,889   copying pymlst/pytyper/commands/__init__.py -> build/lib/pymlst/pytyper/commands
2025-03-28T16:54:18,891   copying pymlst/pytyper/commands/search.py -> build/lib/pymlst/pytyper/commands
2025-03-28T16:54:18,893   creating build/lib/pymlst/common/commands
2025-03-28T16:54:18,894   copying pymlst/common/commands/configure.py -> build/lib/pymlst/common/commands
2025-03-28T16:54:18,897   copying pymlst/common/commands/__init__.py -> build/lib/pymlst/common/commands
2025-03-28T16:54:18,899   creating build/lib/pymlst/cla/commands
2025-03-28T16:54:18,900   copying pymlst/cla/commands/import.py -> build/lib/pymlst/cla/commands
2025-03-28T16:54:18,902   copying pymlst/cla/commands/remove.py -> build/lib/pymlst/cla/commands
2025-03-28T16:54:18,904   copying pymlst/cla/commands/__init__.py -> build/lib/pymlst/cla/commands
2025-03-28T16:54:18,905   copying pymlst/cla/commands/search.py -> build/lib/pymlst/cla/commands
2025-03-28T16:54:18,907   copying pymlst/cla/commands/info.py -> build/lib/pymlst/cla/commands
2025-03-28T16:54:18,909   copying pymlst/cla/commands/create.py -> build/lib/pymlst/cla/commands
2025-03-28T16:54:18,911   copying pymlst/cla/commands/search2.py -> build/lib/pymlst/cla/commands
2025-03-28T16:54:18,912   running egg_info
2025-03-28T16:54:18,940   writing PyMLST.egg-info/PKG-INFO
2025-03-28T16:54:18,943   writing dependency_links to PyMLST.egg-info/dependency_links.txt
2025-03-28T16:54:18,945   writing entry points to PyMLST.egg-info/entry_points.txt
2025-03-28T16:54:18,947   writing requirements to PyMLST.egg-info/requires.txt
2025-03-28T16:54:18,948   writing top-level names to PyMLST.egg-info/top_level.txt
2025-03-28T16:54:18,986   reading manifest file 'PyMLST.egg-info/SOURCES.txt'
2025-03-28T16:54:18,994   reading manifest template 'MANIFEST.in'
2025-03-28T16:54:18,998   adding license file 'LICENSE'
2025-03-28T16:54:19,003   writing manifest file 'PyMLST.egg-info/SOURCES.txt'
2025-03-28T16:54:19,006   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'pymlst.data.alembic' is absent from the `packages` configuration.
2025-03-28T16:54:19,007   !!

2025-03-28T16:54:19,008           ********************************************************************************
2025-03-28T16:54:19,008           ############################
2025-03-28T16:54:19,009           # Package would be ignored #
2025-03-28T16:54:19,010           ############################
2025-03-28T16:54:19,010           Python recognizes 'pymlst.data.alembic' as an importable package[^1],
2025-03-28T16:54:19,011           but it is absent from setuptools' `packages` configuration.

2025-03-28T16:54:19,012           This leads to an ambiguous overall configuration. If you want to distribute this
2025-03-28T16:54:19,013           package, please make sure that 'pymlst.data.alembic' is explicitly added
2025-03-28T16:54:19,014           to the `packages` configuration field.

2025-03-28T16:54:19,015           Alternatively, you can also rely on setuptools' discovery methods
2025-03-28T16:54:19,015           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-03-28T16:54:19,016           instead of `find_packages(...)`/`find:`).

2025-03-28T16:54:19,017           You can read more about "package discovery" on setuptools documentation page:

2025-03-28T16:54:19,018           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-03-28T16:54:19,020           If you don't want 'pymlst.data.alembic' to be distributed and are
2025-03-28T16:54:19,020           already explicitly excluding 'pymlst.data.alembic' via
2025-03-28T16:54:19,021           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-03-28T16:54:19,022           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-03-28T16:54:19,022           combination with a more fine grained `package-data` configuration.

2025-03-28T16:54:19,024           You can read more about "package data files" on setuptools documentation page:

2025-03-28T16:54:19,025           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-03-28T16:54:19,026           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-03-28T16:54:19,027                 even if it does not contain any `.py` files.
2025-03-28T16:54:19,027                 On the other hand, currently there is no concept of package data
2025-03-28T16:54:19,028                 directory, all directories are treated like packages.
2025-03-28T16:54:19,028           ********************************************************************************

2025-03-28T16:54:19,029   !!
2025-03-28T16:54:19,030     check.warn(importable)
2025-03-28T16:54:19,031   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'pymlst.data.alembic.cla' is absent from the `packages` configuration.
2025-03-28T16:54:19,031   !!

2025-03-28T16:54:19,032           ********************************************************************************
2025-03-28T16:54:19,033           ############################
2025-03-28T16:54:19,033           # Package would be ignored #
2025-03-28T16:54:19,034           ############################
2025-03-28T16:54:19,034           Python recognizes 'pymlst.data.alembic.cla' as an importable package[^1],
2025-03-28T16:54:19,035           but it is absent from setuptools' `packages` configuration.

2025-03-28T16:54:19,036           This leads to an ambiguous overall configuration. If you want to distribute this
2025-03-28T16:54:19,037           package, please make sure that 'pymlst.data.alembic.cla' is explicitly added
2025-03-28T16:54:19,037           to the `packages` configuration field.

2025-03-28T16:54:19,038           Alternatively, you can also rely on setuptools' discovery methods
2025-03-28T16:54:19,039           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-03-28T16:54:19,039           instead of `find_packages(...)`/`find:`).

2025-03-28T16:54:19,041           You can read more about "package discovery" on setuptools documentation page:

2025-03-28T16:54:19,042           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-03-28T16:54:19,043           If you don't want 'pymlst.data.alembic.cla' to be distributed and are
2025-03-28T16:54:19,043           already explicitly excluding 'pymlst.data.alembic.cla' via
2025-03-28T16:54:19,044           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-03-28T16:54:19,044           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-03-28T16:54:19,045           combination with a more fine grained `package-data` configuration.

2025-03-28T16:54:19,046           You can read more about "package data files" on setuptools documentation page:

2025-03-28T16:54:19,047           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-03-28T16:54:19,049           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-03-28T16:54:19,050                 even if it does not contain any `.py` files.
2025-03-28T16:54:19,050                 On the other hand, currently there is no concept of package data
2025-03-28T16:54:19,051                 directory, all directories are treated like packages.
2025-03-28T16:54:19,051           ********************************************************************************

2025-03-28T16:54:19,053   !!
2025-03-28T16:54:19,053     check.warn(importable)
2025-03-28T16:54:19,054   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'pymlst.data.alembic.cla.versions' is absent from the `packages` configuration.
2025-03-28T16:54:19,055   !!

2025-03-28T16:54:19,056           ********************************************************************************
2025-03-28T16:54:19,057           ############################
2025-03-28T16:54:19,057           # Package would be ignored #
2025-03-28T16:54:19,058           ############################
2025-03-28T16:54:19,059           Python recognizes 'pymlst.data.alembic.cla.versions' as an importable package[^1],
2025-03-28T16:54:19,059           but it is absent from setuptools' `packages` configuration.

2025-03-28T16:54:19,060           This leads to an ambiguous overall configuration. If you want to distribute this
2025-03-28T16:54:19,061           package, please make sure that 'pymlst.data.alembic.cla.versions' is explicitly added
2025-03-28T16:54:19,061           to the `packages` configuration field.

2025-03-28T16:54:19,062           Alternatively, you can also rely on setuptools' discovery methods
2025-03-28T16:54:19,063           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-03-28T16:54:19,063           instead of `find_packages(...)`/`find:`).

2025-03-28T16:54:19,065           You can read more about "package discovery" on setuptools documentation page:

2025-03-28T16:54:19,066           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-03-28T16:54:19,067           If you don't want 'pymlst.data.alembic.cla.versions' to be distributed and are
2025-03-28T16:54:19,067           already explicitly excluding 'pymlst.data.alembic.cla.versions' via
2025-03-28T16:54:19,068           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-03-28T16:54:19,068           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-03-28T16:54:19,069           combination with a more fine grained `package-data` configuration.

2025-03-28T16:54:19,070           You can read more about "package data files" on setuptools documentation page:

2025-03-28T16:54:19,071           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-03-28T16:54:19,072           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-03-28T16:54:19,073                 even if it does not contain any `.py` files.
2025-03-28T16:54:19,073                 On the other hand, currently there is no concept of package data
2025-03-28T16:54:19,074                 directory, all directories are treated like packages.
2025-03-28T16:54:19,075           ********************************************************************************

2025-03-28T16:54:19,076   !!
2025-03-28T16:54:19,077     check.warn(importable)
2025-03-28T16:54:19,077   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'pymlst.data.alembic.pytyper' is absent from the `packages` configuration.
2025-03-28T16:54:19,078   !!

2025-03-28T16:54:19,080           ********************************************************************************
2025-03-28T16:54:19,081           ############################
2025-03-28T16:54:19,082           # Package would be ignored #
2025-03-28T16:54:19,084           ############################
2025-03-28T16:54:19,085           Python recognizes 'pymlst.data.alembic.pytyper' as an importable package[^1],
2025-03-28T16:54:19,086           but it is absent from setuptools' `packages` configuration.

2025-03-28T16:54:19,087           This leads to an ambiguous overall configuration. If you want to distribute this
2025-03-28T16:54:19,088           package, please make sure that 'pymlst.data.alembic.pytyper' is explicitly added
2025-03-28T16:54:19,089           to the `packages` configuration field.

2025-03-28T16:54:19,090           Alternatively, you can also rely on setuptools' discovery methods
2025-03-28T16:54:19,090           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-03-28T16:54:19,091           instead of `find_packages(...)`/`find:`).

2025-03-28T16:54:19,092           You can read more about "package discovery" on setuptools documentation page:

2025-03-28T16:54:19,093           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-03-28T16:54:19,095           If you don't want 'pymlst.data.alembic.pytyper' to be distributed and are
2025-03-28T16:54:19,095           already explicitly excluding 'pymlst.data.alembic.pytyper' via
2025-03-28T16:54:19,096           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-03-28T16:54:19,097           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-03-28T16:54:19,097           combination with a more fine grained `package-data` configuration.

2025-03-28T16:54:19,098           You can read more about "package data files" on setuptools documentation page:

2025-03-28T16:54:19,099           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-03-28T16:54:19,100           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-03-28T16:54:19,101                 even if it does not contain any `.py` files.
2025-03-28T16:54:19,101                 On the other hand, currently there is no concept of package data
2025-03-28T16:54:19,102                 directory, all directories are treated like packages.
2025-03-28T16:54:19,102           ********************************************************************************

2025-03-28T16:54:19,103   !!
2025-03-28T16:54:19,104     check.warn(importable)
2025-03-28T16:54:19,104   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'pymlst.data.alembic.pytyper.versions' is absent from the `packages` configuration.
2025-03-28T16:54:19,105   !!

2025-03-28T16:54:19,106           ********************************************************************************
2025-03-28T16:54:19,106           ############################
2025-03-28T16:54:19,107           # Package would be ignored #
2025-03-28T16:54:19,107           ############################
2025-03-28T16:54:19,108           Python recognizes 'pymlst.data.alembic.pytyper.versions' as an importable package[^1],
2025-03-28T16:54:19,108           but it is absent from setuptools' `packages` configuration.

2025-03-28T16:54:19,110           This leads to an ambiguous overall configuration. If you want to distribute this
2025-03-28T16:54:19,110           package, please make sure that 'pymlst.data.alembic.pytyper.versions' is explicitly added
2025-03-28T16:54:19,111           to the `packages` configuration field.

2025-03-28T16:54:19,112           Alternatively, you can also rely on setuptools' discovery methods
2025-03-28T16:54:19,113           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-03-28T16:54:19,113           instead of `find_packages(...)`/`find:`).

2025-03-28T16:54:19,114           You can read more about "package discovery" on setuptools documentation page:

2025-03-28T16:54:19,116           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-03-28T16:54:19,117           If you don't want 'pymlst.data.alembic.pytyper.versions' to be distributed and are
2025-03-28T16:54:19,118           already explicitly excluding 'pymlst.data.alembic.pytyper.versions' via
2025-03-28T16:54:19,118           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-03-28T16:54:19,119           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-03-28T16:54:19,119           combination with a more fine grained `package-data` configuration.

2025-03-28T16:54:19,121           You can read more about "package data files" on setuptools documentation page:

2025-03-28T16:54:19,122           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-03-28T16:54:19,124           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-03-28T16:54:19,124                 even if it does not contain any `.py` files.
2025-03-28T16:54:19,125                 On the other hand, currently there is no concept of package data
2025-03-28T16:54:19,125                 directory, all directories are treated like packages.
2025-03-28T16:54:19,126           ********************************************************************************

2025-03-28T16:54:19,127   !!
2025-03-28T16:54:19,128     check.warn(importable)
2025-03-28T16:54:19,129   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'pymlst.data.alembic.wg' is absent from the `packages` configuration.
2025-03-28T16:54:19,129   !!

2025-03-28T16:54:19,130           ********************************************************************************
2025-03-28T16:54:19,130           ############################
2025-03-28T16:54:19,131           # Package would be ignored #
2025-03-28T16:54:19,131           ############################
2025-03-28T16:54:19,132           Python recognizes 'pymlst.data.alembic.wg' as an importable package[^1],
2025-03-28T16:54:19,132           but it is absent from setuptools' `packages` configuration.

2025-03-28T16:54:19,133           This leads to an ambiguous overall configuration. If you want to distribute this
2025-03-28T16:54:19,134           package, please make sure that 'pymlst.data.alembic.wg' is explicitly added
2025-03-28T16:54:19,134           to the `packages` configuration field.

2025-03-28T16:54:19,135           Alternatively, you can also rely on setuptools' discovery methods
2025-03-28T16:54:19,135           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-03-28T16:54:19,136           instead of `find_packages(...)`/`find:`).

2025-03-28T16:54:19,137           You can read more about "package discovery" on setuptools documentation page:

2025-03-28T16:54:19,138           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-03-28T16:54:19,138           If you don't want 'pymlst.data.alembic.wg' to be distributed and are
2025-03-28T16:54:19,139           already explicitly excluding 'pymlst.data.alembic.wg' via
2025-03-28T16:54:19,139           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-03-28T16:54:19,140           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-03-28T16:54:19,140           combination with a more fine grained `package-data` configuration.

2025-03-28T16:54:19,142           You can read more about "package data files" on setuptools documentation page:

2025-03-28T16:54:19,143           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-03-28T16:54:19,145           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-03-28T16:54:19,145                 even if it does not contain any `.py` files.
2025-03-28T16:54:19,146                 On the other hand, currently there is no concept of package data
2025-03-28T16:54:19,147                 directory, all directories are treated like packages.
2025-03-28T16:54:19,147           ********************************************************************************

2025-03-28T16:54:19,149   !!
2025-03-28T16:54:19,149     check.warn(importable)
2025-03-28T16:54:19,150   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'pymlst.data.alembic.wg.versions' is absent from the `packages` configuration.
2025-03-28T16:54:19,150   !!

2025-03-28T16:54:19,151           ********************************************************************************
2025-03-28T16:54:19,152           ############################
2025-03-28T16:54:19,153           # Package would be ignored #
2025-03-28T16:54:19,153           ############################
2025-03-28T16:54:19,154           Python recognizes 'pymlst.data.alembic.wg.versions' as an importable package[^1],
2025-03-28T16:54:19,154           but it is absent from setuptools' `packages` configuration.

2025-03-28T16:54:19,155           This leads to an ambiguous overall configuration. If you want to distribute this
2025-03-28T16:54:19,156           package, please make sure that 'pymlst.data.alembic.wg.versions' is explicitly added
2025-03-28T16:54:19,157           to the `packages` configuration field.

2025-03-28T16:54:19,158           Alternatively, you can also rely on setuptools' discovery methods
2025-03-28T16:54:19,158           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-03-28T16:54:19,159           instead of `find_packages(...)`/`find:`).

2025-03-28T16:54:19,160           You can read more about "package discovery" on setuptools documentation page:

2025-03-28T16:54:19,161           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-03-28T16:54:19,162           If you don't want 'pymlst.data.alembic.wg.versions' to be distributed and are
2025-03-28T16:54:19,163           already explicitly excluding 'pymlst.data.alembic.wg.versions' via
2025-03-28T16:54:19,163           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-03-28T16:54:19,163           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-03-28T16:54:19,164           combination with a more fine grained `package-data` configuration.

2025-03-28T16:54:19,165           You can read more about "package data files" on setuptools documentation page:

2025-03-28T16:54:19,166           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-03-28T16:54:19,167           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-03-28T16:54:19,168                 even if it does not contain any `.py` files.
2025-03-28T16:54:19,168                 On the other hand, currently there is no concept of package data
2025-03-28T16:54:19,168                 directory, all directories are treated like packages.
2025-03-28T16:54:19,169           ********************************************************************************

2025-03-28T16:54:19,170   !!
2025-03-28T16:54:19,170     check.warn(importable)
2025-03-28T16:54:19,171   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'pymlst.data.pytyper' is absent from the `packages` configuration.
2025-03-28T16:54:19,171   !!

2025-03-28T16:54:19,172           ********************************************************************************
2025-03-28T16:54:19,173           ############################
2025-03-28T16:54:19,173           # Package would be ignored #
2025-03-28T16:54:19,174           ############################
2025-03-28T16:54:19,174           Python recognizes 'pymlst.data.pytyper' as an importable package[^1],
2025-03-28T16:54:19,175           but it is absent from setuptools' `packages` configuration.

2025-03-28T16:54:19,176           This leads to an ambiguous overall configuration. If you want to distribute this
2025-03-28T16:54:19,177           package, please make sure that 'pymlst.data.pytyper' is explicitly added
2025-03-28T16:54:19,177           to the `packages` configuration field.

2025-03-28T16:54:19,178           Alternatively, you can also rely on setuptools' discovery methods
2025-03-28T16:54:19,179           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-03-28T16:54:19,179           instead of `find_packages(...)`/`find:`).

2025-03-28T16:54:19,180           You can read more about "package discovery" on setuptools documentation page:

2025-03-28T16:54:19,182           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-03-28T16:54:19,183           If you don't want 'pymlst.data.pytyper' to be distributed and are
2025-03-28T16:54:19,183           already explicitly excluding 'pymlst.data.pytyper' via
2025-03-28T16:54:19,184           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-03-28T16:54:19,184           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-03-28T16:54:19,185           combination with a more fine grained `package-data` configuration.

2025-03-28T16:54:19,186           You can read more about "package data files" on setuptools documentation page:

2025-03-28T16:54:19,187           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-03-28T16:54:19,189           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-03-28T16:54:19,190                 even if it does not contain any `.py` files.
2025-03-28T16:54:19,190                 On the other hand, currently there is no concept of package data
2025-03-28T16:54:19,191                 directory, all directories are treated like packages.
2025-03-28T16:54:19,192           ********************************************************************************

2025-03-28T16:54:19,192   !!
2025-03-28T16:54:19,193     check.warn(importable)
2025-03-28T16:54:19,193   creating build/lib/pymlst/data/alembic
2025-03-28T16:54:19,194   copying pymlst/data/alembic/alembic.ini -> build/lib/pymlst/data/alembic
2025-03-28T16:54:19,194   creating build/lib/pymlst/data/alembic/cla
2025-03-28T16:54:19,195   copying pymlst/data/alembic/cla/env.py -> build/lib/pymlst/data/alembic/cla
2025-03-28T16:54:19,195   copying pymlst/data/alembic/cla/script.py.mako -> build/lib/pymlst/data/alembic/cla
2025-03-28T16:54:19,195   creating build/lib/pymlst/data/alembic/cla/versions
2025-03-28T16:54:19,196   copying pymlst/data/alembic/cla/versions/21efe503d07d_initial.py -> build/lib/pymlst/data/alembic/cla/versions
2025-03-28T16:54:19,197   copying pymlst/data/alembic/cla/versions/c0f871a99d96_add_database_infos.py -> build/lib/pymlst/data/alembic/cla/versions
2025-03-28T16:54:19,197   creating build/lib/pymlst/data/alembic/pytyper
2025-03-28T16:54:19,197   copying pymlst/data/alembic/pytyper/env.py -> build/lib/pymlst/data/alembic/pytyper
2025-03-28T16:54:19,198   copying pymlst/data/alembic/pytyper/script.py.mako -> build/lib/pymlst/data/alembic/pytyper
2025-03-28T16:54:19,198   creating build/lib/pymlst/data/alembic/pytyper/versions
2025-03-28T16:54:19,199   copying pymlst/data/alembic/pytyper/versions/1f96d027f4aa_initial.py -> build/lib/pymlst/data/alembic/pytyper/versions
2025-03-28T16:54:19,199   creating build/lib/pymlst/data/alembic/wg
2025-03-28T16:54:19,199   copying pymlst/data/alembic/wg/env.py -> build/lib/pymlst/data/alembic/wg
2025-03-28T16:54:19,200   copying pymlst/data/alembic/wg/script.py.mako -> build/lib/pymlst/data/alembic/wg
2025-03-28T16:54:19,201   creating build/lib/pymlst/data/alembic/wg/versions
2025-03-28T16:54:19,201   copying pymlst/data/alembic/wg/versions/52ae99cb5f33_initial.py -> build/lib/pymlst/data/alembic/wg/versions
2025-03-28T16:54:19,202   copying pymlst/data/alembic/wg/versions/a793f8f3fd83_add_database_infos.py -> build/lib/pymlst/data/alembic/wg/versions
2025-03-28T16:54:19,202   creating build/lib/pymlst/data/pytyper
2025-03-28T16:54:19,203   copying pymlst/data/pytyper/clmt.fna -> build/lib/pymlst/data/pytyper
2025-03-28T16:54:19,203   copying pymlst/data/pytyper/clmt.txt -> build/lib/pymlst/data/pytyper
2025-03-28T16:54:19,204   copying pymlst/data/pytyper/fimh.fna -> build/lib/pymlst/data/pytyper
2025-03-28T16:54:19,205   copying pymlst/data/pytyper/spa.fna -> build/lib/pymlst/data/pytyper
2025-03-28T16:54:19,205   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-03-28T16:54:19,206   !!

2025-03-28T16:54:19,207           ********************************************************************************
2025-03-28T16:54:19,207           Please avoid running ``setup.py`` directly.
2025-03-28T16:54:19,208           Instead, use pypa/build, pypa/installer or other
2025-03-28T16:54:19,208           standards-based tools.

2025-03-28T16:54:19,209           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-03-28T16:54:19,210           ********************************************************************************

2025-03-28T16:54:19,211   !!
2025-03-28T16:54:19,212     self.initialize_options()
2025-03-28T16:54:19,212   installing to build/bdist.linux-armv7l/wheel
2025-03-28T16:54:19,213   running install
2025-03-28T16:54:19,219   running install_lib
2025-03-28T16:54:19,246   creating build/bdist.linux-armv7l/wheel
2025-03-28T16:54:19,248   creating build/bdist.linux-armv7l/wheel/pymlst
2025-03-28T16:54:19,249   copying build/lib/pymlst/cmd.py -> build/bdist.linux-armv7l/wheel/./pymlst
2025-03-28T16:54:19,252   creating build/bdist.linux-armv7l/wheel/pymlst/wg
2025-03-28T16:54:19,253   copying build/lib/pymlst/wg/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg
2025-03-28T16:54:19,255   copying build/lib/pymlst/wg/model.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg
2025-03-28T16:54:19,257   copying build/lib/pymlst/wg/core.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg
2025-03-28T16:54:19,260   creating build/bdist.linux-armv7l/wheel/pymlst/wg/commands
2025-03-28T16:54:19,261   copying build/lib/pymlst/wg/commands/add.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,263   copying build/lib/pymlst/wg/commands/import.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,265   copying build/lib/pymlst/wg/commands/add2.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,267   copying build/lib/pymlst/wg/commands/remove.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,269   copying build/lib/pymlst/wg/commands/recombination.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,270   copying build/lib/pymlst/wg/commands/mlst.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,272   copying build/lib/pymlst/wg/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,273   copying build/lib/pymlst/wg/commands/distance.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,275   copying build/lib/pymlst/wg/commands/subgraph.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,277   copying build/lib/pymlst/wg/commands/create.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,279   copying build/lib/pymlst/wg/commands/strain.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,281   copying build/lib/pymlst/wg/commands/sequence.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,283   copying build/lib/pymlst/wg/commands/gene.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,284   copying build/lib/pymlst/wg/commands/msa.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,286   copying build/lib/pymlst/wg/commands/stats.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg/commands
2025-03-28T16:54:19,288   copying build/lib/pymlst/wg/extractors.py -> build/bdist.linux-armv7l/wheel/./pymlst/wg
2025-03-28T16:54:19,291   creating build/bdist.linux-armv7l/wheel/pymlst/pytyper
2025-03-28T16:54:19,292   copying build/lib/pymlst/pytyper/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper
2025-03-28T16:54:19,294   copying build/lib/pymlst/pytyper/model.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper
2025-03-28T16:54:19,295   copying build/lib/pymlst/pytyper/method.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper
2025-03-28T16:54:19,297   copying build/lib/pymlst/pytyper/core.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper
2025-03-28T16:54:19,300   copying build/lib/pymlst/pytyper/url.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper
2025-03-28T16:54:19,302   creating build/bdist.linux-armv7l/wheel/pymlst/pytyper/commands
2025-03-28T16:54:19,304   copying build/lib/pymlst/pytyper/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper/commands
2025-03-28T16:54:19,306   copying build/lib/pymlst/pytyper/commands/search.py -> build/bdist.linux-armv7l/wheel/./pymlst/pytyper/commands
2025-03-28T16:54:19,308   copying build/lib/pymlst/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst
2025-03-28T16:54:19,310   creating build/bdist.linux-armv7l/wheel/pymlst/common
2025-03-28T16:54:19,311   copying build/lib/pymlst/common/blat.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2025-03-28T16:54:19,313   copying build/lib/pymlst/common/utils.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2025-03-28T16:54:19,315   copying build/lib/pymlst/common/psl.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2025-03-28T16:54:19,317   copying build/lib/pymlst/common/web.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2025-03-28T16:54:19,320   copying build/lib/pymlst/common/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2025-03-28T16:54:19,321   copying build/lib/pymlst/common/kma.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2025-03-28T16:54:19,323   copying build/lib/pymlst/common/flag.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2025-03-28T16:54:19,325   copying build/lib/pymlst/common/mafft.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2025-03-28T16:54:19,327   copying build/lib/pymlst/common/exceptions.py -> build/bdist.linux-armv7l/wheel/./pymlst/common
2025-03-28T16:54:19,329   creating build/bdist.linux-armv7l/wheel/pymlst/common/commands
2025-03-28T16:54:19,330   copying build/lib/pymlst/common/commands/configure.py -> build/bdist.linux-armv7l/wheel/./pymlst/common/commands
2025-03-28T16:54:19,332   copying build/lib/pymlst/common/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/common/commands
2025-03-28T16:54:19,335   copying build/lib/pymlst/config.py -> build/bdist.linux-armv7l/wheel/./pymlst
2025-03-28T16:54:19,337   copying build/lib/pymlst/version.py -> build/bdist.linux-armv7l/wheel/./pymlst
2025-03-28T16:54:19,339   creating build/bdist.linux-armv7l/wheel/pymlst/cla
2025-03-28T16:54:19,341   copying build/lib/pymlst/cla/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla
2025-03-28T16:54:19,342   copying build/lib/pymlst/cla/model.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla
2025-03-28T16:54:19,344   copying build/lib/pymlst/cla/core.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla
2025-03-28T16:54:19,347   creating build/bdist.linux-armv7l/wheel/pymlst/cla/commands
2025-03-28T16:54:19,348   copying build/lib/pymlst/cla/commands/import.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2025-03-28T16:54:19,350   copying build/lib/pymlst/cla/commands/remove.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2025-03-28T16:54:19,352   copying build/lib/pymlst/cla/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2025-03-28T16:54:19,354   copying build/lib/pymlst/cla/commands/search.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2025-03-28T16:54:19,355   copying build/lib/pymlst/cla/commands/info.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2025-03-28T16:54:19,357   copying build/lib/pymlst/cla/commands/create.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2025-03-28T16:54:19,359   copying build/lib/pymlst/cla/commands/search2.py -> build/bdist.linux-armv7l/wheel/./pymlst/cla/commands
2025-03-28T16:54:19,362   creating build/bdist.linux-armv7l/wheel/pymlst/data
2025-03-28T16:54:19,363   creating build/bdist.linux-armv7l/wheel/pymlst/data/pytyper
2025-03-28T16:54:19,365   copying build/lib/pymlst/data/pytyper/clmt.fna -> build/bdist.linux-armv7l/wheel/./pymlst/data/pytyper
2025-03-28T16:54:19,367   copying build/lib/pymlst/data/pytyper/fimh.fna -> build/bdist.linux-armv7l/wheel/./pymlst/data/pytyper
2025-03-28T16:54:19,369   copying build/lib/pymlst/data/pytyper/spa.fna -> build/bdist.linux-armv7l/wheel/./pymlst/data/pytyper
2025-03-28T16:54:19,371   copying build/lib/pymlst/data/pytyper/clmt.txt -> build/bdist.linux-armv7l/wheel/./pymlst/data/pytyper
2025-03-28T16:54:19,373   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic
2025-03-28T16:54:19,375   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/wg
2025-03-28T16:54:19,376   copying build/lib/pymlst/data/alembic/wg/env.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/wg
2025-03-28T16:54:19,378   copying build/lib/pymlst/data/alembic/wg/script.py.mako -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/wg
2025-03-28T16:54:19,381   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/wg/versions
2025-03-28T16:54:19,382   copying build/lib/pymlst/data/alembic/wg/versions/a793f8f3fd83_add_database_infos.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/wg/versions
2025-03-28T16:54:19,384   copying build/lib/pymlst/data/alembic/wg/versions/52ae99cb5f33_initial.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/wg/versions
2025-03-28T16:54:19,386   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/pytyper
2025-03-28T16:54:19,387   copying build/lib/pymlst/data/alembic/pytyper/env.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/pytyper
2025-03-28T16:54:19,390   copying build/lib/pymlst/data/alembic/pytyper/script.py.mako -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/pytyper
2025-03-28T16:54:19,392   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/pytyper/versions
2025-03-28T16:54:19,393   copying build/lib/pymlst/data/alembic/pytyper/versions/1f96d027f4aa_initial.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/pytyper/versions
2025-03-28T16:54:19,396   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/cla
2025-03-28T16:54:19,397   copying build/lib/pymlst/data/alembic/cla/env.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/cla
2025-03-28T16:54:19,399   copying build/lib/pymlst/data/alembic/cla/script.py.mako -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/cla
2025-03-28T16:54:19,401   creating build/bdist.linux-armv7l/wheel/pymlst/data/alembic/cla/versions
2025-03-28T16:54:19,402   copying build/lib/pymlst/data/alembic/cla/versions/21efe503d07d_initial.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/cla/versions
2025-03-28T16:54:19,404   copying build/lib/pymlst/data/alembic/cla/versions/c0f871a99d96_add_database_infos.py -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic/cla/versions
2025-03-28T16:54:19,406   copying build/lib/pymlst/data/alembic/alembic.ini -> build/bdist.linux-armv7l/wheel/./pymlst/data/alembic
2025-03-28T16:54:19,407   running install_egg_info
2025-03-28T16:54:19,436   Copying PyMLST.egg-info to build/bdist.linux-armv7l/wheel/./PyMLST-2.2.1-py3.11.egg-info
2025-03-28T16:54:19,447   running install_scripts
2025-03-28T16:54:19,465   creating build/bdist.linux-armv7l/wheel/PyMLST-2.2.1.dist-info/WHEEL
2025-03-28T16:54:19,467   creating '/tmp/pip-wheel-xf3o7qxc/PyMLST-2.2.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-03-28T16:54:19,471   adding 'pymlst/__init__.py'
2025-03-28T16:54:19,472   adding 'pymlst/cmd.py'
2025-03-28T16:54:19,474   adding 'pymlst/config.py'
2025-03-28T16:54:19,475   adding 'pymlst/version.py'
2025-03-28T16:54:19,476   adding 'pymlst/cla/__init__.py'
2025-03-28T16:54:19,480   adding 'pymlst/cla/core.py'
2025-03-28T16:54:19,481   adding 'pymlst/cla/model.py'
2025-03-28T16:54:19,483   adding 'pymlst/cla/commands/__init__.py'
2025-03-28T16:54:19,484   adding 'pymlst/cla/commands/create.py'
2025-03-28T16:54:19,486   adding 'pymlst/cla/commands/import.py'
2025-03-28T16:54:19,487   adding 'pymlst/cla/commands/info.py'
2025-03-28T16:54:19,488   adding 'pymlst/cla/commands/remove.py'
2025-03-28T16:54:19,489   adding 'pymlst/cla/commands/search.py'
2025-03-28T16:54:19,491   adding 'pymlst/cla/commands/search2.py'
2025-03-28T16:54:19,492   adding 'pymlst/common/__init__.py'
2025-03-28T16:54:19,493   adding 'pymlst/common/blat.py'
2025-03-28T16:54:19,495   adding 'pymlst/common/exceptions.py'
2025-03-28T16:54:19,496   adding 'pymlst/common/flag.py'
2025-03-28T16:54:19,497   adding 'pymlst/common/kma.py'
2025-03-28T16:54:19,499   adding 'pymlst/common/mafft.py'
2025-03-28T16:54:19,500   adding 'pymlst/common/psl.py'
2025-03-28T16:54:19,502   adding 'pymlst/common/utils.py'
2025-03-28T16:54:19,505   adding 'pymlst/common/web.py'
2025-03-28T16:54:19,507   adding 'pymlst/common/commands/__init__.py'
2025-03-28T16:54:19,508   adding 'pymlst/common/commands/configure.py'
2025-03-28T16:54:19,511   adding 'pymlst/data/alembic/alembic.ini'
2025-03-28T16:54:19,513   adding 'pymlst/data/alembic/cla/env.py'
2025-03-28T16:54:19,515   adding 'pymlst/data/alembic/cla/script.py.mako'
2025-03-28T16:54:19,517   adding 'pymlst/data/alembic/cla/versions/21efe503d07d_initial.py'
2025-03-28T16:54:19,519   adding 'pymlst/data/alembic/cla/versions/c0f871a99d96_add_database_infos.py'
2025-03-28T16:54:19,521   adding 'pymlst/data/alembic/pytyper/env.py'
2025-03-28T16:54:19,523   adding 'pymlst/data/alembic/pytyper/script.py.mako'
2025-03-28T16:54:19,525   adding 'pymlst/data/alembic/pytyper/versions/1f96d027f4aa_initial.py'
2025-03-28T16:54:19,527   adding 'pymlst/data/alembic/wg/env.py'
2025-03-28T16:54:19,528   adding 'pymlst/data/alembic/wg/script.py.mako'
2025-03-28T16:54:19,531   adding 'pymlst/data/alembic/wg/versions/52ae99cb5f33_initial.py'
2025-03-28T16:54:19,532   adding 'pymlst/data/alembic/wg/versions/a793f8f3fd83_add_database_infos.py'
2025-03-28T16:54:19,536   adding 'pymlst/data/pytyper/clmt.fna'
2025-03-28T16:54:19,537   adding 'pymlst/data/pytyper/clmt.txt'
2025-03-28T16:54:19,538   adding 'pymlst/data/pytyper/fimh.fna'
2025-03-28T16:54:19,540   adding 'pymlst/data/pytyper/spa.fna'
2025-03-28T16:54:19,542   adding 'pymlst/pytyper/__init__.py'
2025-03-28T16:54:19,546   adding 'pymlst/pytyper/core.py'
2025-03-28T16:54:19,547   adding 'pymlst/pytyper/method.py'
2025-03-28T16:54:19,549   adding 'pymlst/pytyper/model.py'
2025-03-28T16:54:19,550   adding 'pymlst/pytyper/url.py'
2025-03-28T16:54:19,552   adding 'pymlst/pytyper/commands/__init__.py'
2025-03-28T16:54:19,554   adding 'pymlst/pytyper/commands/search.py'
2025-03-28T16:54:19,556   adding 'pymlst/wg/__init__.py'
2025-03-28T16:54:19,562   adding 'pymlst/wg/core.py'
2025-03-28T16:54:19,564   adding 'pymlst/wg/extractors.py'
2025-03-28T16:54:19,566   adding 'pymlst/wg/model.py'
2025-03-28T16:54:19,568   adding 'pymlst/wg/commands/__init__.py'
2025-03-28T16:54:19,569   adding 'pymlst/wg/commands/add.py'
2025-03-28T16:54:19,571   adding 'pymlst/wg/commands/add2.py'
2025-03-28T16:54:19,572   adding 'pymlst/wg/commands/create.py'
2025-03-28T16:54:19,574   adding 'pymlst/wg/commands/distance.py'
2025-03-28T16:54:19,575   adding 'pymlst/wg/commands/gene.py'
2025-03-28T16:54:19,577   adding 'pymlst/wg/commands/import.py'
2025-03-28T16:54:19,578   adding 'pymlst/wg/commands/mlst.py'
2025-03-28T16:54:19,580   adding 'pymlst/wg/commands/msa.py'
2025-03-28T16:54:19,581   adding 'pymlst/wg/commands/recombination.py'
2025-03-28T16:54:19,583   adding 'pymlst/wg/commands/remove.py'
2025-03-28T16:54:19,585   adding 'pymlst/wg/commands/sequence.py'
2025-03-28T16:54:19,586   adding 'pymlst/wg/commands/stats.py'
2025-03-28T16:54:19,588   adding 'pymlst/wg/commands/strain.py'
2025-03-28T16:54:19,589   adding 'pymlst/wg/commands/subgraph.py'
2025-03-28T16:54:19,590   adding 'PyMLST-2.2.1.dist-info/LICENSE'
2025-03-28T16:54:19,592   adding 'PyMLST-2.2.1.dist-info/METADATA'
2025-03-28T16:54:19,593   adding 'PyMLST-2.2.1.dist-info/WHEEL'
2025-03-28T16:54:19,594   adding 'PyMLST-2.2.1.dist-info/entry_points.txt'
2025-03-28T16:54:19,596   adding 'PyMLST-2.2.1.dist-info/top_level.txt'
2025-03-28T16:54:19,598   adding 'PyMLST-2.2.1.dist-info/RECORD'
2025-03-28T16:54:19,601   removing build/bdist.linux-armv7l/wheel
2025-03-28T16:54:19,739   Building wheel for pymlst (setup.py): finished with status 'done'
2025-03-28T16:54:19,742   Created wheel for pymlst: filename=PyMLST-2.2.1-py3-none-any.whl size=72524 sha256=bb4e9bee8716053e3cc3fff0551aec157b0b594e887ead0bad2b102dd5343f12
2025-03-28T16:54:19,743   Stored in directory: /tmp/pip-ephem-wheel-cache-zo4l1e8o/wheels/fe/cc/01/291c3b50f2b8b493915cb1d90e3c224bd7bf412d5dfdf242b8
2025-03-28T16:54:19,756 Successfully built pymlst
2025-03-28T16:54:19,761 Removed build tracker: '/tmp/pip-build-tracker-yjlzfow5'