2025-10-10T20:40:52,681 Created temporary directory: /tmp/pip-ephem-wheel-cache-c5l9z9p0
2025-10-10T20:40:52,683 Created temporary directory: /tmp/pip-build-tracker-nvdvdeo3
2025-10-10T20:40:52,683 Initialized build tracking at /tmp/pip-build-tracker-nvdvdeo3
2025-10-10T20:40:52,684 Created build tracker: /tmp/pip-build-tracker-nvdvdeo3
2025-10-10T20:40:52,684 Entered build tracker: /tmp/pip-build-tracker-nvdvdeo3
2025-10-10T20:40:52,685 Created temporary directory: /tmp/pip-wheel-y95ja1rt
2025-10-10T20:40:52,688 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2025-10-10T20:40:52,690 Created temporary directory: /tmp/pip-ephem-wheel-cache-faoo06ll
2025-10-10T20:40:52,712 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-10T20:40:52,716 2 location(s) to search for versions of micrograph-cleaner-em:
2025-10-10T20:40:52,716 * https://pypi.org/simple/micrograph-cleaner-em/
2025-10-10T20:40:52,716 * https://www.piwheels.org/simple/micrograph-cleaner-em/
2025-10-10T20:40:52,717 Fetching project page and analyzing links: https://pypi.org/simple/micrograph-cleaner-em/
2025-10-10T20:40:52,718 Getting page https://pypi.org/simple/micrograph-cleaner-em/
2025-10-10T20:40:52,719 Found index url https://pypi.org/simple
2025-10-10T20:40:52,931 Fetched page https://pypi.org/simple/micrograph-cleaner-em/ as application/vnd.pypi.simple.v1+json
2025-10-10T20:40:52,934   Found link https://files.pythonhosted.org/packages/6e/c6/98e5eddb2b8a8d9d2fccc1cb0580b96a8aeed2c27d7e3f45f505ecf65afb/micrograph_cleaner_em-0.1.tar.gz (from https://pypi.org/simple/micrograph-cleaner-em/), version: 0.1
2025-10-10T20:40:52,935   Found link https://files.pythonhosted.org/packages/94/d7/3e3063f5dc4cb8ae72f6697e6310d1eca24ad95cb0864d77094654b316b2/micrograph_cleaner_em-0.2.tar.gz (from https://pypi.org/simple/micrograph-cleaner-em/), version: 0.2
2025-10-10T20:40:52,935   Found link https://files.pythonhosted.org/packages/5c/09/cc3a69a2409eb3761d7fd54f571f17215fae64eba9a00c624bd76674a181/micrograph_cleaner_em-0.22.tar.gz (from https://pypi.org/simple/micrograph-cleaner-em/), version: 0.22
2025-10-10T20:40:52,936   Found link https://files.pythonhosted.org/packages/b7/2c/f8d1ea83128c98e7014c8d43a871adc0f28db46630afff003d6082e21991/micrograph_cleaner_em-0.26.tar.gz (from https://pypi.org/simple/micrograph-cleaner-em/), version: 0.26
2025-10-10T20:40:52,937   Found link https://files.pythonhosted.org/packages/5e/08/906c1b8eb912a7aef147ac50dd7bb88ebd97d9c047cc67b4c7638ed4f4db/micrograph_cleaner_em-0.31.tar.gz (from https://pypi.org/simple/micrograph-cleaner-em/), version: 0.31
2025-10-10T20:40:52,938   Found link https://files.pythonhosted.org/packages/20/9d/f3ea6968adf72362e9cad0fdd54b365ddb51715e9c137eac56c1da988a14/micrograph_cleaner_em-0.32.tar.gz (from https://pypi.org/simple/micrograph-cleaner-em/), version: 0.32
2025-10-10T20:40:52,939   Found link https://files.pythonhosted.org/packages/cd/e5/dd6497aa3fd62bd3d812bfa6edfc9f9af1964cc7330bdbdf1469422f75ce/micrograph_cleaner_em-0.33.tar.gz (from https://pypi.org/simple/micrograph-cleaner-em/), version: 0.33
2025-10-10T20:40:52,939   Found link https://files.pythonhosted.org/packages/84/79/806179a49a430490d4ac34d023caad0c4c23d9dec22c845347a9855f4100/micrograph_cleaner_em-0.35.tar.gz (from https://pypi.org/simple/micrograph-cleaner-em/), version: 0.35
2025-10-10T20:40:52,940   Found link https://files.pythonhosted.org/packages/b5/39/1e4a116dab73230a24b0203df4a4ff90e52f624f6c4d17a882673e9fc028/micrograph_cleaner_em-0.36.tar.gz (from https://pypi.org/simple/micrograph-cleaner-em/), version: 0.36
2025-10-10T20:40:52,941   Found link https://files.pythonhosted.org/packages/0d/32/6d7a003b769afc0752f947f5cc593ed06abe806c3ded222376cccc25e1db/micrograph_cleaner_em-0.37.tar.gz (from https://pypi.org/simple/micrograph-cleaner-em/), version: 0.37
2025-10-10T20:40:52,942   Skipping link: No binaries permitted for micrograph-cleaner-em: https://files.pythonhosted.org/packages/b6/ab/1f2be5e38fa10cddf9441e4dfe2e694d671b7242b25e5b75c522f7813e2a/micrograph_cleaner_em-1.0.2-py3-none-any.whl (from https://pypi.org/simple/micrograph-cleaner-em/) (requires-python:>=3.9)
2025-10-10T20:40:52,943   Found link https://files.pythonhosted.org/packages/25/32/c34044dd90be429b9ee743cb058ba0efad9079f13a9eee72f8a762b637d4/micrograph_cleaner_em-1.0.2.tar.gz (from https://pypi.org/simple/micrograph-cleaner-em/) (requires-python:>=3.9), version: 1.0.2
2025-10-10T20:40:52,944 Fetching project page and analyzing links: https://www.piwheels.org/simple/micrograph-cleaner-em/
2025-10-10T20:40:52,945 Getting page https://www.piwheels.org/simple/micrograph-cleaner-em/
2025-10-10T20:40:52,946 Found index url https://www.piwheels.org/simple
2025-10-10T20:40:53,098 Fetched page https://www.piwheels.org/simple/micrograph-cleaner-em/ as text/html
2025-10-10T20:40:53,100   Skipping link: No binaries permitted for micrograph-cleaner-em: https://archive1.piwheels.org/simple/micrograph-cleaner-em/micrograph_cleaner_em-0.37-py3-none-any.whl#sha256=f8760b2be3fcb1c810b563fe4c5a9779de6a9559fecef4b3466f37cddb93c1ae (from https://www.piwheels.org/simple/micrograph-cleaner-em/)
2025-10-10T20:40:53,101   Skipping link: No binaries permitted for micrograph-cleaner-em: https://archive1.piwheels.org/simple/micrograph-cleaner-em/micrograph_cleaner_em-0.36-py3-none-any.whl#sha256=2c0420d06129affe75246a275a11f2405cde9e75114be7c30b44b0feaa0f94e1 (from https://www.piwheels.org/simple/micrograph-cleaner-em/)
2025-10-10T20:40:53,101   Skipping link: No binaries permitted for micrograph-cleaner-em: https://archive1.piwheels.org/simple/micrograph-cleaner-em/micrograph_cleaner_em-0.35-py3-none-any.whl#sha256=471cd55c4ac74d119bede06860dc93243674ae88f5307bbd1286fd57fd625151 (from https://www.piwheels.org/simple/micrograph-cleaner-em/)
2025-10-10T20:40:53,102   Skipping link: No binaries permitted for micrograph-cleaner-em: https://archive1.piwheels.org/simple/micrograph-cleaner-em/micrograph_cleaner_em-0.33-py3-none-any.whl#sha256=2cc1187975f0c40ff6d22f9aa3b04f3148b8b7eadc9a2227813295365635dbd2 (from https://www.piwheels.org/simple/micrograph-cleaner-em/)
2025-10-10T20:40:53,103   Skipping link: No binaries permitted for micrograph-cleaner-em: https://archive1.piwheels.org/simple/micrograph-cleaner-em/micrograph_cleaner_em-0.32-py3-none-any.whl#sha256=b2969c69d0c454ae96dcf62f2c2b78f4585503f6474df7456c16463dcbb8bfa2 (from https://www.piwheels.org/simple/micrograph-cleaner-em/)
2025-10-10T20:40:53,103   Skipping link: No binaries permitted for micrograph-cleaner-em: https://archive1.piwheels.org/simple/micrograph-cleaner-em/micrograph_cleaner_em-0.31-py3-none-any.whl#sha256=9232a9e4fc327665ef6b90549415b091b963cece27cbde239842c18f66c918da (from https://www.piwheels.org/simple/micrograph-cleaner-em/)
2025-10-10T20:40:53,104 Skipping link: not a file: https://www.piwheels.org/simple/micrograph-cleaner-em/
2025-10-10T20:40:53,105 Skipping link: not a file: https://pypi.org/simple/micrograph-cleaner-em/
2025-10-10T20:40:53,125 Given no hashes to check 1 links for project 'micrograph-cleaner-em': discarding no candidates
2025-10-10T20:40:53,143 Collecting micrograph-cleaner-em==1.0.2
2025-10-10T20:40:53,145   Created temporary directory: /tmp/pip-unpack-c0eysqtj
2025-10-10T20:40:53,374   Downloading micrograph_cleaner_em-1.0.2.tar.gz (5.2 MB)
2025-10-10T20:40:54,428   Added micrograph-cleaner-em==1.0.2 from https://files.pythonhosted.org/packages/25/32/c34044dd90be429b9ee743cb058ba0efad9079f13a9eee72f8a762b637d4/micrograph_cleaner_em-1.0.2.tar.gz to build tracker '/tmp/pip-build-tracker-nvdvdeo3'
2025-10-10T20:40:54,429   Running setup.py (path:/tmp/pip-wheel-y95ja1rt/micrograph-cleaner-em_c829bb6cbacb4c4ab7eda44c3a2138d3/setup.py) egg_info for package micrograph-cleaner-em
2025-10-10T20:40:54,430   Created temporary directory: /tmp/pip-pip-egg-info-nlzh0mjb
2025-10-10T20:40:54,431   Preparing metadata (setup.py): started
2025-10-10T20:40:54,432   Running command python setup.py egg_info
2025-10-10T20:40:54,982   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2025-10-10T20:40:54,982   !!

2025-10-10T20:40:54,984           ********************************************************************************
2025-10-10T20:40:54,984           Requirements should be satisfied by a PEP 517 installer.
2025-10-10T20:40:54,985           If you are using pip, you can try `pip install --use-pep517`.

2025-10-10T20:40:54,986           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-10-10T20:40:54,987           or your builds will no longer be supported.
2025-10-10T20:40:54,987           ********************************************************************************

2025-10-10T20:40:54,989   !!
2025-10-10T20:40:54,989     dist.fetch_build_eggs(dist.setup_requires)
2025-10-10T20:40:58,723   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-10T20:40:58,724   !!

2025-10-10T20:40:58,725           ********************************************************************************
2025-10-10T20:40:58,725           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-10T20:40:58,726           License :: OSI Approved :: MIT License

2025-10-10T20:40:58,727           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-10T20:40:58,728           ********************************************************************************

2025-10-10T20:40:58,729   !!
2025-10-10T20:40:58,729     self._finalize_license_expression()
2025-10-10T20:40:58,756   running egg_info
2025-10-10T20:40:58,786   creating /tmp/pip-pip-egg-info-nlzh0mjb/micrograph_cleaner_em.egg-info
2025-10-10T20:40:58,787   writing /tmp/pip-pip-egg-info-nlzh0mjb/micrograph_cleaner_em.egg-info/PKG-INFO
2025-10-10T20:40:58,791   writing dependency_links to /tmp/pip-pip-egg-info-nlzh0mjb/micrograph_cleaner_em.egg-info/dependency_links.txt
2025-10-10T20:40:58,792   writing entry points to /tmp/pip-pip-egg-info-nlzh0mjb/micrograph_cleaner_em.egg-info/entry_points.txt
2025-10-10T20:40:58,794   writing requirements to /tmp/pip-pip-egg-info-nlzh0mjb/micrograph_cleaner_em.egg-info/requires.txt
2025-10-10T20:40:58,795   writing top-level names to /tmp/pip-pip-egg-info-nlzh0mjb/micrograph_cleaner_em.egg-info/top_level.txt
2025-10-10T20:40:58,796   writing manifest file '/tmp/pip-pip-egg-info-nlzh0mjb/micrograph_cleaner_em.egg-info/SOURCES.txt'
2025-10-10T20:40:58,972   listing git files failed - pretending there aren't any
2025-10-10T20:40:58,988   reading manifest file '/tmp/pip-pip-egg-info-nlzh0mjb/micrograph_cleaner_em.egg-info/SOURCES.txt'
2025-10-10T20:40:58,990   reading manifest template 'MANIFEST.in'
2025-10-10T20:40:58,997   adding license file 'LICENSE'
2025-10-10T20:40:59,000   writing manifest file '/tmp/pip-pip-egg-info-nlzh0mjb/micrograph_cleaner_em.egg-info/SOURCES.txt'
2025-10-10T20:40:59,117   Preparing metadata (setup.py): finished with status 'done'
2025-10-10T20:40:59,122   Source in /tmp/pip-wheel-y95ja1rt/micrograph-cleaner-em_c829bb6cbacb4c4ab7eda44c3a2138d3 has version 1.0.2, which satisfies requirement micrograph-cleaner-em==1.0.2 from https://files.pythonhosted.org/packages/25/32/c34044dd90be429b9ee743cb058ba0efad9079f13a9eee72f8a762b637d4/micrograph_cleaner_em-1.0.2.tar.gz
2025-10-10T20:40:59,123   Removed micrograph-cleaner-em==1.0.2 from https://files.pythonhosted.org/packages/25/32/c34044dd90be429b9ee743cb058ba0efad9079f13a9eee72f8a762b637d4/micrograph_cleaner_em-1.0.2.tar.gz from build tracker '/tmp/pip-build-tracker-nvdvdeo3'
2025-10-10T20:40:59,130 Created temporary directory: /tmp/pip-unpack-klpr41ky
2025-10-10T20:40:59,130 Building wheels for collected packages: micrograph-cleaner-em
2025-10-10T20:40:59,135   Created temporary directory: /tmp/pip-wheel-2owvp8qm
2025-10-10T20:40:59,135   Building wheel for micrograph-cleaner-em (setup.py): started
2025-10-10T20:40:59,137   Destination directory: /tmp/pip-wheel-2owvp8qm
2025-10-10T20:40:59,137   Running command python setup.py bdist_wheel
2025-10-10T20:40:59,662   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2025-10-10T20:40:59,662   !!

2025-10-10T20:40:59,663           ********************************************************************************
2025-10-10T20:40:59,664           Requirements should be satisfied by a PEP 517 installer.
2025-10-10T20:40:59,664           If you are using pip, you can try `pip install --use-pep517`.

2025-10-10T20:40:59,665           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-10-10T20:40:59,665           or your builds will no longer be supported.
2025-10-10T20:40:59,666           ********************************************************************************

2025-10-10T20:40:59,667   !!
2025-10-10T20:40:59,667     dist.fetch_build_eggs(dist.setup_requires)
2025-10-10T20:41:00,284   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-10T20:41:00,284   !!

2025-10-10T20:41:00,285           ********************************************************************************
2025-10-10T20:41:00,286           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-10T20:41:00,287           License :: OSI Approved :: MIT License

2025-10-10T20:41:00,288           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-10T20:41:00,289           ********************************************************************************

2025-10-10T20:41:00,290   !!
2025-10-10T20:41:00,290     self._finalize_license_expression()
2025-10-10T20:41:00,291   running bdist_wheel
2025-10-10T20:41:00,431   running build
2025-10-10T20:41:00,432   running build_py
2025-10-10T20:41:00,464   creating build/lib/micrograph_cleaner_em
2025-10-10T20:41:00,466   copying micrograph_cleaner_em/cleanOneMic.py -> build/lib/micrograph_cleaner_em
2025-10-10T20:41:00,468   copying micrograph_cleaner_em/predictMask.py -> build/lib/micrograph_cleaner_em
2025-10-10T20:41:00,471   copying micrograph_cleaner_em/utils.py -> build/lib/micrograph_cleaner_em
2025-10-10T20:41:00,473   copying micrograph_cleaner_em/cleanMics.py -> build/lib/micrograph_cleaner_em
2025-10-10T20:41:00,475   copying micrograph_cleaner_em/filesManager.py -> build/lib/micrograph_cleaner_em
2025-10-10T20:41:00,478   copying micrograph_cleaner_em/__init__.py -> build/lib/micrograph_cleaner_em
2025-10-10T20:41:00,479   copying micrograph_cleaner_em/config.py -> build/lib/micrograph_cleaner_em
2025-10-10T20:41:00,481   copying micrograph_cleaner_em/filterCoords.py -> build/lib/micrograph_cleaner_em
2025-10-10T20:41:00,483   copying micrograph_cleaner_em/cmdParser.py -> build/lib/micrograph_cleaner_em
2025-10-10T20:41:00,485   copying micrograph_cleaner_em/preprocessMic.py -> build/lib/micrograph_cleaner_em
2025-10-10T20:41:00,488   creating build/lib/micrograph_cleaner_em/tests
2025-10-10T20:41:00,489   copying micrograph_cleaner_em/tests/test_maskPredictor.py -> build/lib/micrograph_cleaner_em/tests
2025-10-10T20:41:00,491   copying micrograph_cleaner_em/tests/testConfig.py -> build/lib/micrograph_cleaner_em/tests
2025-10-10T20:41:00,493   copying micrograph_cleaner_em/tests/__init__.py -> build/lib/micrograph_cleaner_em/tests
2025-10-10T20:41:00,494   copying micrograph_cleaner_em/tests/test_commanLineFun.py -> build/lib/micrograph_cleaner_em/tests
2025-10-10T20:41:00,496   copying micrograph_cleaner_em/tests/test_getMatchingFiles.py -> build/lib/micrograph_cleaner_em/tests
2025-10-10T20:41:00,497   running egg_info
2025-10-10T20:41:00,527   writing micrograph_cleaner_em.egg-info/PKG-INFO
2025-10-10T20:41:00,531   writing dependency_links to micrograph_cleaner_em.egg-info/dependency_links.txt
2025-10-10T20:41:00,532   writing entry points to micrograph_cleaner_em.egg-info/entry_points.txt
2025-10-10T20:41:00,534   writing requirements to micrograph_cleaner_em.egg-info/requires.txt
2025-10-10T20:41:00,535   writing top-level names to micrograph_cleaner_em.egg-info/top_level.txt
2025-10-10T20:41:00,635   listing git files failed - pretending there aren't any
2025-10-10T20:41:00,639   reading manifest file 'micrograph_cleaner_em.egg-info/SOURCES.txt'
2025-10-10T20:41:00,643   reading manifest template 'MANIFEST.in'
2025-10-10T20:41:00,649   adding license file 'LICENSE'
2025-10-10T20:41:00,653   writing manifest file 'micrograph_cleaner_em.egg-info/SOURCES.txt'
2025-10-10T20:41:00,656   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'micrograph_cleaner_em.tests.data.inCoords.relion' is absent from the `packages` configuration.
2025-10-10T20:41:00,657   !!

2025-10-10T20:41:00,658           ********************************************************************************
2025-10-10T20:41:00,658           ############################
2025-10-10T20:41:00,659           # Package would be ignored #
2025-10-10T20:41:00,659           ############################
2025-10-10T20:41:00,660           Python recognizes 'micrograph_cleaner_em.tests.data.inCoords.relion' as an importable package[^1],
2025-10-10T20:41:00,660           but it is absent from setuptools' `packages` configuration.

2025-10-10T20:41:00,661           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-10T20:41:00,662           package, please make sure that 'micrograph_cleaner_em.tests.data.inCoords.relion' is explicitly added
2025-10-10T20:41:00,662           to the `packages` configuration field.

2025-10-10T20:41:00,663           Alternatively, you can also rely on setuptools' discovery methods
2025-10-10T20:41:00,664           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-10T20:41:00,664           instead of `find_packages(...)`/`find:`).

2025-10-10T20:41:00,665           You can read more about "package discovery" on setuptools documentation page:

2025-10-10T20:41:00,667           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-10T20:41:00,668           If you don't want 'micrograph_cleaner_em.tests.data.inCoords.relion' to be distributed and are
2025-10-10T20:41:00,668           already explicitly excluding 'micrograph_cleaner_em.tests.data.inCoords.relion' via
2025-10-10T20:41:00,669           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-10T20:41:00,669           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-10T20:41:00,670           combination with a more fine grained `package-data` configuration.

2025-10-10T20:41:00,671           You can read more about "package data files" on setuptools documentation page:

2025-10-10T20:41:00,672           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-10T20:41:00,674           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-10T20:41:00,675                 even if it does not contain any `.py` files.
2025-10-10T20:41:00,675                 On the other hand, currently there is no concept of package data
2025-10-10T20:41:00,676                 directory, all directories are treated like packages.
2025-10-10T20:41:00,676           ********************************************************************************

2025-10-10T20:41:00,677   !!
2025-10-10T20:41:00,678     check.warn(importable)
2025-10-10T20:41:00,679   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'micrograph_cleaner_em.tests.data.masks' is absent from the `packages` configuration.
2025-10-10T20:41:00,679   !!

2025-10-10T20:41:00,681           ********************************************************************************
2025-10-10T20:41:00,681           ############################
2025-10-10T20:41:00,689           # Package would be ignored #
2025-10-10T20:41:00,704           ############################
2025-10-10T20:41:00,715           Python recognizes 'micrograph_cleaner_em.tests.data.masks' as an importable package[^1],
2025-10-10T20:41:00,717           but it is absent from setuptools' `packages` configuration.

2025-10-10T20:41:00,717           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-10T20:41:00,718           package, please make sure that 'micrograph_cleaner_em.tests.data.masks' is explicitly added
2025-10-10T20:41:00,723           to the `packages` configuration field.

2025-10-10T20:41:00,743           Alternatively, you can also rely on setuptools' discovery methods
2025-10-10T20:41:00,743           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-10T20:41:00,744           instead of `find_packages(...)`/`find:`).

2025-10-10T20:41:00,745           You can read more about "package discovery" on setuptools documentation page:

2025-10-10T20:41:00,746           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-10T20:41:00,747           If you don't want 'micrograph_cleaner_em.tests.data.masks' to be distributed and are
2025-10-10T20:41:00,747           already explicitly excluding 'micrograph_cleaner_em.tests.data.masks' via
2025-10-10T20:41:00,748           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-10T20:41:00,748           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-10T20:41:00,749           combination with a more fine grained `package-data` configuration.

2025-10-10T20:41:00,750           You can read more about "package data files" on setuptools documentation page:

2025-10-10T20:41:00,751           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-10T20:41:00,753           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-10T20:41:00,754                 even if it does not contain any `.py` files.
2025-10-10T20:41:00,755                 On the other hand, currently there is no concept of package data
2025-10-10T20:41:00,755                 directory, all directories are treated like packages.
2025-10-10T20:41:00,756           ********************************************************************************

2025-10-10T20:41:00,757   !!
2025-10-10T20:41:00,758     check.warn(importable)
2025-10-10T20:41:00,758   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'micrograph_cleaner_em.tests.data.mics' is absent from the `packages` configuration.
2025-10-10T20:41:00,759   !!

2025-10-10T20:41:00,760           ********************************************************************************
2025-10-10T20:41:00,761           ############################
2025-10-10T20:41:00,761           # Package would be ignored #
2025-10-10T20:41:00,762           ############################
2025-10-10T20:41:00,763           Python recognizes 'micrograph_cleaner_em.tests.data.mics' as an importable package[^1],
2025-10-10T20:41:00,763           but it is absent from setuptools' `packages` configuration.

2025-10-10T20:41:00,766           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-10T20:41:00,767           package, please make sure that 'micrograph_cleaner_em.tests.data.mics' is explicitly added
2025-10-10T20:41:00,770           to the `packages` configuration field.

2025-10-10T20:41:00,775           Alternatively, you can also rely on setuptools' discovery methods
2025-10-10T20:41:00,777           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-10T20:41:00,778           instead of `find_packages(...)`/`find:`).

2025-10-10T20:41:00,783           You can read more about "package discovery" on setuptools documentation page:

2025-10-10T20:41:00,799           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-10T20:41:00,801           If you don't want 'micrograph_cleaner_em.tests.data.mics' to be distributed and are
2025-10-10T20:41:00,802           already explicitly excluding 'micrograph_cleaner_em.tests.data.mics' via
2025-10-10T20:41:00,802           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-10T20:41:00,803           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-10T20:41:00,803           combination with a more fine grained `package-data` configuration.

2025-10-10T20:41:00,805           You can read more about "package data files" on setuptools documentation page:

2025-10-10T20:41:00,805           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-10T20:41:00,809           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-10T20:41:00,809                 even if it does not contain any `.py` files.
2025-10-10T20:41:00,809                 On the other hand, currently there is no concept of package data
2025-10-10T20:41:00,810                 directory, all directories are treated like packages.
2025-10-10T20:41:00,810           ********************************************************************************

2025-10-10T20:41:00,811   !!
2025-10-10T20:41:00,812     check.warn(importable)
2025-10-10T20:41:00,812   creating build/lib/micrograph_cleaner_em/tests/data/inCoords/relion
2025-10-10T20:41:00,813   copying micrograph_cleaner_em/tests/data/inCoords/relion/Ucsf_stack_1142_DW_autopick.star -> build/lib/micrograph_cleaner_em/tests/data/inCoords/relion
2025-10-10T20:41:00,813   creating build/lib/micrograph_cleaner_em/tests/data/masks
2025-10-10T20:41:00,814   copying micrograph_cleaner_em/tests/data/masks/Ucsf_stack_1142_DW.mrc -> build/lib/micrograph_cleaner_em/tests/data/masks
2025-10-10T20:41:00,814   creating build/lib/micrograph_cleaner_em/tests/data/mics
2025-10-10T20:41:00,815   copying micrograph_cleaner_em/tests/data/mics/Ucsf_stack_1142_DW.mrc -> build/lib/micrograph_cleaner_em/tests/data/mics
2025-10-10T20:41:00,841   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-10-10T20:41:00,842   !!

2025-10-10T20:41:00,843           ********************************************************************************
2025-10-10T20:41:00,844           Please avoid running ``setup.py`` directly.
2025-10-10T20:41:00,844           Instead, use pypa/build, pypa/installer or other
2025-10-10T20:41:00,845           standards-based tools.

2025-10-10T20:41:00,846           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-10-10T20:41:00,847           or your builds will no longer be supported.

2025-10-10T20:41:00,848           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-10-10T20:41:00,848           ********************************************************************************

2025-10-10T20:41:00,849   !!
2025-10-10T20:41:00,850     self.initialize_options()
2025-10-10T20:41:00,876   installing to build/bdist.linux-armv7l/wheel
2025-10-10T20:41:00,877   running install
2025-10-10T20:41:00,902   running install_lib
2025-10-10T20:41:00,933   creating build/bdist.linux-armv7l/wheel
2025-10-10T20:41:00,935   creating build/bdist.linux-armv7l/wheel/micrograph_cleaner_em
2025-10-10T20:41:00,937   copying build/lib/micrograph_cleaner_em/cleanOneMic.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em
2025-10-10T20:41:00,939   copying build/lib/micrograph_cleaner_em/predictMask.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em
2025-10-10T20:41:00,942   copying build/lib/micrograph_cleaner_em/utils.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em
2025-10-10T20:41:00,944   copying build/lib/micrograph_cleaner_em/cleanMics.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em
2025-10-10T20:41:00,947   copying build/lib/micrograph_cleaner_em/filesManager.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em
2025-10-10T20:41:00,949   copying build/lib/micrograph_cleaner_em/__init__.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em
2025-10-10T20:41:00,951   copying build/lib/micrograph_cleaner_em/config.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em
2025-10-10T20:41:00,954   creating build/bdist.linux-armv7l/wheel/micrograph_cleaner_em/tests
2025-10-10T20:41:00,955   copying build/lib/micrograph_cleaner_em/tests/test_maskPredictor.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em/tests
2025-10-10T20:41:00,957   copying build/lib/micrograph_cleaner_em/tests/testConfig.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em/tests
2025-10-10T20:41:00,959   copying build/lib/micrograph_cleaner_em/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em/tests
2025-10-10T20:41:00,961   copying build/lib/micrograph_cleaner_em/tests/test_commanLineFun.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em/tests
2025-10-10T20:41:00,963   creating build/bdist.linux-armv7l/wheel/micrograph_cleaner_em/tests/data
2025-10-10T20:41:00,965   creating build/bdist.linux-armv7l/wheel/micrograph_cleaner_em/tests/data/masks
2025-10-10T20:41:00,966   copying build/lib/micrograph_cleaner_em/tests/data/masks/Ucsf_stack_1142_DW.mrc -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em/tests/data/masks
2025-10-10T20:41:01,023   creating build/bdist.linux-armv7l/wheel/micrograph_cleaner_em/tests/data/mics
2025-10-10T20:41:01,024   copying build/lib/micrograph_cleaner_em/tests/data/mics/Ucsf_stack_1142_DW.mrc -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em/tests/data/mics
2025-10-10T20:41:01,081   creating build/bdist.linux-armv7l/wheel/micrograph_cleaner_em/tests/data/inCoords
2025-10-10T20:41:01,082   creating build/bdist.linux-armv7l/wheel/micrograph_cleaner_em/tests/data/inCoords/relion
2025-10-10T20:41:01,083   copying build/lib/micrograph_cleaner_em/tests/data/inCoords/relion/Ucsf_stack_1142_DW_autopick.star -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em/tests/data/inCoords/relion
2025-10-10T20:41:01,085   copying build/lib/micrograph_cleaner_em/tests/test_getMatchingFiles.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em/tests
2025-10-10T20:41:01,087   copying build/lib/micrograph_cleaner_em/filterCoords.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em
2025-10-10T20:41:01,089   copying build/lib/micrograph_cleaner_em/cmdParser.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em
2025-10-10T20:41:01,091   copying build/lib/micrograph_cleaner_em/preprocessMic.py -> build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em
2025-10-10T20:41:01,093   running install_egg_info
2025-10-10T20:41:01,124   Copying micrograph_cleaner_em.egg-info to build/bdist.linux-armv7l/wheel/./micrograph_cleaner_em-1.0.2-py3.11.egg-info
2025-10-10T20:41:01,135   running install_scripts
2025-10-10T20:41:01,149   creating build/bdist.linux-armv7l/wheel/micrograph_cleaner_em-1.0.2.dist-info/WHEEL
2025-10-10T20:41:01,152   creating '/tmp/pip-wheel-2owvp8qm/micrograph_cleaner_em-1.0.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-10-10T20:41:01,154   adding 'micrograph_cleaner_em/__init__.py'
2025-10-10T20:41:01,155   adding 'micrograph_cleaner_em/cleanMics.py'
2025-10-10T20:41:01,157   adding 'micrograph_cleaner_em/cleanOneMic.py'
2025-10-10T20:41:01,159   adding 'micrograph_cleaner_em/cmdParser.py'
2025-10-10T20:41:01,160   adding 'micrograph_cleaner_em/config.py'
2025-10-10T20:41:01,162   adding 'micrograph_cleaner_em/filesManager.py'
2025-10-10T20:41:01,164   adding 'micrograph_cleaner_em/filterCoords.py'
2025-10-10T20:41:01,166   adding 'micrograph_cleaner_em/predictMask.py'
2025-10-10T20:41:01,167   adding 'micrograph_cleaner_em/preprocessMic.py'
2025-10-10T20:41:01,169   adding 'micrograph_cleaner_em/utils.py'
2025-10-10T20:41:01,170   adding 'micrograph_cleaner_em/tests/__init__.py'
2025-10-10T20:41:01,172   adding 'micrograph_cleaner_em/tests/testConfig.py'
2025-10-10T20:41:01,173   adding 'micrograph_cleaner_em/tests/test_commanLineFun.py'
2025-10-10T20:41:01,174   adding 'micrograph_cleaner_em/tests/test_getMatchingFiles.py'
2025-10-10T20:41:01,175   adding 'micrograph_cleaner_em/tests/test_maskPredictor.py'
2025-10-10T20:41:01,178   adding 'micrograph_cleaner_em/tests/data/inCoords/relion/Ucsf_stack_1142_DW_autopick.star'
2025-10-10T20:41:01,774   adding 'micrograph_cleaner_em/tests/data/masks/Ucsf_stack_1142_DW.mrc'
2025-10-10T20:41:03,589   adding 'micrograph_cleaner_em/tests/data/mics/Ucsf_stack_1142_DW.mrc'
2025-10-10T20:41:03,614   adding 'micrograph_cleaner_em-1.0.2.dist-info/licenses/LICENSE'
2025-10-10T20:41:03,616   adding 'micrograph_cleaner_em-1.0.2.dist-info/METADATA'
2025-10-10T20:41:03,617   adding 'micrograph_cleaner_em-1.0.2.dist-info/WHEEL'
2025-10-10T20:41:03,618   adding 'micrograph_cleaner_em-1.0.2.dist-info/entry_points.txt'
2025-10-10T20:41:03,619   adding 'micrograph_cleaner_em-1.0.2.dist-info/top_level.txt'
2025-10-10T20:41:03,619   adding 'micrograph_cleaner_em-1.0.2.dist-info/RECORD'
2025-10-10T20:41:03,681   removing build/bdist.linux-armv7l/wheel
2025-10-10T20:41:03,808   Building wheel for micrograph-cleaner-em (setup.py): finished with status 'done'
2025-10-10T20:41:03,862   Created wheel for micrograph-cleaner-em: filename=micrograph_cleaner_em-1.0.2-py3-none-any.whl size=5243549 sha256=cd432436178e37c3054cbf0ac1a8294f352821ad10ff7c2ab650cb97f7419f58
2025-10-10T20:41:03,864   Stored in directory: /tmp/pip-ephem-wheel-cache-faoo06ll/wheels/35/85/4d/233a4fa4a7a19d0af96531dfd8dbbf7e1ee3785d235ec55319
2025-10-10T20:41:03,877 Successfully built micrograph-cleaner-em
2025-10-10T20:41:04,012 Removed build tracker: '/tmp/pip-build-tracker-nvdvdeo3'