2025-10-13T09:37:22,729 Created temporary directory: /tmp/pip-ephem-wheel-cache-op45k85o
2025-10-13T09:37:22,731 Created temporary directory: /tmp/pip-build-tracker-1ja36c9s
2025-10-13T09:37:22,731 Initialized build tracking at /tmp/pip-build-tracker-1ja36c9s
2025-10-13T09:37:22,732 Created build tracker: /tmp/pip-build-tracker-1ja36c9s
2025-10-13T09:37:22,732 Entered build tracker: /tmp/pip-build-tracker-1ja36c9s
2025-10-13T09:37:22,733 Created temporary directory: /tmp/pip-wheel-4l8tanxr
2025-10-13T09:37:22,736 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
2025-10-13T09:37:22,738 Created temporary directory: /tmp/pip-ephem-wheel-cache-konnrz3m
2025-10-13T09:37:22,760 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-13T09:37:22,764 2 location(s) to search for versions of pichemist:
2025-10-13T09:37:22,764 * https://pypi.org/simple/pichemist/
2025-10-13T09:37:22,764 * https://www.piwheels.org/simple/pichemist/
2025-10-13T09:37:22,765 Fetching project page and analyzing links: https://pypi.org/simple/pichemist/
2025-10-13T09:37:22,765 Getting page https://pypi.org/simple/pichemist/
2025-10-13T09:37:22,767 Found index url https://pypi.org/simple
2025-10-13T09:37:22,974 Fetched page https://pypi.org/simple/pichemist/ as application/vnd.pypi.simple.v1+json
2025-10-13T09:37:22,976   Skipping link: No binaries permitted for pichemist: https://files.pythonhosted.org/packages/87/1a/bb171094da5c6a6829a2043fc67059297628311a144d79b7aa7dc156d8fd/pichemist-0.1.0-py3-none-any.whl (from https://pypi.org/simple/pichemist/)
2025-10-13T09:37:22,977   Found link https://files.pythonhosted.org/packages/0d/d8/1621751aa5081e2b1fa62f4cef7de3a2c38a3cad4e4a2b21fc35e08103b0/pichemist-0.1.0.tar.gz (from https://pypi.org/simple/pichemist/), version: 0.1.0
2025-10-13T09:37:22,978   Skipping link: No binaries permitted for pichemist: https://files.pythonhosted.org/packages/76/3d/a5bfd0d8d48f95fb95fa503e6a79651c547d9bd4802d8335db181b6434f3/pichemist-0.2.0-py3-none-any.whl (from https://pypi.org/simple/pichemist/)
2025-10-13T09:37:22,979   Found link https://files.pythonhosted.org/packages/4b/b4/28c15528b9742ec95abdec64b71e2bbf7fed2e0fcf8efdd1dfa817482f4d/pichemist-0.2.0.tar.gz (from https://pypi.org/simple/pichemist/), version: 0.2.0
2025-10-13T09:37:22,979   Skipping link: No binaries permitted for pichemist: https://files.pythonhosted.org/packages/95/e1/593a882b2aa97fee127966c220cbce688d2c0fa5117553a5b6453bf76b5e/pichemist-2.1.0-py3-none-any.whl (from https://pypi.org/simple/pichemist/)
2025-10-13T09:37:22,980   Found link https://files.pythonhosted.org/packages/20/f8/1ec3c063ee404967c683550a9acbdbd5ecc2dbeced339c770236e650ce3f/pichemist-2.1.0.tar.gz (from https://pypi.org/simple/pichemist/), version: 2.1.0
2025-10-13T09:37:22,981   Skipping link: No binaries permitted for pichemist: https://files.pythonhosted.org/packages/96/22/9cdc6c5526b50f1c599ab3a92966a30f6fb12a171090edb6bf292ca66e16/pichemist-2.1.1-py3-none-any.whl (from https://pypi.org/simple/pichemist/)
2025-10-13T09:37:22,981   Found link https://files.pythonhosted.org/packages/ec/eb/a99fe78cd64b3dbf2abcb38a563ddb3f5aeeced7029e8350863b6c5846d4/pichemist-2.1.1.tar.gz (from https://pypi.org/simple/pichemist/), version: 2.1.1
2025-10-13T09:37:22,982 Fetching project page and analyzing links: https://www.piwheels.org/simple/pichemist/
2025-10-13T09:37:22,983 Getting page https://www.piwheels.org/simple/pichemist/
2025-10-13T09:37:22,984 Found index url https://www.piwheels.org/simple
2025-10-13T09:37:23,220 Fetched page https://www.piwheels.org/simple/pichemist/ as text/html
2025-10-13T09:37:23,222   Skipping link: No binaries permitted for pichemist: https://www.piwheels.org/simple/pichemist/pichemist-2.1.0-py3-none-any.whl#sha256=b45c744354a1f1b18aae6d629193386f17a2c07a3ff5e5574aca8d96bb2a2b14 (from https://www.piwheels.org/simple/pichemist/)
2025-10-13T09:37:23,223   Skipping link: No binaries permitted for pichemist: https://archive1.piwheels.org/simple/pichemist/pichemist-0.2.0-py3-none-any.whl#sha256=3a9cc2439aeb60a99d3c9024d55885469d6ad761041e96c9c149b9ae25be981b (from https://www.piwheels.org/simple/pichemist/)
2025-10-13T09:37:23,224   Skipping link: No binaries permitted for pichemist: https://archive1.piwheels.org/simple/pichemist/pichemist-0.1.0-py3-none-any.whl#sha256=10ce770e0a009cb84b3c82ca75ecebb061677f32cc3a2a138a5f3c4baa41c1ab (from https://www.piwheels.org/simple/pichemist/)
2025-10-13T09:37:23,224 Skipping link: not a file: https://www.piwheels.org/simple/pichemist/
2025-10-13T09:37:23,225 Skipping link: not a file: https://pypi.org/simple/pichemist/
2025-10-13T09:37:23,244 Given no hashes to check 1 links for project 'pichemist': discarding no candidates
2025-10-13T09:37:23,262 Collecting pichemist==2.1.1
2025-10-13T09:37:23,264   Created temporary directory: /tmp/pip-unpack-_he3aj5c
2025-10-13T09:37:23,471   Downloading pichemist-2.1.1.tar.gz (49 kB)
2025-10-13T09:37:23,685   Added pichemist==2.1.1 from https://files.pythonhosted.org/packages/ec/eb/a99fe78cd64b3dbf2abcb38a563ddb3f5aeeced7029e8350863b6c5846d4/pichemist-2.1.1.tar.gz to build tracker '/tmp/pip-build-tracker-1ja36c9s'
2025-10-13T09:37:23,687   Running setup.py (path:/tmp/pip-wheel-4l8tanxr/pichemist_190f7667719e4982895b0f719aa957a2/setup.py) egg_info for package pichemist
2025-10-13T09:37:23,688   Created temporary directory: /tmp/pip-pip-egg-info-_qnbhs_8
2025-10-13T09:37:23,689   Preparing metadata (setup.py): started
2025-10-13T09:37:23,690   Running command python setup.py egg_info
2025-10-13T09:37:24,245   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2025-10-13T09:37:24,245   !!

2025-10-13T09:37:24,246           ********************************************************************************
2025-10-13T09:37:24,247           Requirements should be satisfied by a PEP 517 installer.
2025-10-13T09:37:24,248           If you are using pip, you can try `pip install --use-pep517`.

2025-10-13T09:37:24,249           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-10-13T09:37:24,249           or your builds will no longer be supported.
2025-10-13T09:37:24,250           ********************************************************************************

2025-10-13T09:37:24,251   !!
2025-10-13T09:37:24,252     dist.fetch_build_eggs(dist.setup_requires)
2025-10-13T09:37:29,926   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
2025-10-13T09:37:29,927     warnings.warn(msg)
2025-10-13T09:37:29,928   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
2025-10-13T09:37:29,928     warnings.warn(msg)
2025-10-13T09:37:30,023   running egg_info
2025-10-13T09:37:30,056   creating /tmp/pip-pip-egg-info-_qnbhs_8/pichemist.egg-info
2025-10-13T09:37:30,057   writing /tmp/pip-pip-egg-info-_qnbhs_8/pichemist.egg-info/PKG-INFO
2025-10-13T09:37:30,060   writing dependency_links to /tmp/pip-pip-egg-info-_qnbhs_8/pichemist.egg-info/dependency_links.txt
2025-10-13T09:37:30,062   writing entry points to /tmp/pip-pip-egg-info-_qnbhs_8/pichemist.egg-info/entry_points.txt
2025-10-13T09:37:30,063   writing requirements to /tmp/pip-pip-egg-info-_qnbhs_8/pichemist.egg-info/requires.txt
2025-10-13T09:37:30,065   writing top-level names to /tmp/pip-pip-egg-info-_qnbhs_8/pichemist.egg-info/top_level.txt
2025-10-13T09:37:30,066   writing manifest file '/tmp/pip-pip-egg-info-_qnbhs_8/pichemist.egg-info/SOURCES.txt'
2025-10-13T09:37:30,174   reading manifest file '/tmp/pip-pip-egg-info-_qnbhs_8/pichemist.egg-info/SOURCES.txt'
2025-10-13T09:37:30,176   reading manifest template 'MANIFEST.in'
2025-10-13T09:37:30,201   adding license file 'LICENSE'
2025-10-13T09:37:30,206   writing manifest file '/tmp/pip-pip-egg-info-_qnbhs_8/pichemist.egg-info/SOURCES.txt'
2025-10-13T09:37:30,314   Preparing metadata (setup.py): finished with status 'done'
2025-10-13T09:37:30,318   Source in /tmp/pip-wheel-4l8tanxr/pichemist_190f7667719e4982895b0f719aa957a2 has version 2.1.1, which satisfies requirement pichemist==2.1.1 from https://files.pythonhosted.org/packages/ec/eb/a99fe78cd64b3dbf2abcb38a563ddb3f5aeeced7029e8350863b6c5846d4/pichemist-2.1.1.tar.gz
2025-10-13T09:37:30,319   Removed pichemist==2.1.1 from https://files.pythonhosted.org/packages/ec/eb/a99fe78cd64b3dbf2abcb38a563ddb3f5aeeced7029e8350863b6c5846d4/pichemist-2.1.1.tar.gz from build tracker '/tmp/pip-build-tracker-1ja36c9s'
2025-10-13T09:37:30,324 Created temporary directory: /tmp/pip-unpack-p87vlsog
2025-10-13T09:37:30,325 Building wheels for collected packages: pichemist
2025-10-13T09:37:30,329   Created temporary directory: /tmp/pip-wheel-7hgkmuef
2025-10-13T09:37:30,330   Building wheel for pichemist (setup.py): started
2025-10-13T09:37:30,331   Destination directory: /tmp/pip-wheel-7hgkmuef
2025-10-13T09:37:30,331   Running command python setup.py bdist_wheel
2025-10-13T09:37:30,860   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2025-10-13T09:37:30,860   !!

2025-10-13T09:37:30,861           ********************************************************************************
2025-10-13T09:37:30,862           Requirements should be satisfied by a PEP 517 installer.
2025-10-13T09:37:30,862           If you are using pip, you can try `pip install --use-pep517`.

2025-10-13T09:37:30,863           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-10-13T09:37:30,864           or your builds will no longer be supported.
2025-10-13T09:37:30,864           ********************************************************************************

2025-10-13T09:37:30,866   !!
2025-10-13T09:37:30,866     dist.fetch_build_eggs(dist.setup_requires)
2025-10-13T09:37:31,292   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
2025-10-13T09:37:31,293     warnings.warn(msg)
2025-10-13T09:37:31,293   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
2025-10-13T09:37:31,294     warnings.warn(msg)
2025-10-13T09:37:31,576   running bdist_wheel
2025-10-13T09:37:31,732   running build
2025-10-13T09:37:31,733   running build_py
2025-10-13T09:37:31,767   creating build/lib/pichemist
2025-10-13T09:37:31,770   copying pichemist/config.py -> build/lib/pichemist
2025-10-13T09:37:31,772   copying pichemist/io.py -> build/lib/pichemist
2025-10-13T09:37:31,774   copying pichemist/__init__.py -> build/lib/pichemist
2025-10-13T09:37:31,776   copying pichemist/charges.py -> build/lib/pichemist
2025-10-13T09:37:31,778   copying pichemist/model.py -> build/lib/pichemist
2025-10-13T09:37:31,780   copying pichemist/plot.py -> build/lib/pichemist
2025-10-13T09:37:31,782   copying pichemist/cli.py -> build/lib/pichemist
2025-10-13T09:37:31,784   copying pichemist/isoelectric.py -> build/lib/pichemist
2025-10-13T09:37:31,786   copying pichemist/stats.py -> build/lib/pichemist
2025-10-13T09:37:31,788   copying pichemist/molecule.py -> build/lib/pichemist
2025-10-13T09:37:31,790   copying pichemist/utils.py -> build/lib/pichemist
2025-10-13T09:37:31,792   copying pichemist/api.py -> build/lib/pichemist
2025-10-13T09:37:31,794   copying pichemist/core.py -> build/lib/pichemist
2025-10-13T09:37:31,797   creating build/lib/pichemist/smarts
2025-10-13T09:37:31,798   copying pichemist/smarts/pka_set.py -> build/lib/pichemist/smarts
2025-10-13T09:37:31,800   copying pichemist/smarts/__init__.py -> build/lib/pichemist/smarts
2025-10-13T09:37:31,802   creating build/lib/pichemist/fasta
2025-10-13T09:37:31,803   copying pichemist/fasta/scrambler.py -> build/lib/pichemist/fasta
2025-10-13T09:37:31,805   copying pichemist/fasta/matcher.py -> build/lib/pichemist/fasta
2025-10-13T09:37:31,808   copying pichemist/fasta/__init__.py -> build/lib/pichemist/fasta
2025-10-13T09:37:31,809   copying pichemist/fasta/smarts.py -> build/lib/pichemist/fasta
2025-10-13T09:37:31,811   copying pichemist/fasta/helpers.py -> build/lib/pichemist/fasta
2025-10-13T09:37:31,813   copying pichemist/fasta/pka_sets.py -> build/lib/pichemist/fasta
2025-10-13T09:37:31,815   creating build/lib/pichemist/pka
2025-10-13T09:37:31,816   copying pichemist/pka/__init__.py -> build/lib/pichemist/pka
2025-10-13T09:37:31,818   copying pichemist/pka/acd.py -> build/lib/pichemist/pka
2025-10-13T09:37:31,820   copying pichemist/pka/pkamatcher.py -> build/lib/pichemist/pka
2025-10-13T09:37:31,821   copying pichemist/pka/utils.py -> build/lib/pichemist/pka
2025-10-13T09:37:31,823   running egg_info
2025-10-13T09:37:31,854   writing pichemist.egg-info/PKG-INFO
2025-10-13T09:37:31,857   writing dependency_links to pichemist.egg-info/dependency_links.txt
2025-10-13T09:37:31,859   writing entry points to pichemist.egg-info/entry_points.txt
2025-10-13T09:37:31,860   writing requirements to pichemist.egg-info/requires.txt
2025-10-13T09:37:31,861   writing top-level names to pichemist.egg-info/top_level.txt
2025-10-13T09:37:31,897   reading manifest file 'pichemist.egg-info/SOURCES.txt'
2025-10-13T09:37:31,904   reading manifest template 'MANIFEST.in'
2025-10-13T09:37:31,923   adding license file 'LICENSE'
2025-10-13T09:37:31,929   writing manifest file 'pichemist.egg-info/SOURCES.txt'
2025-10-13T09:37:31,931   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.fasta' is absent from the `packages` configuration.
2025-10-13T09:37:31,932   !!

2025-10-13T09:37:31,933           ********************************************************************************
2025-10-13T09:37:31,934           ############################
2025-10-13T09:37:31,934           # Package would be ignored #
2025-10-13T09:37:31,935           ############################
2025-10-13T09:37:31,935           Python recognizes 'pichemist.data.fasta' as an importable package[^1],
2025-10-13T09:37:31,936           but it is absent from setuptools' `packages` configuration.

2025-10-13T09:37:31,937           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-13T09:37:31,938           package, please make sure that 'pichemist.data.fasta' is explicitly added
2025-10-13T09:37:31,939           to the `packages` configuration field.

2025-10-13T09:37:31,940           Alternatively, you can also rely on setuptools' discovery methods
2025-10-13T09:37:31,941           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-13T09:37:31,941           instead of `find_packages(...)`/`find:`).

2025-10-13T09:37:31,942           You can read more about "package discovery" on setuptools documentation page:

2025-10-13T09:37:31,943           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-13T09:37:31,944           If you don't want 'pichemist.data.fasta' to be distributed and are
2025-10-13T09:37:31,945           already explicitly excluding 'pichemist.data.fasta' via
2025-10-13T09:37:31,945           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-13T09:37:31,946           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-13T09:37:31,947           combination with a more fine grained `package-data` configuration.

2025-10-13T09:37:31,947           You can read more about "package data files" on setuptools documentation page:

2025-10-13T09:37:31,949           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-13T09:37:31,950           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-13T09:37:31,951                 even if it does not contain any `.py` files.
2025-10-13T09:37:31,951                 On the other hand, currently there is no concept of package data
2025-10-13T09:37:31,952                 directory, all directories are treated like packages.
2025-10-13T09:37:31,953           ********************************************************************************

2025-10-13T09:37:31,953   !!
2025-10-13T09:37:31,954     check.warn(importable)
2025-10-13T09:37:31,954   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.fasta.legacy' is absent from the `packages` configuration.
2025-10-13T09:37:31,955   !!

2025-10-13T09:37:31,956           ********************************************************************************
2025-10-13T09:37:31,956           ############################
2025-10-13T09:37:31,957           # Package would be ignored #
2025-10-13T09:37:31,957           ############################
2025-10-13T09:37:31,957           Python recognizes 'pichemist.data.fasta.legacy' as an importable package[^1],
2025-10-13T09:37:31,958           but it is absent from setuptools' `packages` configuration.

2025-10-13T09:37:31,959           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-13T09:37:31,960           package, please make sure that 'pichemist.data.fasta.legacy' is explicitly added
2025-10-13T09:37:31,960           to the `packages` configuration field.

2025-10-13T09:37:31,961           Alternatively, you can also rely on setuptools' discovery methods
2025-10-13T09:37:31,962           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-13T09:37:31,962           instead of `find_packages(...)`/`find:`).

2025-10-13T09:37:31,963           You can read more about "package discovery" on setuptools documentation page:

2025-10-13T09:37:31,964           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-13T09:37:31,965           If you don't want 'pichemist.data.fasta.legacy' to be distributed and are
2025-10-13T09:37:31,966           already explicitly excluding 'pichemist.data.fasta.legacy' via
2025-10-13T09:37:31,966           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-13T09:37:31,967           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-13T09:37:31,967           combination with a more fine grained `package-data` configuration.

2025-10-13T09:37:31,968           You can read more about "package data files" on setuptools documentation page:

2025-10-13T09:37:31,969           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-13T09:37:31,971           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-13T09:37:31,972                 even if it does not contain any `.py` files.
2025-10-13T09:37:31,972                 On the other hand, currently there is no concept of package data
2025-10-13T09:37:31,973                 directory, all directories are treated like packages.
2025-10-13T09:37:31,973           ********************************************************************************

2025-10-13T09:37:31,974   !!
2025-10-13T09:37:31,975     check.warn(importable)
2025-10-13T09:37:31,975   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.fasta.original_enriched' is absent from the `packages` configuration.
2025-10-13T09:37:31,976   !!

2025-10-13T09:37:31,977           ********************************************************************************
2025-10-13T09:37:31,977           ############################
2025-10-13T09:37:31,978           # Package would be ignored #
2025-10-13T09:37:31,978           ############################
2025-10-13T09:37:31,979           Python recognizes 'pichemist.data.fasta.original_enriched' as an importable package[^1],
2025-10-13T09:37:31,980           but it is absent from setuptools' `packages` configuration.

2025-10-13T09:37:31,981           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-13T09:37:31,982           package, please make sure that 'pichemist.data.fasta.original_enriched' is explicitly added
2025-10-13T09:37:31,982           to the `packages` configuration field.

2025-10-13T09:37:31,983           Alternatively, you can also rely on setuptools' discovery methods
2025-10-13T09:37:31,984           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-13T09:37:31,984           instead of `find_packages(...)`/`find:`).

2025-10-13T09:37:31,985           You can read more about "package discovery" on setuptools documentation page:

2025-10-13T09:37:31,986           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-13T09:37:31,987           If you don't want 'pichemist.data.fasta.original_enriched' to be distributed and are
2025-10-13T09:37:31,987           already explicitly excluding 'pichemist.data.fasta.original_enriched' via
2025-10-13T09:37:31,987           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-13T09:37:31,988           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-13T09:37:31,988           combination with a more fine grained `package-data` configuration.

2025-10-13T09:37:31,989           You can read more about "package data files" on setuptools documentation page:

2025-10-13T09:37:31,990           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-13T09:37:31,991           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-13T09:37:31,992                 even if it does not contain any `.py` files.
2025-10-13T09:37:31,992                 On the other hand, currently there is no concept of package data
2025-10-13T09:37:31,993                 directory, all directories are treated like packages.
2025-10-13T09:37:31,993           ********************************************************************************

2025-10-13T09:37:31,994   !!
2025-10-13T09:37:31,995     check.warn(importable)
2025-10-13T09:37:31,995   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.fasta.original_short' is absent from the `packages` configuration.
2025-10-13T09:37:31,996   !!

2025-10-13T09:37:31,997           ********************************************************************************
2025-10-13T09:37:31,997           ############################
2025-10-13T09:37:31,998           # Package would be ignored #
2025-10-13T09:37:31,998           ############################
2025-10-13T09:37:31,999           Python recognizes 'pichemist.data.fasta.original_short' as an importable package[^1],
2025-10-13T09:37:31,999           but it is absent from setuptools' `packages` configuration.

2025-10-13T09:37:32,000           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-13T09:37:32,001           package, please make sure that 'pichemist.data.fasta.original_short' is explicitly added
2025-10-13T09:37:32,001           to the `packages` configuration field.

2025-10-13T09:37:32,002           Alternatively, you can also rely on setuptools' discovery methods
2025-10-13T09:37:32,003           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-13T09:37:32,003           instead of `find_packages(...)`/`find:`).

2025-10-13T09:37:32,004           You can read more about "package discovery" on setuptools documentation page:

2025-10-13T09:37:32,005           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-13T09:37:32,007           If you don't want 'pichemist.data.fasta.original_short' to be distributed and are
2025-10-13T09:37:32,007           already explicitly excluding 'pichemist.data.fasta.original_short' via
2025-10-13T09:37:32,008           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-13T09:37:32,008           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-13T09:37:32,009           combination with a more fine grained `package-data` configuration.

2025-10-13T09:37:32,009           You can read more about "package data files" on setuptools documentation page:

2025-10-13T09:37:32,010           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-13T09:37:32,012           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-13T09:37:32,012                 even if it does not contain any `.py` files.
2025-10-13T09:37:32,012                 On the other hand, currently there is no concept of package data
2025-10-13T09:37:32,013                 directory, all directories are treated like packages.
2025-10-13T09:37:32,013           ********************************************************************************

2025-10-13T09:37:32,014   !!
2025-10-13T09:37:32,015     check.warn(importable)
2025-10-13T09:37:32,015   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.fasta.standardised' is absent from the `packages` configuration.
2025-10-13T09:37:32,016   !!

2025-10-13T09:37:32,016           ********************************************************************************
2025-10-13T09:37:32,017           ############################
2025-10-13T09:37:32,017           # Package would be ignored #
2025-10-13T09:37:32,018           ############################
2025-10-13T09:37:32,018           Python recognizes 'pichemist.data.fasta.standardised' as an importable package[^1],
2025-10-13T09:37:32,019           but it is absent from setuptools' `packages` configuration.

2025-10-13T09:37:32,020           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-13T09:37:32,020           package, please make sure that 'pichemist.data.fasta.standardised' is explicitly added
2025-10-13T09:37:32,021           to the `packages` configuration field.

2025-10-13T09:37:32,022           Alternatively, you can also rely on setuptools' discovery methods
2025-10-13T09:37:32,022           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-13T09:37:32,023           instead of `find_packages(...)`/`find:`).

2025-10-13T09:37:32,024           You can read more about "package discovery" on setuptools documentation page:

2025-10-13T09:37:32,025           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-13T09:37:32,026           If you don't want 'pichemist.data.fasta.standardised' to be distributed and are
2025-10-13T09:37:32,026           already explicitly excluding 'pichemist.data.fasta.standardised' via
2025-10-13T09:37:32,027           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-13T09:37:32,028           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-13T09:37:32,028           combination with a more fine grained `package-data` configuration.

2025-10-13T09:37:32,029           You can read more about "package data files" on setuptools documentation page:

2025-10-13T09:37:32,030           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-13T09:37:32,032           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-13T09:37:32,032                 even if it does not contain any `.py` files.
2025-10-13T09:37:32,033                 On the other hand, currently there is no concept of package data
2025-10-13T09:37:32,033                 directory, all directories are treated like packages.
2025-10-13T09:37:32,034           ********************************************************************************

2025-10-13T09:37:32,035   !!
2025-10-13T09:37:32,036     check.warn(importable)
2025-10-13T09:37:32,036   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.smarts' is absent from the `packages` configuration.
2025-10-13T09:37:32,037   !!

2025-10-13T09:37:32,038           ********************************************************************************
2025-10-13T09:37:32,039           ############################
2025-10-13T09:37:32,039           # Package would be ignored #
2025-10-13T09:37:32,040           ############################
2025-10-13T09:37:32,040           Python recognizes 'pichemist.data.smarts' as an importable package[^1],
2025-10-13T09:37:32,041           but it is absent from setuptools' `packages` configuration.

2025-10-13T09:37:32,042           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-13T09:37:32,042           package, please make sure that 'pichemist.data.smarts' is explicitly added
2025-10-13T09:37:32,043           to the `packages` configuration field.

2025-10-13T09:37:32,044           Alternatively, you can also rely on setuptools' discovery methods
2025-10-13T09:37:32,044           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-13T09:37:32,044           instead of `find_packages(...)`/`find:`).

2025-10-13T09:37:32,045           You can read more about "package discovery" on setuptools documentation page:

2025-10-13T09:37:32,047           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-13T09:37:32,047           If you don't want 'pichemist.data.smarts' to be distributed and are
2025-10-13T09:37:32,048           already explicitly excluding 'pichemist.data.smarts' via
2025-10-13T09:37:32,048           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-13T09:37:32,049           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-13T09:37:32,049           combination with a more fine grained `package-data` configuration.

2025-10-13T09:37:32,050           You can read more about "package data files" on setuptools documentation page:

2025-10-13T09:37:32,052           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-13T09:37:32,053           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-13T09:37:32,054                 even if it does not contain any `.py` files.
2025-10-13T09:37:32,054                 On the other hand, currently there is no concept of package data
2025-10-13T09:37:32,055                 directory, all directories are treated like packages.
2025-10-13T09:37:32,055           ********************************************************************************

2025-10-13T09:37:32,056   !!
2025-10-13T09:37:32,057     check.warn(importable)
2025-10-13T09:37:32,057   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.smarts.legacy' is absent from the `packages` configuration.
2025-10-13T09:37:32,058   !!

2025-10-13T09:37:32,059           ********************************************************************************
2025-10-13T09:37:32,060           ############################
2025-10-13T09:37:32,060           # Package would be ignored #
2025-10-13T09:37:32,060           ############################
2025-10-13T09:37:32,061           Python recognizes 'pichemist.data.smarts.legacy' as an importable package[^1],
2025-10-13T09:37:32,062           but it is absent from setuptools' `packages` configuration.

2025-10-13T09:37:32,063           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-13T09:37:32,063           package, please make sure that 'pichemist.data.smarts.legacy' is explicitly added
2025-10-13T09:37:32,064           to the `packages` configuration field.

2025-10-13T09:37:32,065           Alternatively, you can also rely on setuptools' discovery methods
2025-10-13T09:37:32,065           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-13T09:37:32,066           instead of `find_packages(...)`/`find:`).

2025-10-13T09:37:32,067           You can read more about "package discovery" on setuptools documentation page:

2025-10-13T09:37:32,068           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-13T09:37:32,069           If you don't want 'pichemist.data.smarts.legacy' to be distributed and are
2025-10-13T09:37:32,069           already explicitly excluding 'pichemist.data.smarts.legacy' via
2025-10-13T09:37:32,070           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-13T09:37:32,070           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-13T09:37:32,071           combination with a more fine grained `package-data` configuration.

2025-10-13T09:37:32,071           You can read more about "package data files" on setuptools documentation page:

2025-10-13T09:37:32,072           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-13T09:37:32,073           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-13T09:37:32,074                 even if it does not contain any `.py` files.
2025-10-13T09:37:32,074                 On the other hand, currently there is no concept of package data
2025-10-13T09:37:32,075                 directory, all directories are treated like packages.
2025-10-13T09:37:32,075           ********************************************************************************

2025-10-13T09:37:32,076   !!
2025-10-13T09:37:32,077     check.warn(importable)
2025-10-13T09:37:32,077   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.smarts.standardised' is absent from the `packages` configuration.
2025-10-13T09:37:32,078   !!

2025-10-13T09:37:32,078           ********************************************************************************
2025-10-13T09:37:32,079           ############################
2025-10-13T09:37:32,079           # Package would be ignored #
2025-10-13T09:37:32,080           ############################
2025-10-13T09:37:32,080           Python recognizes 'pichemist.data.smarts.standardised' as an importable package[^1],
2025-10-13T09:37:32,081           but it is absent from setuptools' `packages` configuration.

2025-10-13T09:37:32,082           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-13T09:37:32,083           package, please make sure that 'pichemist.data.smarts.standardised' is explicitly added
2025-10-13T09:37:32,083           to the `packages` configuration field.

2025-10-13T09:37:32,084           Alternatively, you can also rely on setuptools' discovery methods
2025-10-13T09:37:32,085           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-13T09:37:32,085           instead of `find_packages(...)`/`find:`).

2025-10-13T09:37:32,086           You can read more about "package discovery" on setuptools documentation page:

2025-10-13T09:37:32,087           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-13T09:37:32,088           If you don't want 'pichemist.data.smarts.standardised' to be distributed and are
2025-10-13T09:37:32,089           already explicitly excluding 'pichemist.data.smarts.standardised' via
2025-10-13T09:37:32,090           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-13T09:37:32,090           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-13T09:37:32,091           combination with a more fine grained `package-data` configuration.

2025-10-13T09:37:32,092           You can read more about "package data files" on setuptools documentation page:

2025-10-13T09:37:32,093           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-13T09:37:32,095           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-13T09:37:32,095                 even if it does not contain any `.py` files.
2025-10-13T09:37:32,096                 On the other hand, currently there is no concept of package data
2025-10-13T09:37:32,096                 directory, all directories are treated like packages.
2025-10-13T09:37:32,097           ********************************************************************************

2025-10-13T09:37:32,099   !!
2025-10-13T09:37:32,099     check.warn(importable)
2025-10-13T09:37:32,100   creating build/lib/pichemist/data/fasta
2025-10-13T09:37:32,100   copying pichemist/data/fasta/convert_legacy_gauci_to_original_and_standardised.py -> build/lib/pichemist/data/fasta
2025-10-13T09:37:32,100   copying pichemist/data/fasta/convert_legacy_promost_into_standardised.py -> build/lib/pichemist/data/fasta
2025-10-13T09:37:32,101   copying pichemist/data/fasta/convert_legacy_short_set_to_original.py -> build/lib/pichemist/data/fasta
2025-10-13T09:37:32,101   copying pichemist/data/fasta/convert_original_short_set_to_standardised.py -> build/lib/pichemist/data/fasta
2025-10-13T09:37:32,102   copying pichemist/data/fasta/legacy_conversion.py -> build/lib/pichemist/data/fasta
2025-10-13T09:37:32,102   creating build/lib/pichemist/data/fasta/legacy
2025-10-13T09:37:32,103   copying pichemist/data/fasta/legacy/aa_legend.tsv -> build/lib/pichemist/data/fasta/legacy
2025-10-13T09:37:32,103   copying pichemist/data/fasta/legacy/gauci.py -> build/lib/pichemist/data/fasta/legacy
2025-10-13T09:37:32,104   copying pichemist/data/fasta/legacy/promost.py -> build/lib/pichemist/data/fasta/legacy
2025-10-13T09:37:32,104   copying pichemist/data/fasta/legacy/short_pka_sets.py -> build/lib/pichemist/data/fasta/legacy
2025-10-13T09:37:32,105   creating build/lib/pichemist/data/fasta/original_enriched
2025-10-13T09:37:32,105   copying pichemist/data/fasta/original_enriched/pka_set_gauci_original.json -> build/lib/pichemist/data/fasta/original_enriched
2025-10-13T09:37:32,106   creating build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,106   copying pichemist/data/fasta/original_short/pka_set_bjellqvist_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,107   copying pichemist/data/fasta/original_short/pka_set_dawson_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,107   copying pichemist/data/fasta/original_short/pka_set_dtaselect_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,108   copying pichemist/data/fasta/original_short/pka_set_emboss_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,108   copying pichemist/data/fasta/original_short/pka_set_grimsley_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,109   copying pichemist/data/fasta/original_short/pka_set_ipc2_peptide_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,110   copying pichemist/data/fasta/original_short/pka_set_ipc_peptide_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,110   copying pichemist/data/fasta/original_short/pka_set_lehninger_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,111   copying pichemist/data/fasta/original_short/pka_set_nozaki_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,111   copying pichemist/data/fasta/original_short/pka_set_rodwell_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,112   copying pichemist/data/fasta/original_short/pka_set_sillero_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,113   copying pichemist/data/fasta/original_short/pka_set_solomon_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,113   copying pichemist/data/fasta/original_short/pka_set_thurlkill_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,114   copying pichemist/data/fasta/original_short/pka_set_toseland_original.json -> build/lib/pichemist/data/fasta/original_short
2025-10-13T09:37:32,114   creating build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,115   copying pichemist/data/fasta/standardised/pka_set_bjellqvist_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,115   copying pichemist/data/fasta/standardised/pka_set_dawson_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,116   copying pichemist/data/fasta/standardised/pka_set_dtaselect_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,117   copying pichemist/data/fasta/standardised/pka_set_emboss_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,117   copying pichemist/data/fasta/standardised/pka_set_gauci_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,118   copying pichemist/data/fasta/standardised/pka_set_grimsley_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,118   copying pichemist/data/fasta/standardised/pka_set_ipc2_peptide_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,119   copying pichemist/data/fasta/standardised/pka_set_ipc_peptide_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,119   copying pichemist/data/fasta/standardised/pka_set_lehninger_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,120   copying pichemist/data/fasta/standardised/pka_set_nozaki_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,120   copying pichemist/data/fasta/standardised/pka_set_promost_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,121   copying pichemist/data/fasta/standardised/pka_set_rodwell_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,121   copying pichemist/data/fasta/standardised/pka_set_sillero_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,122   copying pichemist/data/fasta/standardised/pka_set_solomon_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,122   copying pichemist/data/fasta/standardised/pka_set_thurlkill_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,123   copying pichemist/data/fasta/standardised/pka_set_toseland_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-10-13T09:37:32,123   creating build/lib/pichemist/data/smarts
2025-10-13T09:37:32,124   copying pichemist/data/smarts/convert_legacy_aa_smarts_to_standardised.py -> build/lib/pichemist/data/smarts
2025-10-13T09:37:32,124   copying pichemist/data/smarts/convert_legacy_ss_smarts_to_standardised.py -> build/lib/pichemist/data/smarts
2025-10-13T09:37:32,125   creating build/lib/pichemist/data/smarts/legacy
2025-10-13T09:37:32,126   copying pichemist/data/smarts/legacy/smarts_naturalAAs.py -> build/lib/pichemist/data/smarts/legacy
2025-10-13T09:37:32,126   copying pichemist/data/smarts/legacy/smarts_notes.py -> build/lib/pichemist/data/smarts/legacy
2025-10-13T09:37:32,127   copying pichemist/data/smarts/legacy/smarts_pKaMatcher.dat -> build/lib/pichemist/data/smarts/legacy
2025-10-13T09:37:32,127   copying pichemist/data/smarts/legacy/smarts_pKaMatcher.py -> build/lib/pichemist/data/smarts/legacy
2025-10-13T09:37:32,128   creating build/lib/pichemist/data/smarts/standardised
2025-10-13T09:37:32,129   copying pichemist/data/smarts/standardised/aa_smarts_set_standardised.json -> build/lib/pichemist/data/smarts/standardised
2025-10-13T09:37:32,129   copying pichemist/data/smarts/standardised/ss_smarts_set_standardised.json -> build/lib/pichemist/data/smarts/standardised
2025-10-13T09:37:32,132   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-10-13T09:37:32,132   !!

2025-10-13T09:37:32,134           ********************************************************************************
2025-10-13T09:37:32,134           Please avoid running ``setup.py`` directly.
2025-10-13T09:37:32,135           Instead, use pypa/build, pypa/installer or other
2025-10-13T09:37:32,135           standards-based tools.

2025-10-13T09:37:32,137           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-10-13T09:37:32,137           or your builds will no longer be supported.

2025-10-13T09:37:32,138           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-10-13T09:37:32,139           ********************************************************************************

2025-10-13T09:37:32,140   !!
2025-10-13T09:37:32,140     self.initialize_options()
2025-10-13T09:37:32,163   installing to build/bdist.linux-armv7l/wheel
2025-10-13T09:37:32,164   running install
2025-10-13T09:37:32,188   running install_lib
2025-10-13T09:37:32,219   creating build/bdist.linux-armv7l/wheel
2025-10-13T09:37:32,221   creating build/bdist.linux-armv7l/wheel/pichemist
2025-10-13T09:37:32,222   copying build/lib/pichemist/config.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,224   copying build/lib/pichemist/io.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,227   creating build/bdist.linux-armv7l/wheel/pichemist/smarts
2025-10-13T09:37:32,228   copying build/lib/pichemist/smarts/pka_set.py -> build/bdist.linux-armv7l/wheel/./pichemist/smarts
2025-10-13T09:37:32,230   copying build/lib/pichemist/smarts/__init__.py -> build/bdist.linux-armv7l/wheel/./pichemist/smarts
2025-10-13T09:37:32,232   creating build/bdist.linux-armv7l/wheel/pichemist/data
2025-10-13T09:37:32,233   creating build/bdist.linux-armv7l/wheel/pichemist/data/smarts
2025-10-13T09:37:32,235   creating build/bdist.linux-armv7l/wheel/pichemist/data/smarts/standardised
2025-10-13T09:37:32,236   copying build/lib/pichemist/data/smarts/standardised/ss_smarts_set_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/standardised
2025-10-13T09:37:32,239   copying build/lib/pichemist/data/smarts/standardised/aa_smarts_set_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/standardised
2025-10-13T09:37:32,242   creating build/bdist.linux-armv7l/wheel/pichemist/data/smarts/legacy
2025-10-13T09:37:32,243   copying build/lib/pichemist/data/smarts/legacy/smarts_notes.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/legacy
2025-10-13T09:37:32,245   copying build/lib/pichemist/data/smarts/legacy/smarts_pKaMatcher.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/legacy
2025-10-13T09:37:32,247   copying build/lib/pichemist/data/smarts/legacy/smarts_naturalAAs.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/legacy
2025-10-13T09:37:32,250   copying build/lib/pichemist/data/smarts/legacy/smarts_pKaMatcher.dat -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/legacy
2025-10-13T09:37:32,252   copying build/lib/pichemist/data/smarts/convert_legacy_ss_smarts_to_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts
2025-10-13T09:37:32,254   copying build/lib/pichemist/data/smarts/convert_legacy_aa_smarts_to_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts
2025-10-13T09:37:32,257   creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta
2025-10-13T09:37:32,258   creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta/original_short
2025-10-13T09:37:32,259   copying build/lib/pichemist/data/fasta/original_short/pka_set_emboss_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,261   copying build/lib/pichemist/data/fasta/original_short/pka_set_nozaki_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,263   copying build/lib/pichemist/data/fasta/original_short/pka_set_bjellqvist_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,265   copying build/lib/pichemist/data/fasta/original_short/pka_set_rodwell_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,267   copying build/lib/pichemist/data/fasta/original_short/pka_set_toseland_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,269   copying build/lib/pichemist/data/fasta/original_short/pka_set_dtaselect_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,271   copying build/lib/pichemist/data/fasta/original_short/pka_set_solomon_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,273   copying build/lib/pichemist/data/fasta/original_short/pka_set_sillero_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,274   copying build/lib/pichemist/data/fasta/original_short/pka_set_dawson_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,276   copying build/lib/pichemist/data/fasta/original_short/pka_set_thurlkill_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,278   copying build/lib/pichemist/data/fasta/original_short/pka_set_ipc_peptide_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,280   copying build/lib/pichemist/data/fasta/original_short/pka_set_lehninger_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,281   copying build/lib/pichemist/data/fasta/original_short/pka_set_grimsley_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,283   copying build/lib/pichemist/data/fasta/original_short/pka_set_ipc2_peptide_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-10-13T09:37:32,285   creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta/standardised
2025-10-13T09:37:32,286   copying build/lib/pichemist/data/fasta/standardised/pka_set_grimsley_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,289   copying build/lib/pichemist/data/fasta/standardised/pka_set_thurlkill_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,291   copying build/lib/pichemist/data/fasta/standardised/pka_set_solomon_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,293   copying build/lib/pichemist/data/fasta/standardised/pka_set_ipc_peptide_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,295   copying build/lib/pichemist/data/fasta/standardised/pka_set_sillero_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,297   copying build/lib/pichemist/data/fasta/standardised/pka_set_ipc2_peptide_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,300   copying build/lib/pichemist/data/fasta/standardised/pka_set_gauci_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,302   copying build/lib/pichemist/data/fasta/standardised/pka_set_emboss_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,304   copying build/lib/pichemist/data/fasta/standardised/pka_set_dawson_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,306   copying build/lib/pichemist/data/fasta/standardised/pka_set_promost_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,308   copying build/lib/pichemist/data/fasta/standardised/pka_set_lehninger_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,310   copying build/lib/pichemist/data/fasta/standardised/pka_set_toseland_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,312   copying build/lib/pichemist/data/fasta/standardised/pka_set_dtaselect_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,315   copying build/lib/pichemist/data/fasta/standardised/pka_set_rodwell_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,317   copying build/lib/pichemist/data/fasta/standardised/pka_set_nozaki_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,319   copying build/lib/pichemist/data/fasta/standardised/pka_set_bjellqvist_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-10-13T09:37:32,322   creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta/legacy
2025-10-13T09:37:32,323   copying build/lib/pichemist/data/fasta/legacy/promost.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/legacy
2025-10-13T09:37:32,325   copying build/lib/pichemist/data/fasta/legacy/gauci.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/legacy
2025-10-13T09:37:32,327   copying build/lib/pichemist/data/fasta/legacy/short_pka_sets.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/legacy
2025-10-13T09:37:32,328   copying build/lib/pichemist/data/fasta/legacy/aa_legend.tsv -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/legacy
2025-10-13T09:37:32,330   copying build/lib/pichemist/data/fasta/convert_original_short_set_to_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta
2025-10-13T09:37:32,332   copying build/lib/pichemist/data/fasta/convert_legacy_promost_into_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta
2025-10-13T09:37:32,334   copying build/lib/pichemist/data/fasta/convert_legacy_short_set_to_original.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta
2025-10-13T09:37:32,336   copying build/lib/pichemist/data/fasta/legacy_conversion.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta
2025-10-13T09:37:32,338   creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta/original_enriched
2025-10-13T09:37:32,339   copying build/lib/pichemist/data/fasta/original_enriched/pka_set_gauci_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_enriched
2025-10-13T09:37:32,341   copying build/lib/pichemist/data/fasta/convert_legacy_gauci_to_original_and_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta
2025-10-13T09:37:32,344   creating build/bdist.linux-armv7l/wheel/pichemist/fasta
2025-10-13T09:37:32,345   copying build/lib/pichemist/fasta/scrambler.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta
2025-10-13T09:37:32,347   copying build/lib/pichemist/fasta/matcher.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta
2025-10-13T09:37:32,349   copying build/lib/pichemist/fasta/__init__.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta
2025-10-13T09:37:32,350   copying build/lib/pichemist/fasta/smarts.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta
2025-10-13T09:37:32,352   copying build/lib/pichemist/fasta/helpers.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta
2025-10-13T09:37:32,354   copying build/lib/pichemist/fasta/pka_sets.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta
2025-10-13T09:37:32,356   copying build/lib/pichemist/__init__.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,357   copying build/lib/pichemist/charges.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,359   copying build/lib/pichemist/model.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,361   copying build/lib/pichemist/plot.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,363   copying build/lib/pichemist/cli.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,366   copying build/lib/pichemist/isoelectric.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,368   copying build/lib/pichemist/stats.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,370   copying build/lib/pichemist/molecule.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,372   copying build/lib/pichemist/utils.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,374   copying build/lib/pichemist/api.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,377   creating build/bdist.linux-armv7l/wheel/pichemist/pka
2025-10-13T09:37:32,378   copying build/lib/pichemist/pka/__init__.py -> build/bdist.linux-armv7l/wheel/./pichemist/pka
2025-10-13T09:37:32,379   copying build/lib/pichemist/pka/acd.py -> build/bdist.linux-armv7l/wheel/./pichemist/pka
2025-10-13T09:37:32,381   copying build/lib/pichemist/pka/pkamatcher.py -> build/bdist.linux-armv7l/wheel/./pichemist/pka
2025-10-13T09:37:32,383   copying build/lib/pichemist/pka/utils.py -> build/bdist.linux-armv7l/wheel/./pichemist/pka
2025-10-13T09:37:32,385   copying build/lib/pichemist/core.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-10-13T09:37:32,387   running install_egg_info
2025-10-13T09:37:32,420   Copying pichemist.egg-info to build/bdist.linux-armv7l/wheel/./pichemist-2.1.1-py3.11.egg-info
2025-10-13T09:37:32,432   running install_scripts
2025-10-13T09:37:32,444   creating build/bdist.linux-armv7l/wheel/pichemist-2.1.1.dist-info/WHEEL
2025-10-13T09:37:32,447   creating '/tmp/pip-wheel-7hgkmuef/pichemist-2.1.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-10-13T09:37:32,449   adding 'pichemist/__init__.py'
2025-10-13T09:37:32,451   adding 'pichemist/api.py'
2025-10-13T09:37:32,452   adding 'pichemist/charges.py'
2025-10-13T09:37:32,453   adding 'pichemist/cli.py'
2025-10-13T09:37:32,455   adding 'pichemist/config.py'
2025-10-13T09:37:32,456   adding 'pichemist/core.py'
2025-10-13T09:37:32,458   adding 'pichemist/io.py'
2025-10-13T09:37:32,460   adding 'pichemist/isoelectric.py'
2025-10-13T09:37:32,461   adding 'pichemist/model.py'
2025-10-13T09:37:32,462   adding 'pichemist/molecule.py'
2025-10-13T09:37:32,464   adding 'pichemist/plot.py'
2025-10-13T09:37:32,465   adding 'pichemist/stats.py'
2025-10-13T09:37:32,466   adding 'pichemist/utils.py'
2025-10-13T09:37:32,468   adding 'pichemist/data/fasta/convert_legacy_gauci_to_original_and_standardised.py'
2025-10-13T09:37:32,469   adding 'pichemist/data/fasta/convert_legacy_promost_into_standardised.py'
2025-10-13T09:37:32,471   adding 'pichemist/data/fasta/convert_legacy_short_set_to_original.py'
2025-10-13T09:37:32,472   adding 'pichemist/data/fasta/convert_original_short_set_to_standardised.py'
2025-10-13T09:37:32,473   adding 'pichemist/data/fasta/legacy_conversion.py'
2025-10-13T09:37:32,475   adding 'pichemist/data/fasta/legacy/aa_legend.tsv'
2025-10-13T09:37:32,476   adding 'pichemist/data/fasta/legacy/gauci.py'
2025-10-13T09:37:32,478   adding 'pichemist/data/fasta/legacy/promost.py'
2025-10-13T09:37:32,479   adding 'pichemist/data/fasta/legacy/short_pka_sets.py'
2025-10-13T09:37:32,481   adding 'pichemist/data/fasta/original_enriched/pka_set_gauci_original.json'
2025-10-13T09:37:32,483   adding 'pichemist/data/fasta/original_short/pka_set_bjellqvist_original.json'
2025-10-13T09:37:32,484   adding 'pichemist/data/fasta/original_short/pka_set_dawson_original.json'
2025-10-13T09:37:32,485   adding 'pichemist/data/fasta/original_short/pka_set_dtaselect_original.json'
2025-10-13T09:37:32,486   adding 'pichemist/data/fasta/original_short/pka_set_emboss_original.json'
2025-10-13T09:37:32,487   adding 'pichemist/data/fasta/original_short/pka_set_grimsley_original.json'
2025-10-13T09:37:32,488   adding 'pichemist/data/fasta/original_short/pka_set_ipc2_peptide_original.json'
2025-10-13T09:37:32,489   adding 'pichemist/data/fasta/original_short/pka_set_ipc_peptide_original.json'
2025-10-13T09:37:32,491   adding 'pichemist/data/fasta/original_short/pka_set_lehninger_original.json'
2025-10-13T09:37:32,492   adding 'pichemist/data/fasta/original_short/pka_set_nozaki_original.json'
2025-10-13T09:37:32,493   adding 'pichemist/data/fasta/original_short/pka_set_rodwell_original.json'
2025-10-13T09:37:32,494   adding 'pichemist/data/fasta/original_short/pka_set_sillero_original.json'
2025-10-13T09:37:32,495   adding 'pichemist/data/fasta/original_short/pka_set_solomon_original.json'
2025-10-13T09:37:32,496   adding 'pichemist/data/fasta/original_short/pka_set_thurlkill_original.json'
2025-10-13T09:37:32,498   adding 'pichemist/data/fasta/original_short/pka_set_toseland_original.json'
2025-10-13T09:37:32,499   adding 'pichemist/data/fasta/standardised/pka_set_bjellqvist_standardised.json'
2025-10-13T09:37:32,501   adding 'pichemist/data/fasta/standardised/pka_set_dawson_standardised.json'
2025-10-13T09:37:32,502   adding 'pichemist/data/fasta/standardised/pka_set_dtaselect_standardised.json'
2025-10-13T09:37:32,503   adding 'pichemist/data/fasta/standardised/pka_set_emboss_standardised.json'
2025-10-13T09:37:32,504   adding 'pichemist/data/fasta/standardised/pka_set_gauci_standardised.json'
2025-10-13T09:37:32,506   adding 'pichemist/data/fasta/standardised/pka_set_grimsley_standardised.json'
2025-10-13T09:37:32,507   adding 'pichemist/data/fasta/standardised/pka_set_ipc2_peptide_standardised.json'
2025-10-13T09:37:32,508   adding 'pichemist/data/fasta/standardised/pka_set_ipc_peptide_standardised.json'
2025-10-13T09:37:32,509   adding 'pichemist/data/fasta/standardised/pka_set_lehninger_standardised.json'
2025-10-13T09:37:32,511   adding 'pichemist/data/fasta/standardised/pka_set_nozaki_standardised.json'
2025-10-13T09:37:32,512   adding 'pichemist/data/fasta/standardised/pka_set_promost_standardised.json'
2025-10-13T09:37:32,513   adding 'pichemist/data/fasta/standardised/pka_set_rodwell_standardised.json'
2025-10-13T09:37:32,515   adding 'pichemist/data/fasta/standardised/pka_set_sillero_standardised.json'
2025-10-13T09:37:32,516   adding 'pichemist/data/fasta/standardised/pka_set_solomon_standardised.json'
2025-10-13T09:37:32,517   adding 'pichemist/data/fasta/standardised/pka_set_thurlkill_standardised.json'
2025-10-13T09:37:32,519   adding 'pichemist/data/fasta/standardised/pka_set_toseland_standardised.json'
2025-10-13T09:37:32,521   adding 'pichemist/data/smarts/convert_legacy_aa_smarts_to_standardised.py'
2025-10-13T09:37:32,522   adding 'pichemist/data/smarts/convert_legacy_ss_smarts_to_standardised.py'
2025-10-13T09:37:32,524   adding 'pichemist/data/smarts/legacy/smarts_naturalAAs.py'
2025-10-13T09:37:32,525   adding 'pichemist/data/smarts/legacy/smarts_notes.py'
2025-10-13T09:37:32,527   adding 'pichemist/data/smarts/legacy/smarts_pKaMatcher.dat'
2025-10-13T09:37:32,528   adding 'pichemist/data/smarts/legacy/smarts_pKaMatcher.py'
2025-10-13T09:37:32,531   adding 'pichemist/data/smarts/standardised/aa_smarts_set_standardised.json'
2025-10-13T09:37:32,532   adding 'pichemist/data/smarts/standardised/ss_smarts_set_standardised.json'
2025-10-13T09:37:32,534   adding 'pichemist/fasta/__init__.py'
2025-10-13T09:37:32,536   adding 'pichemist/fasta/helpers.py'
2025-10-13T09:37:32,537   adding 'pichemist/fasta/matcher.py'
2025-10-13T09:37:32,539   adding 'pichemist/fasta/pka_sets.py'
2025-10-13T09:37:32,540   adding 'pichemist/fasta/scrambler.py'
2025-10-13T09:37:32,541   adding 'pichemist/fasta/smarts.py'
2025-10-13T09:37:32,543   adding 'pichemist/pka/__init__.py'
2025-10-13T09:37:32,544   adding 'pichemist/pka/acd.py'
2025-10-13T09:37:32,546   adding 'pichemist/pka/pkamatcher.py'
2025-10-13T09:37:32,547   adding 'pichemist/pka/utils.py'
2025-10-13T09:37:32,549   adding 'pichemist/smarts/__init__.py'
2025-10-13T09:37:32,550   adding 'pichemist/smarts/pka_set.py'
2025-10-13T09:37:32,552   adding 'pichemist-2.1.1.dist-info/licenses/LICENSE'
2025-10-13T09:37:32,554   adding 'pichemist-2.1.1.dist-info/METADATA'
2025-10-13T09:37:32,555   adding 'pichemist-2.1.1.dist-info/WHEEL'
2025-10-13T09:37:32,556   adding 'pichemist-2.1.1.dist-info/entry_points.txt'
2025-10-13T09:37:32,557   adding 'pichemist-2.1.1.dist-info/top_level.txt'
2025-10-13T09:37:32,559   adding 'pichemist-2.1.1.dist-info/RECORD'
2025-10-13T09:37:32,561   removing build/bdist.linux-armv7l/wheel
2025-10-13T09:37:32,689   Building wheel for pichemist (setup.py): finished with status 'done'
2025-10-13T09:37:32,692   Created wheel for pichemist: filename=pichemist-2.1.1-py3-none-any.whl size=65702 sha256=5ebafaa5caba1c30a6864fcb3788180732f55a24e6cbd21586c4ae8940c22b81
2025-10-13T09:37:32,693   Stored in directory: /tmp/pip-ephem-wheel-cache-konnrz3m/wheels/9d/5f/da/b2b705180c9b304406983df47834d74b3936be0acb686aefd6
2025-10-13T09:37:32,707 Successfully built pichemist
2025-10-13T09:37:32,712 Removed build tracker: '/tmp/pip-build-tracker-1ja36c9s'