2025-09-17T21:21:26,631 Created temporary directory: /tmp/pip-ephem-wheel-cache-9p2fkuff
2025-09-17T21:21:26,633 Created temporary directory: /tmp/pip-build-tracker-xsheoyih
2025-09-17T21:21:26,634 Initialized build tracking at /tmp/pip-build-tracker-xsheoyih
2025-09-17T21:21:26,634 Created build tracker: /tmp/pip-build-tracker-xsheoyih
2025-09-17T21:21:26,634 Entered build tracker: /tmp/pip-build-tracker-xsheoyih
2025-09-17T21:21:26,635 Created temporary directory: /tmp/pip-wheel-97tl20nv
2025-09-17T21:21:26,638 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
2025-09-17T21:21:26,640 Created temporary directory: /tmp/pip-ephem-wheel-cache-zanvi8zo
2025-09-17T21:21:26,664 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-09-17T21:21:26,667 2 location(s) to search for versions of pichemist:
2025-09-17T21:21:26,667 * https://pypi.org/simple/pichemist/
2025-09-17T21:21:26,667 * https://www.piwheels.org/simple/pichemist/
2025-09-17T21:21:26,668 Fetching project page and analyzing links: https://pypi.org/simple/pichemist/
2025-09-17T21:21:26,669 Getting page https://pypi.org/simple/pichemist/
2025-09-17T21:21:26,670 Found index url https://pypi.org/simple
2025-09-17T21:21:26,884 Fetched page https://pypi.org/simple/pichemist/ as application/vnd.pypi.simple.v1+json
2025-09-17T21:21:26,886   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/)
2025-09-17T21:21:26,887   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
2025-09-17T21:21:26,888   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/)
2025-09-17T21:21:26,888   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
2025-09-17T21:21:26,889   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/)
2025-09-17T21:21:26,890   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
2025-09-17T21:21:26,891 Fetching project page and analyzing links: https://www.piwheels.org/simple/pichemist/
2025-09-17T21:21:26,891 Getting page https://www.piwheels.org/simple/pichemist/
2025-09-17T21:21:26,893 Found index url https://www.piwheels.org/simple
2025-09-17T21:21:27,062 Fetched page https://www.piwheels.org/simple/pichemist/ as text/html
2025-09-17T21:21:27,064   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/)
2025-09-17T21:21:27,064   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/)
2025-09-17T21:21:27,065 Skipping link: not a file: https://www.piwheels.org/simple/pichemist/
2025-09-17T21:21:27,066 Skipping link: not a file: https://pypi.org/simple/pichemist/
2025-09-17T21:21:27,085 Given no hashes to check 1 links for project 'pichemist': discarding no candidates
2025-09-17T21:21:27,102 Collecting pichemist==2.1.0
2025-09-17T21:21:27,105   Created temporary directory: /tmp/pip-unpack-56fgnt5w
2025-09-17T21:21:27,320   Downloading pichemist-2.1.0.tar.gz (49 kB)
2025-09-17T21:21:27,531   Added pichemist==2.1.0 from https://files.pythonhosted.org/packages/20/f8/1ec3c063ee404967c683550a9acbdbd5ecc2dbeced339c770236e650ce3f/pichemist-2.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-xsheoyih'
2025-09-17T21:21:27,533   Running setup.py (path:/tmp/pip-wheel-97tl20nv/pichemist_4bb42936fb674e84ab717275616e6dbb/setup.py) egg_info for package pichemist
2025-09-17T21:21:27,533   Created temporary directory: /tmp/pip-pip-egg-info-22r0pj27
2025-09-17T21:21:27,534   Preparing metadata (setup.py): started
2025-09-17T21:21:27,535   Running command python setup.py egg_info
2025-09-17T21:21:28,083   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2025-09-17T21:21:28,083   !!

2025-09-17T21:21:28,084           ********************************************************************************
2025-09-17T21:21:28,085           Requirements should be satisfied by a PEP 517 installer.
2025-09-17T21:21:28,085           If you are using pip, you can try `pip install --use-pep517`.

2025-09-17T21:21:28,086           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-09-17T21:21:28,086           or your builds will no longer be supported.
2025-09-17T21:21:28,087           ********************************************************************************

2025-09-17T21:21:28,088   !!
2025-09-17T21:21:28,088     dist.fetch_build_eggs(dist.setup_requires)
2025-09-17T21:21:33,786   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
2025-09-17T21:21:33,786     warnings.warn(msg)
2025-09-17T21:21:33,787   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
2025-09-17T21:21:33,787     warnings.warn(msg)
2025-09-17T21:21:33,879   running egg_info
2025-09-17T21:21:33,910   creating /tmp/pip-pip-egg-info-22r0pj27/pichemist.egg-info
2025-09-17T21:21:33,911   writing /tmp/pip-pip-egg-info-22r0pj27/pichemist.egg-info/PKG-INFO
2025-09-17T21:21:33,915   writing dependency_links to /tmp/pip-pip-egg-info-22r0pj27/pichemist.egg-info/dependency_links.txt
2025-09-17T21:21:33,917   writing entry points to /tmp/pip-pip-egg-info-22r0pj27/pichemist.egg-info/entry_points.txt
2025-09-17T21:21:33,918   writing requirements to /tmp/pip-pip-egg-info-22r0pj27/pichemist.egg-info/requires.txt
2025-09-17T21:21:33,919   writing top-level names to /tmp/pip-pip-egg-info-22r0pj27/pichemist.egg-info/top_level.txt
2025-09-17T21:21:33,920   writing manifest file '/tmp/pip-pip-egg-info-22r0pj27/pichemist.egg-info/SOURCES.txt'
2025-09-17T21:21:34,313   reading manifest file '/tmp/pip-pip-egg-info-22r0pj27/pichemist.egg-info/SOURCES.txt'
2025-09-17T21:21:34,395   reading manifest template 'MANIFEST.in'
2025-09-17T21:21:34,657   adding license file 'LICENSE'
2025-09-17T21:21:34,669   writing manifest file '/tmp/pip-pip-egg-info-22r0pj27/pichemist.egg-info/SOURCES.txt'
2025-09-17T21:21:34,794   Preparing metadata (setup.py): finished with status 'done'
2025-09-17T21:21:34,798   Source in /tmp/pip-wheel-97tl20nv/pichemist_4bb42936fb674e84ab717275616e6dbb has version 2.1.0, which satisfies requirement pichemist==2.1.0 from https://files.pythonhosted.org/packages/20/f8/1ec3c063ee404967c683550a9acbdbd5ecc2dbeced339c770236e650ce3f/pichemist-2.1.0.tar.gz
2025-09-17T21:21:34,799   Removed pichemist==2.1.0 from https://files.pythonhosted.org/packages/20/f8/1ec3c063ee404967c683550a9acbdbd5ecc2dbeced339c770236e650ce3f/pichemist-2.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-xsheoyih'
2025-09-17T21:21:34,804 Created temporary directory: /tmp/pip-unpack-jr337cd8
2025-09-17T21:21:34,805 Building wheels for collected packages: pichemist
2025-09-17T21:21:34,809   Created temporary directory: /tmp/pip-wheel-vvfes9ru
2025-09-17T21:21:34,810   Building wheel for pichemist (setup.py): started
2025-09-17T21:21:34,811   Destination directory: /tmp/pip-wheel-vvfes9ru
2025-09-17T21:21:34,811   Running command python setup.py bdist_wheel
2025-09-17T21:21:35,346   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2025-09-17T21:21:35,346   !!

2025-09-17T21:21:35,347           ********************************************************************************
2025-09-17T21:21:35,348           Requirements should be satisfied by a PEP 517 installer.
2025-09-17T21:21:35,348           If you are using pip, you can try `pip install --use-pep517`.

2025-09-17T21:21:35,349           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-09-17T21:21:35,349           or your builds will no longer be supported.
2025-09-17T21:21:35,350           ********************************************************************************

2025-09-17T21:21:35,351   !!
2025-09-17T21:21:35,351     dist.fetch_build_eggs(dist.setup_requires)
2025-09-17T21:21:35,770   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
2025-09-17T21:21:35,770     warnings.warn(msg)
2025-09-17T21:21:35,771   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
2025-09-17T21:21:35,771     warnings.warn(msg)
2025-09-17T21:21:36,050   running bdist_wheel
2025-09-17T21:21:36,209   running build
2025-09-17T21:21:36,210   running build_py
2025-09-17T21:21:36,244   creating build/lib/pichemist
2025-09-17T21:21:36,246   copying pichemist/model.py -> build/lib/pichemist
2025-09-17T21:21:36,248   copying pichemist/isoelectric.py -> build/lib/pichemist
2025-09-17T21:21:36,250   copying pichemist/charges.py -> build/lib/pichemist
2025-09-17T21:21:36,252   copying pichemist/utils.py -> build/lib/pichemist
2025-09-17T21:21:36,254   copying pichemist/api.py -> build/lib/pichemist
2025-09-17T21:21:36,256   copying pichemist/config.py -> build/lib/pichemist
2025-09-17T21:21:36,258   copying pichemist/io.py -> build/lib/pichemist
2025-09-17T21:21:36,260   copying pichemist/core.py -> build/lib/pichemist
2025-09-17T21:21:36,262   copying pichemist/cli.py -> build/lib/pichemist
2025-09-17T21:21:36,265   copying pichemist/plot.py -> build/lib/pichemist
2025-09-17T21:21:36,267   copying pichemist/stats.py -> build/lib/pichemist
2025-09-17T21:21:36,268   copying pichemist/__init__.py -> build/lib/pichemist
2025-09-17T21:21:36,270   copying pichemist/molecule.py -> build/lib/pichemist
2025-09-17T21:21:36,272   creating build/lib/pichemist/pka
2025-09-17T21:21:36,273   copying pichemist/pka/pkamatcher.py -> build/lib/pichemist/pka
2025-09-17T21:21:36,276   copying pichemist/pka/utils.py -> build/lib/pichemist/pka
2025-09-17T21:21:36,277   copying pichemist/pka/acd.py -> build/lib/pichemist/pka
2025-09-17T21:21:36,279   copying pichemist/pka/__init__.py -> build/lib/pichemist/pka
2025-09-17T21:21:36,281   creating build/lib/pichemist/fasta
2025-09-17T21:21:36,282   copying pichemist/fasta/matcher.py -> build/lib/pichemist/fasta
2025-09-17T21:21:36,285   copying pichemist/fasta/pka_sets.py -> build/lib/pichemist/fasta
2025-09-17T21:21:36,287   copying pichemist/fasta/smarts.py -> build/lib/pichemist/fasta
2025-09-17T21:21:36,288   copying pichemist/fasta/scrambler.py -> build/lib/pichemist/fasta
2025-09-17T21:21:36,290   copying pichemist/fasta/helpers.py -> build/lib/pichemist/fasta
2025-09-17T21:21:36,292   copying pichemist/fasta/__init__.py -> build/lib/pichemist/fasta
2025-09-17T21:21:36,294   creating build/lib/pichemist/smarts
2025-09-17T21:21:36,295   copying pichemist/smarts/pka_set.py -> build/lib/pichemist/smarts
2025-09-17T21:21:36,297   copying pichemist/smarts/__init__.py -> build/lib/pichemist/smarts
2025-09-17T21:21:36,298   running egg_info
2025-09-17T21:21:36,330   writing pichemist.egg-info/PKG-INFO
2025-09-17T21:21:36,333   writing dependency_links to pichemist.egg-info/dependency_links.txt
2025-09-17T21:21:36,334   writing entry points to pichemist.egg-info/entry_points.txt
2025-09-17T21:21:36,336   writing requirements to pichemist.egg-info/requires.txt
2025-09-17T21:21:36,337   writing top-level names to pichemist.egg-info/top_level.txt
2025-09-17T21:21:36,374   reading manifest file 'pichemist.egg-info/SOURCES.txt'
2025-09-17T21:21:36,380   reading manifest template 'MANIFEST.in'
2025-09-17T21:21:36,401   adding license file 'LICENSE'
2025-09-17T21:21:36,407   writing manifest file 'pichemist.egg-info/SOURCES.txt'
2025-09-17T21:21:36,409   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.fasta' is absent from the `packages` configuration.
2025-09-17T21:21:36,410   !!

2025-09-17T21:21:36,411           ********************************************************************************
2025-09-17T21:21:36,411           ############################
2025-09-17T21:21:36,411           # Package would be ignored #
2025-09-17T21:21:36,412           ############################
2025-09-17T21:21:36,412           Python recognizes 'pichemist.data.fasta' as an importable package[^1],
2025-09-17T21:21:36,413           but it is absent from setuptools' `packages` configuration.

2025-09-17T21:21:36,414           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-17T21:21:36,414           package, please make sure that 'pichemist.data.fasta' is explicitly added
2025-09-17T21:21:36,415           to the `packages` configuration field.

2025-09-17T21:21:36,416           Alternatively, you can also rely on setuptools' discovery methods
2025-09-17T21:21:36,417           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-17T21:21:36,417           instead of `find_packages(...)`/`find:`).

2025-09-17T21:21:36,418           You can read more about "package discovery" on setuptools documentation page:

2025-09-17T21:21:36,420           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-17T21:21:36,421           If you don't want 'pichemist.data.fasta' to be distributed and are
2025-09-17T21:21:36,421           already explicitly excluding 'pichemist.data.fasta' via
2025-09-17T21:21:36,422           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-17T21:21:36,422           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-17T21:21:36,423           combination with a more fine grained `package-data` configuration.

2025-09-17T21:21:36,424           You can read more about "package data files" on setuptools documentation page:

2025-09-17T21:21:36,425           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-17T21:21:36,426           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-17T21:21:36,427                 even if it does not contain any `.py` files.
2025-09-17T21:21:36,428                 On the other hand, currently there is no concept of package data
2025-09-17T21:21:36,428                 directory, all directories are treated like packages.
2025-09-17T21:21:36,463           ********************************************************************************

2025-09-17T21:21:36,464   !!
2025-09-17T21:21:36,465     check.warn(importable)
2025-09-17T21:21:36,465   /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.
2025-09-17T21:21:36,466   !!

2025-09-17T21:21:36,467           ********************************************************************************
2025-09-17T21:21:36,468           ############################
2025-09-17T21:21:36,468           # Package would be ignored #
2025-09-17T21:21:36,469           ############################
2025-09-17T21:21:36,469           Python recognizes 'pichemist.data.fasta.legacy' as an importable package[^1],
2025-09-17T21:21:36,470           but it is absent from setuptools' `packages` configuration.

2025-09-17T21:21:36,471           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-17T21:21:36,471           package, please make sure that 'pichemist.data.fasta.legacy' is explicitly added
2025-09-17T21:21:36,472           to the `packages` configuration field.

2025-09-17T21:21:36,473           Alternatively, you can also rely on setuptools' discovery methods
2025-09-17T21:21:36,473           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-17T21:21:36,473           instead of `find_packages(...)`/`find:`).

2025-09-17T21:21:36,474           You can read more about "package discovery" on setuptools documentation page:

2025-09-17T21:21:36,475           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-17T21:21:36,476           If you don't want 'pichemist.data.fasta.legacy' to be distributed and are
2025-09-17T21:21:36,477           already explicitly excluding 'pichemist.data.fasta.legacy' via
2025-09-17T21:21:36,477           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-17T21:21:36,478           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-17T21:21:36,478           combination with a more fine grained `package-data` configuration.

2025-09-17T21:21:36,479           You can read more about "package data files" on setuptools documentation page:

2025-09-17T21:21:36,480           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-17T21:21:36,481           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-17T21:21:36,482                 even if it does not contain any `.py` files.
2025-09-17T21:21:36,483                 On the other hand, currently there is no concept of package data
2025-09-17T21:21:36,483                 directory, all directories are treated like packages.
2025-09-17T21:21:36,484           ********************************************************************************

2025-09-17T21:21:36,485   !!
2025-09-17T21:21:36,485     check.warn(importable)
2025-09-17T21:21:36,486   /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.
2025-09-17T21:21:36,486   !!

2025-09-17T21:21:36,487           ********************************************************************************
2025-09-17T21:21:36,488           ############################
2025-09-17T21:21:36,488           # Package would be ignored #
2025-09-17T21:21:36,489           ############################
2025-09-17T21:21:36,489           Python recognizes 'pichemist.data.fasta.original_enriched' as an importable package[^1],
2025-09-17T21:21:36,490           but it is absent from setuptools' `packages` configuration.

2025-09-17T21:21:36,491           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-17T21:21:36,491           package, please make sure that 'pichemist.data.fasta.original_enriched' is explicitly added
2025-09-17T21:21:36,492           to the `packages` configuration field.

2025-09-17T21:21:36,493           Alternatively, you can also rely on setuptools' discovery methods
2025-09-17T21:21:36,493           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-17T21:21:36,494           instead of `find_packages(...)`/`find:`).

2025-09-17T21:21:36,496           You can read more about "package discovery" on setuptools documentation page:

2025-09-17T21:21:36,497           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-17T21:21:36,498           If you don't want 'pichemist.data.fasta.original_enriched' to be distributed and are
2025-09-17T21:21:36,498           already explicitly excluding 'pichemist.data.fasta.original_enriched' via
2025-09-17T21:21:36,499           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-17T21:21:36,500           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-17T21:21:36,500           combination with a more fine grained `package-data` configuration.

2025-09-17T21:21:36,501           You can read more about "package data files" on setuptools documentation page:

2025-09-17T21:21:36,502           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-17T21:21:36,503           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-17T21:21:36,503                 even if it does not contain any `.py` files.
2025-09-17T21:21:36,504                 On the other hand, currently there is no concept of package data
2025-09-17T21:21:36,504                 directory, all directories are treated like packages.
2025-09-17T21:21:36,504           ********************************************************************************

2025-09-17T21:21:36,505   !!
2025-09-17T21:21:36,506     check.warn(importable)
2025-09-17T21:21:36,506   /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.
2025-09-17T21:21:36,506   !!

2025-09-17T21:21:36,507           ********************************************************************************
2025-09-17T21:21:36,508           ############################
2025-09-17T21:21:36,508           # Package would be ignored #
2025-09-17T21:21:36,509           ############################
2025-09-17T21:21:36,509           Python recognizes 'pichemist.data.fasta.original_short' as an importable package[^1],
2025-09-17T21:21:36,509           but it is absent from setuptools' `packages` configuration.

2025-09-17T21:21:36,510           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-17T21:21:36,511           package, please make sure that 'pichemist.data.fasta.original_short' is explicitly added
2025-09-17T21:21:36,511           to the `packages` configuration field.

2025-09-17T21:21:36,512           Alternatively, you can also rely on setuptools' discovery methods
2025-09-17T21:21:36,513           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-17T21:21:36,513           instead of `find_packages(...)`/`find:`).

2025-09-17T21:21:36,514           You can read more about "package discovery" on setuptools documentation page:

2025-09-17T21:21:36,515           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-17T21:21:36,516           If you don't want 'pichemist.data.fasta.original_short' to be distributed and are
2025-09-17T21:21:36,517           already explicitly excluding 'pichemist.data.fasta.original_short' via
2025-09-17T21:21:36,518           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-17T21:21:36,518           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-17T21:21:36,519           combination with a more fine grained `package-data` configuration.

2025-09-17T21:21:36,520           You can read more about "package data files" on setuptools documentation page:

2025-09-17T21:21:36,521           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-17T21:21:36,523           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-17T21:21:36,524                 even if it does not contain any `.py` files.
2025-09-17T21:21:36,524                 On the other hand, currently there is no concept of package data
2025-09-17T21:21:36,525                 directory, all directories are treated like packages.
2025-09-17T21:21:36,525           ********************************************************************************

2025-09-17T21:21:36,527   !!
2025-09-17T21:21:36,527     check.warn(importable)
2025-09-17T21:21:36,527   /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.
2025-09-17T21:21:36,528   !!

2025-09-17T21:21:36,529           ********************************************************************************
2025-09-17T21:21:36,529           ############################
2025-09-17T21:21:36,529           # Package would be ignored #
2025-09-17T21:21:36,530           ############################
2025-09-17T21:21:36,530           Python recognizes 'pichemist.data.fasta.standardised' as an importable package[^1],
2025-09-17T21:21:36,531           but it is absent from setuptools' `packages` configuration.

2025-09-17T21:21:36,531           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-17T21:21:36,532           package, please make sure that 'pichemist.data.fasta.standardised' is explicitly added
2025-09-17T21:21:36,532           to the `packages` configuration field.

2025-09-17T21:21:36,533           Alternatively, you can also rely on setuptools' discovery methods
2025-09-17T21:21:36,534           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-17T21:21:36,534           instead of `find_packages(...)`/`find:`).

2025-09-17T21:21:36,535           You can read more about "package discovery" on setuptools documentation page:

2025-09-17T21:21:36,536           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-17T21:21:36,537           If you don't want 'pichemist.data.fasta.standardised' to be distributed and are
2025-09-17T21:21:36,537           already explicitly excluding 'pichemist.data.fasta.standardised' via
2025-09-17T21:21:36,538           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-17T21:21:36,538           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-17T21:21:36,539           combination with a more fine grained `package-data` configuration.

2025-09-17T21:21:36,540           You can read more about "package data files" on setuptools documentation page:

2025-09-17T21:21:36,541           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-17T21:21:36,542           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-17T21:21:36,543                 even if it does not contain any `.py` files.
2025-09-17T21:21:36,544                 On the other hand, currently there is no concept of package data
2025-09-17T21:21:36,544                 directory, all directories are treated like packages.
2025-09-17T21:21:36,545           ********************************************************************************

2025-09-17T21:21:36,546   !!
2025-09-17T21:21:36,546     check.warn(importable)
2025-09-17T21:21:36,547   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pichemist.data.smarts' is absent from the `packages` configuration.
2025-09-17T21:21:36,547   !!

2025-09-17T21:21:36,548           ********************************************************************************
2025-09-17T21:21:36,549           ############################
2025-09-17T21:21:36,549           # Package would be ignored #
2025-09-17T21:21:36,550           ############################
2025-09-17T21:21:36,551           Python recognizes 'pichemist.data.smarts' as an importable package[^1],
2025-09-17T21:21:36,551           but it is absent from setuptools' `packages` configuration.

2025-09-17T21:21:36,552           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-17T21:21:36,553           package, please make sure that 'pichemist.data.smarts' is explicitly added
2025-09-17T21:21:36,553           to the `packages` configuration field.

2025-09-17T21:21:36,555           Alternatively, you can also rely on setuptools' discovery methods
2025-09-17T21:21:36,555           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-17T21:21:36,556           instead of `find_packages(...)`/`find:`).

2025-09-17T21:21:36,557           You can read more about "package discovery" on setuptools documentation page:

2025-09-17T21:21:36,558           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-17T21:21:36,558           If you don't want 'pichemist.data.smarts' to be distributed and are
2025-09-17T21:21:36,559           already explicitly excluding 'pichemist.data.smarts' via
2025-09-17T21:21:36,559           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-17T21:21:36,560           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-17T21:21:36,560           combination with a more fine grained `package-data` configuration.

2025-09-17T21:21:36,561           You can read more about "package data files" on setuptools documentation page:

2025-09-17T21:21:36,562           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-17T21:21:36,564           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-17T21:21:36,564                 even if it does not contain any `.py` files.
2025-09-17T21:21:36,565                 On the other hand, currently there is no concept of package data
2025-09-17T21:21:36,565                 directory, all directories are treated like packages.
2025-09-17T21:21:36,566           ********************************************************************************

2025-09-17T21:21:36,567   !!
2025-09-17T21:21:36,567     check.warn(importable)
2025-09-17T21:21:36,568   /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.
2025-09-17T21:21:36,568   !!

2025-09-17T21:21:36,569           ********************************************************************************
2025-09-17T21:21:36,570           ############################
2025-09-17T21:21:36,571           # Package would be ignored #
2025-09-17T21:21:36,571           ############################
2025-09-17T21:21:36,572           Python recognizes 'pichemist.data.smarts.legacy' as an importable package[^1],
2025-09-17T21:21:36,572           but it is absent from setuptools' `packages` configuration.

2025-09-17T21:21:36,573           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-17T21:21:36,574           package, please make sure that 'pichemist.data.smarts.legacy' is explicitly added
2025-09-17T21:21:36,574           to the `packages` configuration field.

2025-09-17T21:21:36,575           Alternatively, you can also rely on setuptools' discovery methods
2025-09-17T21:21:36,576           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-17T21:21:36,576           instead of `find_packages(...)`/`find:`).

2025-09-17T21:21:36,578           You can read more about "package discovery" on setuptools documentation page:

2025-09-17T21:21:36,579           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-17T21:21:36,580           If you don't want 'pichemist.data.smarts.legacy' to be distributed and are
2025-09-17T21:21:36,580           already explicitly excluding 'pichemist.data.smarts.legacy' via
2025-09-17T21:21:36,581           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-17T21:21:36,581           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-17T21:21:36,582           combination with a more fine grained `package-data` configuration.

2025-09-17T21:21:36,583           You can read more about "package data files" on setuptools documentation page:

2025-09-17T21:21:36,584           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-17T21:21:36,585           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-17T21:21:36,586                 even if it does not contain any `.py` files.
2025-09-17T21:21:36,587                 On the other hand, currently there is no concept of package data
2025-09-17T21:21:36,587                 directory, all directories are treated like packages.
2025-09-17T21:21:36,588           ********************************************************************************

2025-09-17T21:21:36,588   !!
2025-09-17T21:21:36,589     check.warn(importable)
2025-09-17T21:21:36,589   /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.
2025-09-17T21:21:36,589   !!

2025-09-17T21:21:36,590           ********************************************************************************
2025-09-17T21:21:36,591           ############################
2025-09-17T21:21:36,591           # Package would be ignored #
2025-09-17T21:21:36,592           ############################
2025-09-17T21:21:36,592           Python recognizes 'pichemist.data.smarts.standardised' as an importable package[^1],
2025-09-17T21:21:36,593           but it is absent from setuptools' `packages` configuration.

2025-09-17T21:21:36,594           This leads to an ambiguous overall configuration. If you want to distribute this
2025-09-17T21:21:36,594           package, please make sure that 'pichemist.data.smarts.standardised' is explicitly added
2025-09-17T21:21:36,595           to the `packages` configuration field.

2025-09-17T21:21:36,596           Alternatively, you can also rely on setuptools' discovery methods
2025-09-17T21:21:36,596           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-09-17T21:21:36,597           instead of `find_packages(...)`/`find:`).

2025-09-17T21:21:36,598           You can read more about "package discovery" on setuptools documentation page:

2025-09-17T21:21:36,599           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-09-17T21:21:36,600           If you don't want 'pichemist.data.smarts.standardised' to be distributed and are
2025-09-17T21:21:36,600           already explicitly excluding 'pichemist.data.smarts.standardised' via
2025-09-17T21:21:36,601           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-09-17T21:21:36,601           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-09-17T21:21:36,602           combination with a more fine grained `package-data` configuration.

2025-09-17T21:21:36,603           You can read more about "package data files" on setuptools documentation page:

2025-09-17T21:21:36,604           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-09-17T21:21:36,606           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-09-17T21:21:36,606                 even if it does not contain any `.py` files.
2025-09-17T21:21:36,607                 On the other hand, currently there is no concept of package data
2025-09-17T21:21:36,607                 directory, all directories are treated like packages.
2025-09-17T21:21:36,608           ********************************************************************************

2025-09-17T21:21:36,609   !!
2025-09-17T21:21:36,609     check.warn(importable)
2025-09-17T21:21:36,610   creating build/lib/pichemist/data/fasta
2025-09-17T21:21:36,610   copying pichemist/data/fasta/convert_legacy_gauci_to_original_and_standardised.py -> build/lib/pichemist/data/fasta
2025-09-17T21:21:36,611   copying pichemist/data/fasta/convert_legacy_promost_into_standardised.py -> build/lib/pichemist/data/fasta
2025-09-17T21:21:36,611   copying pichemist/data/fasta/convert_legacy_short_set_to_original.py -> build/lib/pichemist/data/fasta
2025-09-17T21:21:36,612   copying pichemist/data/fasta/convert_original_short_set_to_standardised.py -> build/lib/pichemist/data/fasta
2025-09-17T21:21:36,613   copying pichemist/data/fasta/legacy_conversion.py -> build/lib/pichemist/data/fasta
2025-09-17T21:21:36,613   creating build/lib/pichemist/data/fasta/legacy
2025-09-17T21:21:36,614   copying pichemist/data/fasta/legacy/aa_legend.tsv -> build/lib/pichemist/data/fasta/legacy
2025-09-17T21:21:36,615   copying pichemist/data/fasta/legacy/gauci.py -> build/lib/pichemist/data/fasta/legacy
2025-09-17T21:21:36,615   copying pichemist/data/fasta/legacy/promost.py -> build/lib/pichemist/data/fasta/legacy
2025-09-17T21:21:36,615   copying pichemist/data/fasta/legacy/short_pka_sets.py -> build/lib/pichemist/data/fasta/legacy
2025-09-17T21:21:36,616   creating build/lib/pichemist/data/fasta/original_enriched
2025-09-17T21:21:36,616   copying pichemist/data/fasta/original_enriched/pka_set_gauci_original.json -> build/lib/pichemist/data/fasta/original_enriched
2025-09-17T21:21:36,617   creating build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,617   copying pichemist/data/fasta/original_short/pka_set_bjellqvist_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,618   copying pichemist/data/fasta/original_short/pka_set_dawson_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,618   copying pichemist/data/fasta/original_short/pka_set_dtaselect_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,619   copying pichemist/data/fasta/original_short/pka_set_emboss_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,619   copying pichemist/data/fasta/original_short/pka_set_grimsley_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,620   copying pichemist/data/fasta/original_short/pka_set_ipc2_peptide_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,620   copying pichemist/data/fasta/original_short/pka_set_ipc_peptide_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,621   copying pichemist/data/fasta/original_short/pka_set_lehninger_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,621   copying pichemist/data/fasta/original_short/pka_set_nozaki_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,622   copying pichemist/data/fasta/original_short/pka_set_rodwell_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,622   copying pichemist/data/fasta/original_short/pka_set_sillero_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,623   copying pichemist/data/fasta/original_short/pka_set_solomon_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,624   copying pichemist/data/fasta/original_short/pka_set_thurlkill_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,624   copying pichemist/data/fasta/original_short/pka_set_toseland_original.json -> build/lib/pichemist/data/fasta/original_short
2025-09-17T21:21:36,625   creating build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,625   copying pichemist/data/fasta/standardised/pka_set_bjellqvist_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,626   copying pichemist/data/fasta/standardised/pka_set_dawson_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,626   copying pichemist/data/fasta/standardised/pka_set_dtaselect_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,627   copying pichemist/data/fasta/standardised/pka_set_emboss_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,628   copying pichemist/data/fasta/standardised/pka_set_gauci_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,628   copying pichemist/data/fasta/standardised/pka_set_grimsley_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,629   copying pichemist/data/fasta/standardised/pka_set_ipc2_peptide_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,629   copying pichemist/data/fasta/standardised/pka_set_ipc_peptide_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,630   copying pichemist/data/fasta/standardised/pka_set_lehninger_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,631   copying pichemist/data/fasta/standardised/pka_set_nozaki_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,631   copying pichemist/data/fasta/standardised/pka_set_promost_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,631   copying pichemist/data/fasta/standardised/pka_set_rodwell_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,632   copying pichemist/data/fasta/standardised/pka_set_sillero_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,632   copying pichemist/data/fasta/standardised/pka_set_solomon_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,633   copying pichemist/data/fasta/standardised/pka_set_thurlkill_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,633   copying pichemist/data/fasta/standardised/pka_set_toseland_standardised.json -> build/lib/pichemist/data/fasta/standardised
2025-09-17T21:21:36,634   creating build/lib/pichemist/data/smarts
2025-09-17T21:21:36,634   copying pichemist/data/smarts/convert_legacy_aa_smarts_to_standardised.py -> build/lib/pichemist/data/smarts
2025-09-17T21:21:36,634   copying pichemist/data/smarts/convert_legacy_ss_smarts_to_standardised.py -> build/lib/pichemist/data/smarts
2025-09-17T21:21:36,635   creating build/lib/pichemist/data/smarts/legacy
2025-09-17T21:21:36,636   copying pichemist/data/smarts/legacy/smarts_naturalAAs.py -> build/lib/pichemist/data/smarts/legacy
2025-09-17T21:21:36,636   copying pichemist/data/smarts/legacy/smarts_notes.py -> build/lib/pichemist/data/smarts/legacy
2025-09-17T21:21:36,637   copying pichemist/data/smarts/legacy/smarts_pKaMatcher.dat -> build/lib/pichemist/data/smarts/legacy
2025-09-17T21:21:36,637   copying pichemist/data/smarts/legacy/smarts_pKaMatcher.py -> build/lib/pichemist/data/smarts/legacy
2025-09-17T21:21:36,638   creating build/lib/pichemist/data/smarts/standardised
2025-09-17T21:21:36,639   copying pichemist/data/smarts/standardised/aa_smarts_set_standardised.json -> build/lib/pichemist/data/smarts/standardised
2025-09-17T21:21:36,639   copying pichemist/data/smarts/standardised/ss_smarts_set_standardised.json -> build/lib/pichemist/data/smarts/standardised
2025-09-17T21:21:36,650   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-09-17T21:21:36,651   !!

2025-09-17T21:21:36,652           ********************************************************************************
2025-09-17T21:21:36,653           Please avoid running ``setup.py`` directly.
2025-09-17T21:21:36,653           Instead, use pypa/build, pypa/installer or other
2025-09-17T21:21:36,654           standards-based tools.

2025-09-17T21:21:36,655           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-09-17T21:21:36,656           or your builds will no longer be supported.

2025-09-17T21:21:36,657           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-09-17T21:21:36,658           ********************************************************************************

2025-09-17T21:21:36,659   !!
2025-09-17T21:21:36,660     self.initialize_options()
2025-09-17T21:21:36,688   installing to build/bdist.linux-armv7l/wheel
2025-09-17T21:21:36,688   running install
2025-09-17T21:21:36,711   running install_lib
2025-09-17T21:21:36,742   creating build/bdist.linux-armv7l/wheel
2025-09-17T21:21:36,745   creating build/bdist.linux-armv7l/wheel/pichemist
2025-09-17T21:21:36,747   creating build/bdist.linux-armv7l/wheel/pichemist/pka
2025-09-17T21:21:36,748   copying build/lib/pichemist/pka/pkamatcher.py -> build/bdist.linux-armv7l/wheel/./pichemist/pka
2025-09-17T21:21:36,750   copying build/lib/pichemist/pka/utils.py -> build/bdist.linux-armv7l/wheel/./pichemist/pka
2025-09-17T21:21:36,752   copying build/lib/pichemist/pka/acd.py -> build/bdist.linux-armv7l/wheel/./pichemist/pka
2025-09-17T21:21:36,753   copying build/lib/pichemist/pka/__init__.py -> build/bdist.linux-armv7l/wheel/./pichemist/pka
2025-09-17T21:21:36,756   creating build/bdist.linux-armv7l/wheel/pichemist/fasta
2025-09-17T21:21:36,757   copying build/lib/pichemist/fasta/matcher.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta
2025-09-17T21:21:36,759   copying build/lib/pichemist/fasta/pka_sets.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta
2025-09-17T21:21:36,761   copying build/lib/pichemist/fasta/smarts.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta
2025-09-17T21:21:36,763   copying build/lib/pichemist/fasta/scrambler.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta
2025-09-17T21:21:36,764   copying build/lib/pichemist/fasta/helpers.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta
2025-09-17T21:21:36,766   copying build/lib/pichemist/fasta/__init__.py -> build/bdist.linux-armv7l/wheel/./pichemist/fasta
2025-09-17T21:21:36,767   copying build/lib/pichemist/model.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,769   creating build/bdist.linux-armv7l/wheel/pichemist/smarts
2025-09-17T21:21:36,770   copying build/lib/pichemist/smarts/pka_set.py -> build/bdist.linux-armv7l/wheel/./pichemist/smarts
2025-09-17T21:21:36,772   copying build/lib/pichemist/smarts/__init__.py -> build/bdist.linux-armv7l/wheel/./pichemist/smarts
2025-09-17T21:21:36,774   copying build/lib/pichemist/isoelectric.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,776   copying build/lib/pichemist/charges.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,777   copying build/lib/pichemist/utils.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,779   copying build/lib/pichemist/api.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,782   creating build/bdist.linux-armv7l/wheel/pichemist/data
2025-09-17T21:21:36,783   creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta
2025-09-17T21:21:36,785   copying build/lib/pichemist/data/fasta/convert_legacy_promost_into_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta
2025-09-17T21:21:36,787   creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta/original_enriched
2025-09-17T21:21:36,788   copying build/lib/pichemist/data/fasta/original_enriched/pka_set_gauci_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_enriched
2025-09-17T21:21:36,791   creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta/original_short
2025-09-17T21:21:36,792   copying build/lib/pichemist/data/fasta/original_short/pka_set_grimsley_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,794   copying build/lib/pichemist/data/fasta/original_short/pka_set_toseland_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,796   copying build/lib/pichemist/data/fasta/original_short/pka_set_rodwell_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,797   copying build/lib/pichemist/data/fasta/original_short/pka_set_ipc2_peptide_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,799   copying build/lib/pichemist/data/fasta/original_short/pka_set_dawson_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,801   copying build/lib/pichemist/data/fasta/original_short/pka_set_emboss_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,802   copying build/lib/pichemist/data/fasta/original_short/pka_set_dtaselect_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,804   copying build/lib/pichemist/data/fasta/original_short/pka_set_nozaki_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,806   copying build/lib/pichemist/data/fasta/original_short/pka_set_solomon_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,808   copying build/lib/pichemist/data/fasta/original_short/pka_set_bjellqvist_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,810   copying build/lib/pichemist/data/fasta/original_short/pka_set_sillero_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,811   copying build/lib/pichemist/data/fasta/original_short/pka_set_lehninger_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,813   copying build/lib/pichemist/data/fasta/original_short/pka_set_ipc_peptide_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,815   copying build/lib/pichemist/data/fasta/original_short/pka_set_thurlkill_original.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/original_short
2025-09-17T21:21:36,817   creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta/legacy
2025-09-17T21:21:36,818   copying build/lib/pichemist/data/fasta/legacy/gauci.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/legacy
2025-09-17T21:21:36,820   copying build/lib/pichemist/data/fasta/legacy/aa_legend.tsv -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/legacy
2025-09-17T21:21:36,821   copying build/lib/pichemist/data/fasta/legacy/promost.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/legacy
2025-09-17T21:21:36,823   copying build/lib/pichemist/data/fasta/legacy/short_pka_sets.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/legacy
2025-09-17T21:21:36,826   creating build/bdist.linux-armv7l/wheel/pichemist/data/fasta/standardised
2025-09-17T21:21:36,827   copying build/lib/pichemist/data/fasta/standardised/pka_set_nozaki_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,829   copying build/lib/pichemist/data/fasta/standardised/pka_set_solomon_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,831   copying build/lib/pichemist/data/fasta/standardised/pka_set_lehninger_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,833   copying build/lib/pichemist/data/fasta/standardised/pka_set_ipc_peptide_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,836   copying build/lib/pichemist/data/fasta/standardised/pka_set_ipc2_peptide_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,838   copying build/lib/pichemist/data/fasta/standardised/pka_set_bjellqvist_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,840   copying build/lib/pichemist/data/fasta/standardised/pka_set_toseland_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,842   copying build/lib/pichemist/data/fasta/standardised/pka_set_gauci_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,845   copying build/lib/pichemist/data/fasta/standardised/pka_set_sillero_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,847   copying build/lib/pichemist/data/fasta/standardised/pka_set_rodwell_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,849   copying build/lib/pichemist/data/fasta/standardised/pka_set_dawson_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,851   copying build/lib/pichemist/data/fasta/standardised/pka_set_grimsley_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,853   copying build/lib/pichemist/data/fasta/standardised/pka_set_emboss_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,856   copying build/lib/pichemist/data/fasta/standardised/pka_set_dtaselect_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,858   copying build/lib/pichemist/data/fasta/standardised/pka_set_thurlkill_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,860   copying build/lib/pichemist/data/fasta/standardised/pka_set_promost_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta/standardised
2025-09-17T21:21:36,862   copying build/lib/pichemist/data/fasta/convert_legacy_gauci_to_original_and_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta
2025-09-17T21:21:36,864   copying build/lib/pichemist/data/fasta/legacy_conversion.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta
2025-09-17T21:21:36,866   copying build/lib/pichemist/data/fasta/convert_legacy_short_set_to_original.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta
2025-09-17T21:21:36,867   copying build/lib/pichemist/data/fasta/convert_original_short_set_to_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/fasta
2025-09-17T21:21:36,870   creating build/bdist.linux-armv7l/wheel/pichemist/data/smarts
2025-09-17T21:21:36,871   copying build/lib/pichemist/data/smarts/convert_legacy_aa_smarts_to_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts
2025-09-17T21:21:36,873   creating build/bdist.linux-armv7l/wheel/pichemist/data/smarts/legacy
2025-09-17T21:21:36,874   copying build/lib/pichemist/data/smarts/legacy/smarts_naturalAAs.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/legacy
2025-09-17T21:21:36,877   copying build/lib/pichemist/data/smarts/legacy/smarts_notes.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/legacy
2025-09-17T21:21:36,879   copying build/lib/pichemist/data/smarts/legacy/smarts_pKaMatcher.dat -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/legacy
2025-09-17T21:21:36,881   copying build/lib/pichemist/data/smarts/legacy/smarts_pKaMatcher.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/legacy
2025-09-17T21:21:36,883   creating build/bdist.linux-armv7l/wheel/pichemist/data/smarts/standardised
2025-09-17T21:21:36,884   copying build/lib/pichemist/data/smarts/standardised/ss_smarts_set_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/standardised
2025-09-17T21:21:36,887   copying build/lib/pichemist/data/smarts/standardised/aa_smarts_set_standardised.json -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts/standardised
2025-09-17T21:21:36,890   copying build/lib/pichemist/data/smarts/convert_legacy_ss_smarts_to_standardised.py -> build/bdist.linux-armv7l/wheel/./pichemist/data/smarts
2025-09-17T21:21:36,891   copying build/lib/pichemist/config.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,893   copying build/lib/pichemist/io.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,896   copying build/lib/pichemist/core.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,898   copying build/lib/pichemist/cli.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,900   copying build/lib/pichemist/plot.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,902   copying build/lib/pichemist/stats.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,904   copying build/lib/pichemist/__init__.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,905   copying build/lib/pichemist/molecule.py -> build/bdist.linux-armv7l/wheel/./pichemist
2025-09-17T21:21:36,907   running install_egg_info
2025-09-17T21:21:36,940   Copying pichemist.egg-info to build/bdist.linux-armv7l/wheel/./pichemist-2.1.0-py3.11.egg-info
2025-09-17T21:21:36,951   running install_scripts
2025-09-17T21:21:36,963   creating build/bdist.linux-armv7l/wheel/pichemist-2.1.0.dist-info/WHEEL
2025-09-17T21:21:36,966   creating '/tmp/pip-wheel-vvfes9ru/pichemist-2.1.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-09-17T21:21:36,968   adding 'pichemist/__init__.py'
2025-09-17T21:21:36,969   adding 'pichemist/api.py'
2025-09-17T21:21:36,971   adding 'pichemist/charges.py'
2025-09-17T21:21:36,972   adding 'pichemist/cli.py'
2025-09-17T21:21:36,974   adding 'pichemist/config.py'
2025-09-17T21:21:36,975   adding 'pichemist/core.py'
2025-09-17T21:21:36,977   adding 'pichemist/io.py'
2025-09-17T21:21:36,979   adding 'pichemist/isoelectric.py'
2025-09-17T21:21:36,980   adding 'pichemist/model.py'
2025-09-17T21:21:36,982   adding 'pichemist/molecule.py'
2025-09-17T21:21:36,983   adding 'pichemist/plot.py'
2025-09-17T21:21:36,984   adding 'pichemist/stats.py'
2025-09-17T21:21:36,985   adding 'pichemist/utils.py'
2025-09-17T21:21:36,987   adding 'pichemist/data/fasta/convert_legacy_gauci_to_original_and_standardised.py'
2025-09-17T21:21:36,988   adding 'pichemist/data/fasta/convert_legacy_promost_into_standardised.py'
2025-09-17T21:21:36,990   adding 'pichemist/data/fasta/convert_legacy_short_set_to_original.py'
2025-09-17T21:21:36,991   adding 'pichemist/data/fasta/convert_original_short_set_to_standardised.py'
2025-09-17T21:21:36,992   adding 'pichemist/data/fasta/legacy_conversion.py'
2025-09-17T21:21:36,994   adding 'pichemist/data/fasta/legacy/aa_legend.tsv'
2025-09-17T21:21:36,995   adding 'pichemist/data/fasta/legacy/gauci.py'
2025-09-17T21:21:36,996   adding 'pichemist/data/fasta/legacy/promost.py'
2025-09-17T21:21:36,998   adding 'pichemist/data/fasta/legacy/short_pka_sets.py'
2025-09-17T21:21:37,000   adding 'pichemist/data/fasta/original_enriched/pka_set_gauci_original.json'
2025-09-17T21:21:37,002   adding 'pichemist/data/fasta/original_short/pka_set_bjellqvist_original.json'
2025-09-17T21:21:37,003   adding 'pichemist/data/fasta/original_short/pka_set_dawson_original.json'
2025-09-17T21:21:37,004   adding 'pichemist/data/fasta/original_short/pka_set_dtaselect_original.json'
2025-09-17T21:21:37,006   adding 'pichemist/data/fasta/original_short/pka_set_emboss_original.json'
2025-09-17T21:21:37,007   adding 'pichemist/data/fasta/original_short/pka_set_grimsley_original.json'
2025-09-17T21:21:37,008   adding 'pichemist/data/fasta/original_short/pka_set_ipc2_peptide_original.json'
2025-09-17T21:21:37,009   adding 'pichemist/data/fasta/original_short/pka_set_ipc_peptide_original.json'
2025-09-17T21:21:37,010   adding 'pichemist/data/fasta/original_short/pka_set_lehninger_original.json'
2025-09-17T21:21:37,011   adding 'pichemist/data/fasta/original_short/pka_set_nozaki_original.json'
2025-09-17T21:21:37,012   adding 'pichemist/data/fasta/original_short/pka_set_rodwell_original.json'
2025-09-17T21:21:37,013   adding 'pichemist/data/fasta/original_short/pka_set_sillero_original.json'
2025-09-17T21:21:37,015   adding 'pichemist/data/fasta/original_short/pka_set_solomon_original.json'
2025-09-17T21:21:37,016   adding 'pichemist/data/fasta/original_short/pka_set_thurlkill_original.json'
2025-09-17T21:21:37,017   adding 'pichemist/data/fasta/original_short/pka_set_toseland_original.json'
2025-09-17T21:21:37,019   adding 'pichemist/data/fasta/standardised/pka_set_bjellqvist_standardised.json'
2025-09-17T21:21:37,021   adding 'pichemist/data/fasta/standardised/pka_set_dawson_standardised.json'
2025-09-17T21:21:37,022   adding 'pichemist/data/fasta/standardised/pka_set_dtaselect_standardised.json'
2025-09-17T21:21:37,023   adding 'pichemist/data/fasta/standardised/pka_set_emboss_standardised.json'
2025-09-17T21:21:37,025   adding 'pichemist/data/fasta/standardised/pka_set_gauci_standardised.json'
2025-09-17T21:21:37,026   adding 'pichemist/data/fasta/standardised/pka_set_grimsley_standardised.json'
2025-09-17T21:21:37,027   adding 'pichemist/data/fasta/standardised/pka_set_ipc2_peptide_standardised.json'
2025-09-17T21:21:37,028   adding 'pichemist/data/fasta/standardised/pka_set_ipc_peptide_standardised.json'
2025-09-17T21:21:37,030   adding 'pichemist/data/fasta/standardised/pka_set_lehninger_standardised.json'
2025-09-17T21:21:37,031   adding 'pichemist/data/fasta/standardised/pka_set_nozaki_standardised.json'
2025-09-17T21:21:37,032   adding 'pichemist/data/fasta/standardised/pka_set_promost_standardised.json'
2025-09-17T21:21:37,033   adding 'pichemist/data/fasta/standardised/pka_set_rodwell_standardised.json'
2025-09-17T21:21:37,034   adding 'pichemist/data/fasta/standardised/pka_set_sillero_standardised.json'
2025-09-17T21:21:37,036   adding 'pichemist/data/fasta/standardised/pka_set_solomon_standardised.json'
2025-09-17T21:21:37,037   adding 'pichemist/data/fasta/standardised/pka_set_thurlkill_standardised.json'
2025-09-17T21:21:37,038   adding 'pichemist/data/fasta/standardised/pka_set_toseland_standardised.json'
2025-09-17T21:21:37,040   adding 'pichemist/data/smarts/convert_legacy_aa_smarts_to_standardised.py'
2025-09-17T21:21:37,041   adding 'pichemist/data/smarts/convert_legacy_ss_smarts_to_standardised.py'
2025-09-17T21:21:37,043   adding 'pichemist/data/smarts/legacy/smarts_naturalAAs.py'
2025-09-17T21:21:37,044   adding 'pichemist/data/smarts/legacy/smarts_notes.py'
2025-09-17T21:21:37,046   adding 'pichemist/data/smarts/legacy/smarts_pKaMatcher.dat'
2025-09-17T21:21:37,047   adding 'pichemist/data/smarts/legacy/smarts_pKaMatcher.py'
2025-09-17T21:21:37,050   adding 'pichemist/data/smarts/standardised/aa_smarts_set_standardised.json'
2025-09-17T21:21:37,051   adding 'pichemist/data/smarts/standardised/ss_smarts_set_standardised.json'
2025-09-17T21:21:37,053   adding 'pichemist/fasta/__init__.py'
2025-09-17T21:21:37,054   adding 'pichemist/fasta/helpers.py'
2025-09-17T21:21:37,056   adding 'pichemist/fasta/matcher.py'
2025-09-17T21:21:37,057   adding 'pichemist/fasta/pka_sets.py'
2025-09-17T21:21:37,059   adding 'pichemist/fasta/scrambler.py'
2025-09-17T21:21:37,060   adding 'pichemist/fasta/smarts.py'
2025-09-17T21:21:37,061   adding 'pichemist/pka/__init__.py'
2025-09-17T21:21:37,063   adding 'pichemist/pka/acd.py'
2025-09-17T21:21:37,064   adding 'pichemist/pka/pkamatcher.py'
2025-09-17T21:21:37,066   adding 'pichemist/pka/utils.py'
2025-09-17T21:21:37,067   adding 'pichemist/smarts/__init__.py'
2025-09-17T21:21:37,068   adding 'pichemist/smarts/pka_set.py'
2025-09-17T21:21:37,071   adding 'pichemist-2.1.0.dist-info/licenses/LICENSE'
2025-09-17T21:21:37,072   adding 'pichemist-2.1.0.dist-info/METADATA'
2025-09-17T21:21:37,073   adding 'pichemist-2.1.0.dist-info/WHEEL'
2025-09-17T21:21:37,074   adding 'pichemist-2.1.0.dist-info/entry_points.txt'
2025-09-17T21:21:37,075   adding 'pichemist-2.1.0.dist-info/top_level.txt'
2025-09-17T21:21:37,077   adding 'pichemist-2.1.0.dist-info/RECORD'
2025-09-17T21:21:37,080   removing build/bdist.linux-armv7l/wheel
2025-09-17T21:21:37,208   Building wheel for pichemist (setup.py): finished with status 'done'
2025-09-17T21:21:37,211   Created wheel for pichemist: filename=pichemist-2.1.0-py3-none-any.whl size=65626 sha256=b45c744354a1f1b18aae6d629193386f17a2c07a3ff5e5574aca8d96bb2a2b14
2025-09-17T21:21:37,212   Stored in directory: /tmp/pip-ephem-wheel-cache-zanvi8zo/wheels/d4/6d/3f/b285e229254af29a63f662d645f590f2fa88f58bb0745c7376
2025-09-17T21:21:37,225 Successfully built pichemist
2025-09-17T21:21:37,230 Removed build tracker: '/tmp/pip-build-tracker-xsheoyih'