2024-01-21T01:55:38,833 Created temporary directory: /tmp/pip-build-tracker-_r42v99n
2024-01-21T01:55:38,834 Initialized build tracking at /tmp/pip-build-tracker-_r42v99n
2024-01-21T01:55:38,835 Created build tracker: /tmp/pip-build-tracker-_r42v99n
2024-01-21T01:55:38,835 Entered build tracker: /tmp/pip-build-tracker-_r42v99n
2024-01-21T01:55:38,836 Created temporary directory: /tmp/pip-wheel-ibrlppq4
2024-01-21T01:55:38,839 Created temporary directory: /tmp/pip-ephem-wheel-cache-66q9r__y
2024-01-21T01:55:38,861 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-01-21T01:55:38,865 2 location(s) to search for versions of shephard:
2024-01-21T01:55:38,865 * https://pypi.org/simple/shephard/
2024-01-21T01:55:38,865 * https://www.piwheels.org/simple/shephard/
2024-01-21T01:55:38,866 Fetching project page and analyzing links: https://pypi.org/simple/shephard/
2024-01-21T01:55:38,866 Getting page https://pypi.org/simple/shephard/
2024-01-21T01:55:38,868 Found index url https://pypi.org/simple/
2024-01-21T01:55:39,080 Fetched page https://pypi.org/simple/shephard/ as application/vnd.pypi.simple.v1+json
2024-01-21T01:55:39,083   Found link https://files.pythonhosted.org/packages/a9/95/cbdbdeb72c0c4970872dc8b61c9df622274cc80602640b478e234c921234/shephard-0.1.5.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.5
2024-01-21T01:55:39,083   Found link https://files.pythonhosted.org/packages/e9/11/69a637d6d4e0cb3a2addc9c06587e781747dfee014076fdaab76d466c46f/shephard-0.1.7.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.7
2024-01-21T01:55:39,084   Found link https://files.pythonhosted.org/packages/b7/90/ea0b27088b3586d48ecaaae9743f8289d28c8e602c4aee5bb4e342b06fc5/shephard-0.1.8.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.8
2024-01-21T01:55:39,085   Found link https://files.pythonhosted.org/packages/2d/0b/2c408626a7f199cb04f61d0fffb3372420ad5564e6bffb942646d140232a/shephard-0.1.12.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.12
2024-01-21T01:55:39,085   Found link https://files.pythonhosted.org/packages/60/78/e58f5c608c7cc8363648b8466f262582a7de95a0331f7b3e87085cf31179/shephard-0.1.14.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.14
2024-01-21T01:55:39,086   Found link https://files.pythonhosted.org/packages/78/01/9fc9805f42e59bdf8a00197d349471405e1f27c254562ef81a79f0c67a18/shephard-0.1.15.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.15
2024-01-21T01:55:39,087   Found link https://files.pythonhosted.org/packages/c6/9c/5920ae7fe8ea8af0aa79d7d2554018f6408462d68ac30b501933c9870bc9/shephard-0.1.16.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.16
2024-01-21T01:55:39,088   Found link https://files.pythonhosted.org/packages/b9/7c/03b2d14b68bd74d6dbdef3acd2a59faa9eebb74bc9b5bd623488ae60bf0c/shephard-0.1.17.tar.gz (from https://pypi.org/simple/shephard/), version: 0.1.17
2024-01-21T01:55:39,089   Found link https://files.pythonhosted.org/packages/78/a1/eda32772db5f73f89f29c1827f159ee9715a2adb6c0cd7d4d8272fde7c0a/shephard-0.1.20.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.7,<3.12.0), version: 0.1.20
2024-01-21T01:55:39,090   Found link https://files.pythonhosted.org/packages/1d/74/63cf0dc536cee0215cdee8ea059f7fa2207748646d24e93de829ac0f9b1f/shephard-0.1.21.tar.gz (from https://pypi.org/simple/shephard/) (requires-python:>=3.7,<3.12.0), version: 0.1.21
2024-01-21T01:55:39,091 Fetching project page and analyzing links: https://www.piwheels.org/simple/shephard/
2024-01-21T01:55:39,092 Getting page https://www.piwheels.org/simple/shephard/
2024-01-21T01:55:39,093 Found index url https://www.piwheels.org/simple/
2024-01-21T01:55:39,252 Fetched page https://www.piwheels.org/simple/shephard/ as text/html
2024-01-21T01:55:39,256   Skipping link: No binaries permitted for shephard: https://www.piwheels.org/simple/shephard/shephard-0.1.20-py3-none-any.whl#sha256=24e0e6400e28f09571d88701fe01ae333e945fde39dac06662db18acf07102f7 (from https://www.piwheels.org/simple/shephard/) (requires-python:>=3.7,<3.12.0)
2024-01-21T01:55:39,256   Skipping link: No binaries permitted for shephard: https://www.piwheels.org/simple/shephard/shephard-0.1.17-py3-none-any.whl#sha256=e58970e02d8a29858bffaa02f2b81a682a9ff647ab2d40add23077b69f3ac021 (from https://www.piwheels.org/simple/shephard/)
2024-01-21T01:55:39,257   Skipping link: No binaries permitted for shephard: https://www.piwheels.org/simple/shephard/shephard-0.1.16-py3-none-any.whl#sha256=f8e78c819d4b0150399cc6bb2176f78cba05e409f65559ce80fd765577c27f81 (from https://www.piwheels.org/simple/shephard/)
2024-01-21T01:55:39,258   Skipping link: No binaries permitted for shephard: https://www.piwheels.org/simple/shephard/shephard-0.1.15-py3-none-any.whl#sha256=79ddd35e1cf2c5fc12afbbb7ccd13a338a58db5b7af8b2777c70a6ec6c6a5e6f (from https://www.piwheels.org/simple/shephard/)
2024-01-21T01:55:39,258   Skipping link: No binaries permitted for shephard: https://www.piwheels.org/simple/shephard/shephard-0.1.14-py3-none-any.whl#sha256=475a3c0e8212f4d337f0f1dc4abe953595d119c3b46c8cc25fcc63502c39ac2d (from https://www.piwheels.org/simple/shephard/)
2024-01-21T01:55:39,259   Skipping link: No binaries permitted for shephard: https://www.piwheels.org/simple/shephard/shephard-0.1.12-py3-none-any.whl#sha256=11352de9001ada56ef480863bdad4b36727295a16dfd6bdbbb8b4c13523d07ba (from https://www.piwheels.org/simple/shephard/)
2024-01-21T01:55:39,259   Skipping link: No binaries permitted for shephard: https://www.piwheels.org/simple/shephard/shephard-0.1.8-py3-none-any.whl#sha256=affda4c08aba9e71908aa718a3fdb9851faff0a49135550c7741cbeb0d804582 (from https://www.piwheels.org/simple/shephard/)
2024-01-21T01:55:39,260   Skipping link: No binaries permitted for shephard: https://www.piwheels.org/simple/shephard/shephard-0.1.7-py3-none-any.whl#sha256=e515f924da74d106bd56b75ebb3d14350dfd59ecae19d4004c155b7894558ee9 (from https://www.piwheels.org/simple/shephard/)
2024-01-21T01:55:39,260   Skipping link: No binaries permitted for shephard: https://www.piwheels.org/simple/shephard/shephard-0.1.5-py3-none-any.whl#sha256=920236db73af811e8085b5527ca1713d3434695a2dc7a8a4da603b7034a40f67 (from https://www.piwheels.org/simple/shephard/)
2024-01-21T01:55:39,261 Skipping link: not a file: https://www.piwheels.org/simple/shephard/
2024-01-21T01:55:39,261 Skipping link: not a file: https://pypi.org/simple/shephard/
2024-01-21T01:55:39,281 Given no hashes to check 1 links for project 'shephard': discarding no candidates
2024-01-21T01:55:39,298 Collecting shephard==0.1.21
2024-01-21T01:55:39,301   Created temporary directory: /tmp/pip-unpack-sblhaq8z
2024-01-21T01:55:39,510   Downloading shephard-0.1.21.tar.gz (203 kB)
2024-01-21T01:55:39,827   Added shephard==0.1.21 from https://files.pythonhosted.org/packages/1d/74/63cf0dc536cee0215cdee8ea059f7fa2207748646d24e93de829ac0f9b1f/shephard-0.1.21.tar.gz to build tracker '/tmp/pip-build-tracker-_r42v99n'
2024-01-21T01:55:39,829   Running setup.py (path:/tmp/pip-wheel-ibrlppq4/shephard_efa5c26074454a8cb90c9d588194f54a/setup.py) egg_info for package shephard
2024-01-21T01:55:39,831   Created temporary directory: /tmp/pip-pip-egg-info-o0rpse10
2024-01-21T01:55:39,831   Preparing metadata (setup.py): started
2024-01-21T01:55:39,832   Running command python setup.py egg_info
2024-01-21T01:55:40,897   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:314: InformationOnly: Normalizing 'v0.1.21' to '0.1.21'
2024-01-21T01:55:40,897     self.metadata.version = self._normalize_version(self.metadata.version)
2024-01-21T01:55:40,959   running egg_info
2024-01-21T01:55:40,960   creating /tmp/pip-pip-egg-info-o0rpse10/shephard.egg-info
2024-01-21T01:55:40,984   writing /tmp/pip-pip-egg-info-o0rpse10/shephard.egg-info/PKG-INFO
2024-01-21T01:55:40,988   writing dependency_links to /tmp/pip-pip-egg-info-o0rpse10/shephard.egg-info/dependency_links.txt
2024-01-21T01:55:40,990   writing requirements to /tmp/pip-pip-egg-info-o0rpse10/shephard.egg-info/requires.txt
2024-01-21T01:55:40,991   writing top-level names to /tmp/pip-pip-egg-info-o0rpse10/shephard.egg-info/top_level.txt
2024-01-21T01:55:40,993   writing manifest file '/tmp/pip-pip-egg-info-o0rpse10/shephard.egg-info/SOURCES.txt'
2024-01-21T01:55:41,048   reading manifest file '/tmp/pip-pip-egg-info-o0rpse10/shephard.egg-info/SOURCES.txt'
2024-01-21T01:55:41,050   reading manifest template 'MANIFEST.in'
2024-01-21T01:55:41,058   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2024-01-21T01:55:41,058   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2024-01-21T01:55:41,059   warning: no previously-included files matching '*.so' found anywhere in distribution
2024-01-21T01:55:41,060   adding license file 'LICENSE'
2024-01-21T01:55:41,064   writing manifest file '/tmp/pip-pip-egg-info-o0rpse10/shephard.egg-info/SOURCES.txt'
2024-01-21T01:55:41,172   Preparing metadata (setup.py): finished with status 'done'
2024-01-21T01:55:41,176   Source in /tmp/pip-wheel-ibrlppq4/shephard_efa5c26074454a8cb90c9d588194f54a has version 0.1.21, which satisfies requirement shephard==0.1.21 from https://files.pythonhosted.org/packages/1d/74/63cf0dc536cee0215cdee8ea059f7fa2207748646d24e93de829ac0f9b1f/shephard-0.1.21.tar.gz
2024-01-21T01:55:41,177   Removed shephard==0.1.21 from https://files.pythonhosted.org/packages/1d/74/63cf0dc536cee0215cdee8ea059f7fa2207748646d24e93de829ac0f9b1f/shephard-0.1.21.tar.gz from build tracker '/tmp/pip-build-tracker-_r42v99n'
2024-01-21T01:55:41,183 Created temporary directory: /tmp/pip-unpack-aindaqe2
2024-01-21T01:55:41,185 Created temporary directory: /tmp/pip-unpack-dgim9krt
2024-01-21T01:55:41,190 Building wheels for collected packages: shephard
2024-01-21T01:55:41,194   Created temporary directory: /tmp/pip-wheel-sn7jljh_
2024-01-21T01:55:41,195   Building wheel for shephard (setup.py): started
2024-01-21T01:55:41,196   Destination directory: /tmp/pip-wheel-sn7jljh_
2024-01-21T01:55:41,196   Running command python setup.py bdist_wheel
2024-01-21T01:55:42,162   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:314: InformationOnly: Normalizing 'v0.1.21' to '0.1.21'
2024-01-21T01:55:42,163     self.metadata.version = self._normalize_version(self.metadata.version)
2024-01-21T01:55:42,215   running bdist_wheel
2024-01-21T01:55:42,307   running build
2024-01-21T01:55:42,308   running build_py
2024-01-21T01:55:42,313   creating build
2024-01-21T01:55:42,314   creating build/lib
2024-01-21T01:55:42,315   creating build/lib/shephard
2024-01-21T01:55:42,316   copying shephard/proteome.py -> build/lib/shephard
2024-01-21T01:55:42,319   copying shephard/sequence_utilities.py -> build/lib/shephard
2024-01-21T01:55:42,321   copying shephard/domain.py -> build/lib/shephard
2024-01-21T01:55:42,323   copying shephard/site.py -> build/lib/shephard
2024-01-21T01:55:42,325   copying shephard/general_utilities.py -> build/lib/shephard
2024-01-21T01:55:42,327   copying shephard/protein.py -> build/lib/shephard
2024-01-21T01:55:42,331   copying shephard/__init__.py -> build/lib/shephard
2024-01-21T01:55:42,332   copying shephard/_version.py -> build/lib/shephard
2024-01-21T01:55:42,334   copying shephard/track.py -> build/lib/shephard
2024-01-21T01:55:42,337   copying shephard/exceptions.py -> build/lib/shephard
2024-01-21T01:55:42,338   copying shephard/test_domains_sites.py -> build/lib/shephard
2024-01-21T01:55:42,340   creating build/lib/shephard/tools
2024-01-21T01:55:42,341   copying shephard/tools/domain_tools.py -> build/lib/shephard/tools
2024-01-21T01:55:42,344   copying shephard/tools/track_tools.py -> build/lib/shephard/tools
2024-01-21T01:55:42,346   copying shephard/tools/sequence_tools.py -> build/lib/shephard/tools
2024-01-21T01:55:42,347   copying shephard/tools/site_tools.py -> build/lib/shephard/tools
2024-01-21T01:55:42,349   copying shephard/tools/__init__.py -> build/lib/shephard/tools
2024-01-21T01:55:42,351   copying shephard/tools/experimental.py -> build/lib/shephard/tools
2024-01-21T01:55:42,354   creating build/lib/shephard/tests
2024-01-21T01:55:42,354   copying shephard/tests/test_shephard.py -> build/lib/shephard/tests
2024-01-21T01:55:42,356   copying shephard/tests/example_test_function.py -> build/lib/shephard/tests
2024-01-21T01:55:42,358   copying shephard/tests/test_ProteinInterface.py -> build/lib/shephard/tests
2024-01-21T01:55:42,360   copying shephard/tests/test_sequence_tools.py -> build/lib/shephard/tests
2024-01-21T01:55:42,361   copying shephard/tests/test_interfaces.py -> build/lib/shephard/tests
2024-01-21T01:55:42,363   copying shephard/tests/test_SiteInterface.py -> build/lib/shephard/tests
2024-01-21T01:55:42,364   copying shephard/tests/test_api_metapredict.py -> build/lib/shephard/tests
2024-01-21T01:55:42,366   copying shephard/tests/test_ProteinAttributesInterface.py -> build/lib/shephard/tests
2024-01-21T01:55:42,368   copying shephard/tests/test_tracks.py -> build/lib/shephard/tests
2024-01-21T01:55:42,369   copying shephard/tests/test_protein.py -> build/lib/shephard/tests
2024-01-21T01:55:42,372   copying shephard/tests/__init__.py -> build/lib/shephard/tests
2024-01-21T01:55:42,373   copying shephard/tests/test_DomainInterface.py -> build/lib/shephard/tests
2024-01-21T01:55:42,375   copying shephard/tests/test_sites.py -> build/lib/shephard/tests
2024-01-21T01:55:42,377   copying shephard/tests/conftest.py -> build/lib/shephard/tests
2024-01-21T01:55:42,378   copying shephard/tests/test_protein_site_functions.py -> build/lib/shephard/tests
2024-01-21T01:55:42,380   copying shephard/tests/test_apis_fasta.py -> build/lib/shephard/tests
2024-01-21T01:55:42,382   copying shephard/tests/test_si_sites.py -> build/lib/shephard/tests
2024-01-21T01:55:42,384   copying shephard/tests/test_domain_tools.py -> build/lib/shephard/tests
2024-01-21T01:55:42,386   copying shephard/tests/test_si_domains.py -> build/lib/shephard/tests
2024-01-21T01:55:42,388   copying shephard/tests/test_add_remove_annotations.py -> build/lib/shephard/tests
2024-01-21T01:55:42,390   copying shephard/tests/test_proteome.py -> build/lib/shephard/tests
2024-01-21T01:55:42,392   copying shephard/tests/test_domains.py -> build/lib/shephard/tests
2024-01-21T01:55:42,394   copying shephard/tests/test_logic.py -> build/lib/shephard/tests
2024-01-21T01:55:42,395   copying shephard/tests/test_TrackInterface.py -> build/lib/shephard/tests
2024-01-21T01:55:42,397   copying shephard/tests/test_track_tools.py -> build/lib/shephard/tests
2024-01-21T01:55:42,399   copying shephard/tests/test_si_tracks.py -> build/lib/shephard/tests
2024-01-21T01:55:42,402   creating build/lib/shephard/apis
2024-01-21T01:55:42,402   copying shephard/apis/metapredict_api.py -> build/lib/shephard/apis
2024-01-21T01:55:42,405   copying shephard/apis/fasta.py -> build/lib/shephard/apis
2024-01-21T01:55:42,407   copying shephard/apis/__init__.py -> build/lib/shephard/apis
2024-01-21T01:55:42,409   copying shephard/apis/uniprot.py -> build/lib/shephard/apis
2024-01-21T01:55:42,411   creating build/lib/shephard/interfaces
2024-01-21T01:55:42,412   copying shephard/interfaces/si_sites.py -> build/lib/shephard/interfaces
2024-01-21T01:55:42,415   copying shephard/interfaces/si_protein_attributes.py -> build/lib/shephard/interfaces
2024-01-21T01:55:42,417   copying shephard/interfaces/si_tracks.py -> build/lib/shephard/interfaces
2024-01-21T01:55:42,420   copying shephard/interfaces/__init__.py -> build/lib/shephard/interfaces
2024-01-21T01:55:42,422   copying shephard/interfaces/interface_tools.py -> build/lib/shephard/interfaces
2024-01-21T01:55:42,424   copying shephard/interfaces/si_domains.py -> build/lib/shephard/interfaces
2024-01-21T01:55:42,426   copying shephard/interfaces/si_proteins.py -> build/lib/shephard/interfaces
2024-01-21T01:55:42,428   running egg_info
2024-01-21T01:55:42,482   writing shephard.egg-info/PKG-INFO
2024-01-21T01:55:42,485   writing dependency_links to shephard.egg-info/dependency_links.txt
2024-01-21T01:55:42,486   writing requirements to shephard.egg-info/requires.txt
2024-01-21T01:55:42,488   writing top-level names to shephard.egg-info/top_level.txt
2024-01-21T01:55:42,518   reading manifest file 'shephard.egg-info/SOURCES.txt'
2024-01-21T01:55:42,522   reading manifest template 'MANIFEST.in'
2024-01-21T01:55:42,529   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2024-01-21T01:55:42,530   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2024-01-21T01:55:42,531   warning: no previously-included files matching '*.so' found anywhere in distribution
2024-01-21T01:55:42,531   adding license file 'LICENSE'
2024-01-21T01:55:42,538   writing manifest file 'shephard.egg-info/SOURCES.txt'
2024-01-21T01:55:42,540   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'shephard.data' is absent from the `packages` configuration.
2024-01-21T01:55:42,541   !!

2024-01-21T01:55:42,542           ********************************************************************************
2024-01-21T01:55:42,542           ############################
2024-01-21T01:55:42,542           # Package would be ignored #
2024-01-21T01:55:42,543           ############################
2024-01-21T01:55:42,543           Python recognizes 'shephard.data' as an importable package[^1],
2024-01-21T01:55:42,544           but it is absent from setuptools' `packages` configuration.

2024-01-21T01:55:42,545           This leads to an ambiguous overall configuration. If you want to distribute this
2024-01-21T01:55:42,545           package, please make sure that 'shephard.data' is explicitly added
2024-01-21T01:55:42,546           to the `packages` configuration field.

2024-01-21T01:55:42,546           Alternatively, you can also rely on setuptools' discovery methods
2024-01-21T01:55:42,547           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-01-21T01:55:42,547           instead of `find_packages(...)`/`find:`).

2024-01-21T01:55:42,549           You can read more about "package discovery" on setuptools documentation page:

2024-01-21T01:55:42,550           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-01-21T01:55:42,551           If you don't want 'shephard.data' to be distributed and are
2024-01-21T01:55:42,551           already explicitly excluding 'shephard.data' via
2024-01-21T01:55:42,551           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-01-21T01:55:42,552           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-01-21T01:55:42,552           combination with a more fine grained `package-data` configuration.

2024-01-21T01:55:42,553           You can read more about "package data files" on setuptools documentation page:

2024-01-21T01:55:42,554           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-01-21T01:55:42,556           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-01-21T01:55:42,556                 even if it does not contain any `.py` files.
2024-01-21T01:55:42,557                 On the other hand, currently there is no concept of package data
2024-01-21T01:55:42,557                 directory, all directories are treated like packages.
2024-01-21T01:55:42,558           ********************************************************************************

2024-01-21T01:55:42,559   !!
2024-01-21T01:55:42,559     check.warn(importable)
2024-01-21T01:55:42,560   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'shephard.data.test_data' is absent from the `packages` configuration.
2024-01-21T01:55:42,561   !!

2024-01-21T01:55:42,562           ********************************************************************************
2024-01-21T01:55:42,562           ############################
2024-01-21T01:55:42,562           # Package would be ignored #
2024-01-21T01:55:42,563           ############################
2024-01-21T01:55:42,564           Python recognizes 'shephard.data.test_data' as an importable package[^1],
2024-01-21T01:55:42,564           but it is absent from setuptools' `packages` configuration.

2024-01-21T01:55:42,565           This leads to an ambiguous overall configuration. If you want to distribute this
2024-01-21T01:55:42,566           package, please make sure that 'shephard.data.test_data' is explicitly added
2024-01-21T01:55:42,566           to the `packages` configuration field.

2024-01-21T01:55:42,567           Alternatively, you can also rely on setuptools' discovery methods
2024-01-21T01:55:42,567           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-01-21T01:55:42,568           instead of `find_packages(...)`/`find:`).

2024-01-21T01:55:42,569           You can read more about "package discovery" on setuptools documentation page:

2024-01-21T01:55:42,569           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-01-21T01:55:42,570           If you don't want 'shephard.data.test_data' to be distributed and are
2024-01-21T01:55:42,571           already explicitly excluding 'shephard.data.test_data' via
2024-01-21T01:55:42,571           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-01-21T01:55:42,571           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-01-21T01:55:42,572           combination with a more fine grained `package-data` configuration.

2024-01-21T01:55:42,573           You can read more about "package data files" on setuptools documentation page:

2024-01-21T01:55:42,574           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-01-21T01:55:42,575           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-01-21T01:55:42,575                 even if it does not contain any `.py` files.
2024-01-21T01:55:42,576                 On the other hand, currently there is no concept of package data
2024-01-21T01:55:42,576                 directory, all directories are treated like packages.
2024-01-21T01:55:42,577           ********************************************************************************

2024-01-21T01:55:42,578   !!
2024-01-21T01:55:42,578     check.warn(importable)
2024-01-21T01:55:42,579   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'shephard.tests.output_test' is absent from the `packages` configuration.
2024-01-21T01:55:42,579   !!

2024-01-21T01:55:42,580           ********************************************************************************
2024-01-21T01:55:42,580           ############################
2024-01-21T01:55:42,581           # Package would be ignored #
2024-01-21T01:55:42,581           ############################
2024-01-21T01:55:42,582           Python recognizes 'shephard.tests.output_test' as an importable package[^1],
2024-01-21T01:55:42,582           but it is absent from setuptools' `packages` configuration.

2024-01-21T01:55:42,583           This leads to an ambiguous overall configuration. If you want to distribute this
2024-01-21T01:55:42,584           package, please make sure that 'shephard.tests.output_test' is explicitly added
2024-01-21T01:55:42,584           to the `packages` configuration field.

2024-01-21T01:55:42,585           Alternatively, you can also rely on setuptools' discovery methods
2024-01-21T01:55:42,586           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-01-21T01:55:42,586           instead of `find_packages(...)`/`find:`).

2024-01-21T01:55:42,587           You can read more about "package discovery" on setuptools documentation page:

2024-01-21T01:55:42,588           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-01-21T01:55:42,589           If you don't want 'shephard.tests.output_test' to be distributed and are
2024-01-21T01:55:42,590           already explicitly excluding 'shephard.tests.output_test' via
2024-01-21T01:55:42,590           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-01-21T01:55:42,591           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-01-21T01:55:42,591           combination with a more fine grained `package-data` configuration.

2024-01-21T01:55:42,593           You can read more about "package data files" on setuptools documentation page:

2024-01-21T01:55:42,593           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-01-21T01:55:42,594           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-01-21T01:55:42,595                 even if it does not contain any `.py` files.
2024-01-21T01:55:42,595                 On the other hand, currently there is no concept of package data
2024-01-21T01:55:42,596                 directory, all directories are treated like packages.
2024-01-21T01:55:42,596           ********************************************************************************

2024-01-21T01:55:42,597   !!
2024-01-21T01:55:42,597     check.warn(importable)
2024-01-21T01:55:42,598   copying shephard/.DS_Store -> build/lib/shephard
2024-01-21T01:55:42,598   creating build/lib/shephard/data
2024-01-21T01:55:42,598   copying shephard/data/README.md -> build/lib/shephard/data
2024-01-21T01:55:42,599   copying shephard/data/look_and_say.dat -> build/lib/shephard/data
2024-01-21T01:55:42,599   creating build/lib/shephard/data/test_data
2024-01-21T01:55:42,599   copying shephard/data/test_data/TS1_domains_idr.tsv -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,600   copying shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,600   copying shephard/data/test_data/TS1_domains_pscore.tsv -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,601   copying shephard/data/test_data/TS1_protein_attributes.tsv -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,601   copying shephard/data/test_data/TS1_protein_attributes_several.tsv -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,602   copying shephard/data/test_data/TS1_sites.tsv -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,602   copying shephard/data/test_data/TS1_small_proteins.tsv -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,603   copying shephard/data/test_data/TS1_tracks_pscore.tsv -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,603   copying shephard/data/test_data/names.txt -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,604   copying shephard/data/test_data/seqs.fasta -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,604   copying shephard/data/test_data/testset_1.fasta -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,605   copying shephard/data/test_data/testset_1.fasta.fai -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,605   copying shephard/data/test_data/testset_1_ptms.tsv -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,606   copying shephard/data/test_data/ts1_bonus_sites.tsv -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,606   copying shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,607   copying shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,607   copying shephard/data/test_data/tst.py -> build/lib/shephard/data/test_data
2024-01-21T01:55:42,607   copying shephard/tests/test_scratchpad.ipynb -> build/lib/shephard/tests
2024-01-21T01:55:42,608   creating build/lib/shephard/tests/.ipynb_checkpoints
2024-01-21T01:55:42,608   copying shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/lib/shephard/tests/.ipynb_checkpoints
2024-01-21T01:55:42,609   creating build/lib/shephard/tests/output_test
2024-01-21T01:55:42,609   copying shephard/tests/output_test/all_symbols_test.tsv -> build/lib/shephard/tests/output_test
2024-01-21T01:55:42,610   copying shephard/tests/output_test/all_values_test.tsv -> build/lib/shephard/tests/output_test
2024-01-21T01:55:42,613   copying shephard/tests/output_test/all_values_test_from_list.tsv -> build/lib/shephard/tests/output_test
2024-01-21T01:55:42,615   copying shephard/tests/output_test/out_tracks.tsv -> build/lib/shephard/tests/output_test
2024-01-21T01:55:42,618   copying shephard/tests/output_test/readme.md -> build/lib/shephard/tests/output_test
2024-01-21T01:55:42,620   copying shephard/tests/output_test/shephard_track_phosres.tsv -> build/lib/shephard/tests/output_test
2024-01-21T01:55:42,622   copying shephard/tests/output_test/shephard_track_pscore.tsv -> build/lib/shephard/tests/output_test
2024-01-21T01:55:42,625   copying shephard/tests/output_test/test_domains.tsv -> build/lib/shephard/tests/output_test
2024-01-21T01:55:42,627   copying shephard/tests/output_test/test_domains_types.tsv -> build/lib/shephard/tests/output_test
2024-01-21T01:55:42,628   copying shephard/tests/output_test/test_sites.tsv -> build/lib/shephard/tests/output_test
2024-01-21T01:55:42,632   copying shephard/tests/output_test/track_phospho_track.tsv -> build/lib/shephard/tests/output_test
2024-01-21T01:55:42,634   copying shephard/tests/output_test/track_random_vals.tsv -> build/lib/shephard/tests/output_test
2024-01-21T01:55:42,636   copying shephard/apis/metapredict_api.py~ -> build/lib/shephard/apis
2024-01-21T01:55:42,641   UPDATING build/lib/shephard/_version.py
2024-01-21T01:55:42,642   set build/lib/shephard/_version.py to 'v0.1.21'
2024-01-21T01:55:42,665   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2024-01-21T01:55:42,666   !!

2024-01-21T01:55:42,667           ********************************************************************************
2024-01-21T01:55:42,667           Please avoid running ``setup.py`` directly.
2024-01-21T01:55:42,668           Instead, use pypa/build, pypa/installer or other
2024-01-21T01:55:42,669           standards-based tools.

2024-01-21T01:55:42,670           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2024-01-21T01:55:42,671           ********************************************************************************

2024-01-21T01:55:42,672   !!
2024-01-21T01:55:42,672     self.initialize_options()
2024-01-21T01:55:42,690   installing to build/bdist.linux-armv7l/wheel
2024-01-21T01:55:42,690   running install
2024-01-21T01:55:42,714   running install_lib
2024-01-21T01:55:42,737   creating build/bdist.linux-armv7l
2024-01-21T01:55:42,738   creating build/bdist.linux-armv7l/wheel
2024-01-21T01:55:42,740   creating build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,741   creating build/bdist.linux-armv7l/wheel/shephard/tools
2024-01-21T01:55:42,742   copying build/lib/shephard/tools/domain_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2024-01-21T01:55:42,744   copying build/lib/shephard/tools/track_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2024-01-21T01:55:42,746   copying build/lib/shephard/tools/sequence_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2024-01-21T01:55:42,748   copying build/lib/shephard/tools/site_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2024-01-21T01:55:42,750   copying build/lib/shephard/tools/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2024-01-21T01:55:42,752   copying build/lib/shephard/tools/experimental.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2024-01-21T01:55:42,754   copying build/lib/shephard/proteome.py -> build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,757   creating build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,758   copying build/lib/shephard/tests/test_shephard.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,760   copying build/lib/shephard/tests/example_test_function.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,762   copying build/lib/shephard/tests/test_ProteinInterface.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,764   copying build/lib/shephard/tests/test_scratchpad.ipynb -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,766   copying build/lib/shephard/tests/test_sequence_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,769   creating build/bdist.linux-armv7l/wheel/shephard/tests/.ipynb_checkpoints
2024-01-21T01:55:42,770   copying build/lib/shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/bdist.linux-armv7l/wheel/shephard/tests/.ipynb_checkpoints
2024-01-21T01:55:42,772   copying build/lib/shephard/tests/test_interfaces.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,773   copying build/lib/shephard/tests/test_SiteInterface.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,775   copying build/lib/shephard/tests/test_api_metapredict.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,777   copying build/lib/shephard/tests/test_ProteinAttributesInterface.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,778   copying build/lib/shephard/tests/test_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,780   copying build/lib/shephard/tests/test_protein.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,782   copying build/lib/shephard/tests/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,784   copying build/lib/shephard/tests/test_DomainInterface.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,785   copying build/lib/shephard/tests/test_sites.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,787   copying build/lib/shephard/tests/conftest.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,789   copying build/lib/shephard/tests/test_protein_site_functions.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,791   copying build/lib/shephard/tests/test_apis_fasta.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,793   copying build/lib/shephard/tests/test_si_sites.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,795   copying build/lib/shephard/tests/test_domain_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,797   copying build/lib/shephard/tests/test_si_domains.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,799   copying build/lib/shephard/tests/test_add_remove_annotations.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,801   creating build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,802   copying build/lib/shephard/tests/output_test/shephard_track_phosres.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,804   copying build/lib/shephard/tests/output_test/track_phospho_track.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,806   copying build/lib/shephard/tests/output_test/all_values_test_from_list.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,808   copying build/lib/shephard/tests/output_test/all_values_test.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,811   copying build/lib/shephard/tests/output_test/test_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,815   copying build/lib/shephard/tests/output_test/out_tracks.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,817   copying build/lib/shephard/tests/output_test/all_symbols_test.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,819   copying build/lib/shephard/tests/output_test/test_domains_types.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,821   copying build/lib/shephard/tests/output_test/track_random_vals.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,823   copying build/lib/shephard/tests/output_test/test_domains.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,824   copying build/lib/shephard/tests/output_test/shephard_track_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,827   copying build/lib/shephard/tests/output_test/readme.md -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2024-01-21T01:55:42,829   copying build/lib/shephard/tests/test_proteome.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,831   copying build/lib/shephard/tests/test_domains.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,833   copying build/lib/shephard/tests/test_logic.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,834   copying build/lib/shephard/tests/test_TrackInterface.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,836   copying build/lib/shephard/tests/test_track_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,838   copying build/lib/shephard/tests/test_si_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2024-01-21T01:55:42,840   copying build/lib/shephard/sequence_utilities.py -> build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,842   copying build/lib/shephard/domain.py -> build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,844   copying build/lib/shephard/site.py -> build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,847   copying build/lib/shephard/general_utilities.py -> build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,849   copying build/lib/shephard/protein.py -> build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,852   copying build/lib/shephard/__init__.py -> build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,854   creating build/bdist.linux-armv7l/wheel/shephard/apis
2024-01-21T01:55:42,855   copying build/lib/shephard/apis/metapredict_api.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2024-01-21T01:55:42,858   copying build/lib/shephard/apis/fasta.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2024-01-21T01:55:42,860   copying build/lib/shephard/apis/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2024-01-21T01:55:42,862   copying build/lib/shephard/apis/uniprot.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2024-01-21T01:55:42,864   copying build/lib/shephard/apis/metapredict_api.py~ -> build/bdist.linux-armv7l/wheel/shephard/apis
2024-01-21T01:55:42,867   copying build/lib/shephard/_version.py -> build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,868   copying build/lib/shephard/track.py -> build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,871   copying build/lib/shephard/exceptions.py -> build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,873   copying build/lib/shephard/test_domains_sites.py -> build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,874   copying build/lib/shephard/.DS_Store -> build/bdist.linux-armv7l/wheel/shephard
2024-01-21T01:55:42,877   creating build/bdist.linux-armv7l/wheel/shephard/data
2024-01-21T01:55:42,878   copying build/lib/shephard/data/README.md -> build/bdist.linux-armv7l/wheel/shephard/data
2024-01-21T01:55:42,879   copying build/lib/shephard/data/look_and_say.dat -> build/bdist.linux-armv7l/wheel/shephard/data
2024-01-21T01:55:42,882   creating build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,883   copying build/lib/shephard/data/test_data/TS1_protein_attributes_several.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,885   copying build/lib/shephard/data/test_data/tst.py -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,887   copying build/lib/shephard/data/test_data/testset_1_ptms.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,888   copying build/lib/shephard/data/test_data/TS1_small_proteins.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,892   copying build/lib/shephard/data/test_data/TS1_domains_idr.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,894   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,895   copying build/lib/shephard/data/test_data/TS1_domains_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,897   copying build/lib/shephard/data/test_data/testset_1.fasta -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,899   copying build/lib/shephard/data/test_data/ts1_bonus_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,901   copying build/lib/shephard/data/test_data/seqs.fasta -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,903   copying build/lib/shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,905   copying build/lib/shephard/data/test_data/names.txt -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,907   copying build/lib/shephard/data/test_data/TS1_tracks_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,909   copying build/lib/shephard/data/test_data/TS1_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,912   copying build/lib/shephard/data/test_data/testset_1.fasta.fai -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,913   copying build/lib/shephard/data/test_data/TS1_protein_attributes.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,915   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2024-01-21T01:55:42,917   creating build/bdist.linux-armv7l/wheel/shephard/interfaces
2024-01-21T01:55:42,918   copying build/lib/shephard/interfaces/si_sites.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2024-01-21T01:55:42,921   copying build/lib/shephard/interfaces/si_protein_attributes.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2024-01-21T01:55:42,924   copying build/lib/shephard/interfaces/si_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2024-01-21T01:55:42,927   copying build/lib/shephard/interfaces/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2024-01-21T01:55:42,929   copying build/lib/shephard/interfaces/interface_tools.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2024-01-21T01:55:42,931   copying build/lib/shephard/interfaces/si_domains.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2024-01-21T01:55:42,934   copying build/lib/shephard/interfaces/si_proteins.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2024-01-21T01:55:42,936   running install_egg_info
2024-01-21T01:55:42,967   Copying shephard.egg-info to build/bdist.linux-armv7l/wheel/shephard-0.1.21-py3.11.egg-info
2024-01-21T01:55:42,977   running install_scripts
2024-01-21T01:55:42,997   creating build/bdist.linux-armv7l/wheel/shephard-0.1.21.dist-info/WHEEL
2024-01-21T01:55:43,001   creating '/tmp/pip-wheel-sn7jljh_/shephard-0.1.21-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-01-21T01:55:43,004   adding 'shephard/.DS_Store'
2024-01-21T01:55:43,006   adding 'shephard/__init__.py'
2024-01-21T01:55:43,008   adding 'shephard/_version.py'
2024-01-21T01:55:43,010   adding 'shephard/domain.py'
2024-01-21T01:55:43,012   adding 'shephard/exceptions.py'
2024-01-21T01:55:43,014   adding 'shephard/general_utilities.py'
2024-01-21T01:55:43,023   adding 'shephard/protein.py'
2024-01-21T01:55:43,029   adding 'shephard/proteome.py'
2024-01-21T01:55:43,031   adding 'shephard/sequence_utilities.py'
2024-01-21T01:55:43,033   adding 'shephard/site.py'
2024-01-21T01:55:43,034   adding 'shephard/test_domains_sites.py'
2024-01-21T01:55:43,037   adding 'shephard/track.py'
2024-01-21T01:55:43,039   adding 'shephard/apis/__init__.py'
2024-01-21T01:55:43,041   adding 'shephard/apis/fasta.py'
2024-01-21T01:55:43,043   adding 'shephard/apis/metapredict_api.py'
2024-01-21T01:55:43,045   adding 'shephard/apis/metapredict_api.py~'
2024-01-21T01:55:43,047   adding 'shephard/apis/uniprot.py'
2024-01-21T01:55:43,049   adding 'shephard/data/README.md'
2024-01-21T01:55:43,050   adding 'shephard/data/look_and_say.dat'
2024-01-21T01:55:43,052   adding 'shephard/data/test_data/TS1_domains_idr.tsv'
2024-01-21T01:55:43,053   adding 'shephard/data/test_data/TS1_domains_idr_and_others.tsv'
2024-01-21T01:55:43,054   adding 'shephard/data/test_data/TS1_domains_pscore.tsv'
2024-01-21T01:55:43,055   adding 'shephard/data/test_data/TS1_protein_attributes.tsv'
2024-01-21T01:55:43,056   adding 'shephard/data/test_data/TS1_protein_attributes_several.tsv'
2024-01-21T01:55:43,058   adding 'shephard/data/test_data/TS1_sites.tsv'
2024-01-21T01:55:43,059   adding 'shephard/data/test_data/TS1_small_proteins.tsv'
2024-01-21T01:55:43,067   adding 'shephard/data/test_data/TS1_tracks_pscore.tsv'
2024-01-21T01:55:43,069   adding 'shephard/data/test_data/names.txt'
2024-01-21T01:55:43,070   adding 'shephard/data/test_data/seqs.fasta'
2024-01-21T01:55:43,072   adding 'shephard/data/test_data/testset_1.fasta'
2024-01-21T01:55:43,073   adding 'shephard/data/test_data/testset_1.fasta.fai'
2024-01-21T01:55:43,074   adding 'shephard/data/test_data/testset_1_ptms.tsv'
2024-01-21T01:55:43,075   adding 'shephard/data/test_data/ts1_bonus_sites.tsv'
2024-01-21T01:55:43,077   adding 'shephard/data/test_data/ts1_bonus_sites_bad.tsv'
2024-01-21T01:55:43,078   adding 'shephard/data/test_data/ts1_bonus_sites_bad2.tsv'
2024-01-21T01:55:43,079   adding 'shephard/data/test_data/tst.py'
2024-01-21T01:55:43,081   adding 'shephard/interfaces/__init__.py'
2024-01-21T01:55:43,083   adding 'shephard/interfaces/interface_tools.py'
2024-01-21T01:55:43,086   adding 'shephard/interfaces/si_domains.py'
2024-01-21T01:55:43,088   adding 'shephard/interfaces/si_protein_attributes.py'
2024-01-21T01:55:43,090   adding 'shephard/interfaces/si_proteins.py'
2024-01-21T01:55:43,093   adding 'shephard/interfaces/si_sites.py'
2024-01-21T01:55:43,096   adding 'shephard/interfaces/si_tracks.py'
2024-01-21T01:55:43,099   adding 'shephard/tests/__init__.py'
2024-01-21T01:55:43,100   adding 'shephard/tests/conftest.py'
2024-01-21T01:55:43,101   adding 'shephard/tests/example_test_function.py'
2024-01-21T01:55:43,102   adding 'shephard/tests/test_DomainInterface.py'
2024-01-21T01:55:43,104   adding 'shephard/tests/test_ProteinAttributesInterface.py'
2024-01-21T01:55:43,105   adding 'shephard/tests/test_ProteinInterface.py'
2024-01-21T01:55:43,106   adding 'shephard/tests/test_SiteInterface.py'
2024-01-21T01:55:43,107   adding 'shephard/tests/test_TrackInterface.py'
2024-01-21T01:55:43,109   adding 'shephard/tests/test_add_remove_annotations.py'
2024-01-21T01:55:43,111   adding 'shephard/tests/test_api_metapredict.py'
2024-01-21T01:55:43,112   adding 'shephard/tests/test_apis_fasta.py'
2024-01-21T01:55:43,114   adding 'shephard/tests/test_domain_tools.py'
2024-01-21T01:55:43,115   adding 'shephard/tests/test_domains.py'
2024-01-21T01:55:43,116   adding 'shephard/tests/test_interfaces.py'
2024-01-21T01:55:43,117   adding 'shephard/tests/test_logic.py'
2024-01-21T01:55:43,119   adding 'shephard/tests/test_protein.py'
2024-01-21T01:55:43,121   adding 'shephard/tests/test_protein_site_functions.py'
2024-01-21T01:55:43,122   adding 'shephard/tests/test_proteome.py'
2024-01-21T01:55:43,125   adding 'shephard/tests/test_scratchpad.ipynb'
2024-01-21T01:55:43,126   adding 'shephard/tests/test_sequence_tools.py'
2024-01-21T01:55:43,127   adding 'shephard/tests/test_shephard.py'
2024-01-21T01:55:43,129   adding 'shephard/tests/test_si_domains.py'
2024-01-21T01:55:43,130   adding 'shephard/tests/test_si_sites.py'
2024-01-21T01:55:43,132   adding 'shephard/tests/test_si_tracks.py'
2024-01-21T01:55:43,133   adding 'shephard/tests/test_sites.py'
2024-01-21T01:55:43,135   adding 'shephard/tests/test_track_tools.py'
2024-01-21T01:55:43,136   adding 'shephard/tests/test_tracks.py'
2024-01-21T01:55:43,137   adding 'shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb'
2024-01-21T01:55:43,139   adding 'shephard/tests/output_test/all_symbols_test.tsv'
2024-01-21T01:55:43,142   adding 'shephard/tests/output_test/all_values_test.tsv'
2024-01-21T01:55:43,145   adding 'shephard/tests/output_test/all_values_test_from_list.tsv'
2024-01-21T01:55:43,154   adding 'shephard/tests/output_test/out_tracks.tsv'
2024-01-21T01:55:43,156   adding 'shephard/tests/output_test/readme.md'
2024-01-21T01:55:43,157   adding 'shephard/tests/output_test/shephard_track_phosres.tsv'
2024-01-21T01:55:43,167   adding 'shephard/tests/output_test/shephard_track_pscore.tsv'
2024-01-21T01:55:43,168   adding 'shephard/tests/output_test/test_domains.tsv'
2024-01-21T01:55:43,169   adding 'shephard/tests/output_test/test_domains_types.tsv'
2024-01-21T01:55:43,172   adding 'shephard/tests/output_test/test_sites.tsv'
2024-01-21T01:55:43,174   adding 'shephard/tests/output_test/track_phospho_track.tsv'
2024-01-21T01:55:43,176   adding 'shephard/tests/output_test/track_random_vals.tsv'
2024-01-21T01:55:43,178   adding 'shephard/tools/__init__.py'
2024-01-21T01:55:43,182   adding 'shephard/tools/domain_tools.py'
2024-01-21T01:55:43,183   adding 'shephard/tools/experimental.py'
2024-01-21T01:55:43,185   adding 'shephard/tools/sequence_tools.py'
2024-01-21T01:55:43,187   adding 'shephard/tools/site_tools.py'
2024-01-21T01:55:43,189   adding 'shephard/tools/track_tools.py'
2024-01-21T01:55:43,193   adding 'shephard-0.1.21.dist-info/LICENSE'
2024-01-21T01:55:43,195   adding 'shephard-0.1.21.dist-info/METADATA'
2024-01-21T01:55:43,196   adding 'shephard-0.1.21.dist-info/WHEEL'
2024-01-21T01:55:43,198   adding 'shephard-0.1.21.dist-info/top_level.txt'
2024-01-21T01:55:43,199   adding 'shephard-0.1.21.dist-info/RECORD'
2024-01-21T01:55:43,207   removing build/bdist.linux-armv7l/wheel
2024-01-21T01:55:43,360   Building wheel for shephard (setup.py): finished with status 'done'
2024-01-21T01:55:43,365   Created wheel for shephard: filename=shephard-0.1.21-py3-none-any.whl size=200890 sha256=a7b74868e7b3d7a863c6bcb667f0f6e90071dfcfc14fedffb0f42d538e6cb261
2024-01-21T01:55:43,366   Stored in directory: /tmp/pip-ephem-wheel-cache-66q9r__y/wheels/58/3a/1f/a01be06411d6a3ada84ace739f03e2357dd64750d702c6e4ed
2024-01-21T01:55:43,379 Successfully built shephard
2024-01-21T01:55:43,389 Removed build tracker: '/tmp/pip-build-tracker-_r42v99n'