2023-12-04T14:28:40,981 Created temporary directory: /tmp/pip-build-tracker-8boimf4g
2023-12-04T14:28:40,982 Initialized build tracking at /tmp/pip-build-tracker-8boimf4g
2023-12-04T14:28:40,983 Created build tracker: /tmp/pip-build-tracker-8boimf4g
2023-12-04T14:28:40,983 Entered build tracker: /tmp/pip-build-tracker-8boimf4g
2023-12-04T14:28:40,984 Created temporary directory: /tmp/pip-wheel-ze3gmbq8
2023-12-04T14:28:40,987 Created temporary directory: /tmp/pip-ephem-wheel-cache-118bdnap
2023-12-04T14:28:41,009 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-12-04T14:28:41,012 2 location(s) to search for versions of shephard:
2023-12-04T14:28:41,012 * https://pypi.org/simple/shephard/
2023-12-04T14:28:41,012 * https://www.piwheels.org/simple/shephard/
2023-12-04T14:28:41,013 Fetching project page and analyzing links: https://pypi.org/simple/shephard/
2023-12-04T14:28:41,013 Getting page https://pypi.org/simple/shephard/
2023-12-04T14:28:41,015 Found index url https://pypi.org/simple/
2023-12-04T14:28:41,223 Fetched page https://pypi.org/simple/shephard/ as application/vnd.pypi.simple.v1+json
2023-12-04T14:28:41,226   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
2023-12-04T14:28:41,226   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
2023-12-04T14:28:41,227   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
2023-12-04T14:28:41,228   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
2023-12-04T14:28:41,228   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
2023-12-04T14:28:41,229   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
2023-12-04T14:28:41,230   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
2023-12-04T14:28:41,231   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
2023-12-04T14:28:41,232   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
2023-12-04T14:28:41,233 Fetching project page and analyzing links: https://www.piwheels.org/simple/shephard/
2023-12-04T14:28:41,233 Getting page https://www.piwheels.org/simple/shephard/
2023-12-04T14:28:41,235 Found index url https://www.piwheels.org/simple/
2023-12-04T14:28:41,399 Fetched page https://www.piwheels.org/simple/shephard/ as text/html
2023-12-04T14:28:41,403   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/)
2023-12-04T14:28:41,403   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/)
2023-12-04T14:28:41,404   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/)
2023-12-04T14:28:41,405   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/)
2023-12-04T14:28:41,406   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/)
2023-12-04T14:28:41,406   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/)
2023-12-04T14:28:41,406   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/)
2023-12-04T14:28:41,407   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/)
2023-12-04T14:28:41,407 Skipping link: not a file: https://www.piwheels.org/simple/shephard/
2023-12-04T14:28:41,408 Skipping link: not a file: https://pypi.org/simple/shephard/
2023-12-04T14:28:41,429 Given no hashes to check 1 links for project 'shephard': discarding no candidates
2023-12-04T14:28:41,448 Collecting shephard==0.1.20
2023-12-04T14:28:41,450   Created temporary directory: /tmp/pip-unpack-pgeet478
2023-12-04T14:28:41,658   Downloading shephard-0.1.20.tar.gz (201 kB)
2023-12-04T14:28:41,983   Added shephard==0.1.20 from https://files.pythonhosted.org/packages/78/a1/eda32772db5f73f89f29c1827f159ee9715a2adb6c0cd7d4d8272fde7c0a/shephard-0.1.20.tar.gz to build tracker '/tmp/pip-build-tracker-8boimf4g'
2023-12-04T14:28:41,985   Running setup.py (path:/tmp/pip-wheel-ze3gmbq8/shephard_205509bfbd0f4bc486713409d75a9676/setup.py) egg_info for package shephard
2023-12-04T14:28:41,986   Created temporary directory: /tmp/pip-pip-egg-info-rrktzv22
2023-12-04T14:28:41,987   Preparing metadata (setup.py): started
2023-12-04T14:28:41,988   Running command python setup.py egg_info
2023-12-04T14:28:42,825   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:314: InformationOnly: Normalizing 'v0.1.20' to '0.1.20'
2023-12-04T14:28:42,826     self.metadata.version = self._normalize_version(self.metadata.version)
2023-12-04T14:28:42,888   running egg_info
2023-12-04T14:28:42,889   creating /tmp/pip-pip-egg-info-rrktzv22/shephard.egg-info
2023-12-04T14:28:42,914   writing /tmp/pip-pip-egg-info-rrktzv22/shephard.egg-info/PKG-INFO
2023-12-04T14:28:42,918   writing dependency_links to /tmp/pip-pip-egg-info-rrktzv22/shephard.egg-info/dependency_links.txt
2023-12-04T14:28:42,921   writing requirements to /tmp/pip-pip-egg-info-rrktzv22/shephard.egg-info/requires.txt
2023-12-04T14:28:42,922   writing top-level names to /tmp/pip-pip-egg-info-rrktzv22/shephard.egg-info/top_level.txt
2023-12-04T14:28:42,924   writing manifest file '/tmp/pip-pip-egg-info-rrktzv22/shephard.egg-info/SOURCES.txt'
2023-12-04T14:28:42,981   reading manifest file '/tmp/pip-pip-egg-info-rrktzv22/shephard.egg-info/SOURCES.txt'
2023-12-04T14:28:42,983   reading manifest template 'MANIFEST.in'
2023-12-04T14:28:42,991   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2023-12-04T14:28:42,991   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2023-12-04T14:28:42,992   warning: no previously-included files matching '*.so' found anywhere in distribution
2023-12-04T14:28:42,993   adding license file 'LICENSE'
2023-12-04T14:28:42,997   writing manifest file '/tmp/pip-pip-egg-info-rrktzv22/shephard.egg-info/SOURCES.txt'
2023-12-04T14:28:43,095   Preparing metadata (setup.py): finished with status 'done'
2023-12-04T14:28:43,099   Source in /tmp/pip-wheel-ze3gmbq8/shephard_205509bfbd0f4bc486713409d75a9676 has version 0.1.20, which satisfies requirement shephard==0.1.20 from https://files.pythonhosted.org/packages/78/a1/eda32772db5f73f89f29c1827f159ee9715a2adb6c0cd7d4d8272fde7c0a/shephard-0.1.20.tar.gz
2023-12-04T14:28:43,100   Removed shephard==0.1.20 from https://files.pythonhosted.org/packages/78/a1/eda32772db5f73f89f29c1827f159ee9715a2adb6c0cd7d4d8272fde7c0a/shephard-0.1.20.tar.gz from build tracker '/tmp/pip-build-tracker-8boimf4g'
2023-12-04T14:28:43,106 Created temporary directory: /tmp/pip-unpack-iosvqzuu
2023-12-04T14:28:43,107 Created temporary directory: /tmp/pip-unpack-ixmkt08n
2023-12-04T14:28:43,113 Building wheels for collected packages: shephard
2023-12-04T14:28:43,116   Created temporary directory: /tmp/pip-wheel-wgkrqk_y
2023-12-04T14:28:43,117   Building wheel for shephard (setup.py): started
2023-12-04T14:28:43,118   Destination directory: /tmp/pip-wheel-wgkrqk_y
2023-12-04T14:28:43,119   Running command python setup.py bdist_wheel
2023-12-04T14:28:43,912   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:314: InformationOnly: Normalizing 'v0.1.20' to '0.1.20'
2023-12-04T14:28:43,912     self.metadata.version = self._normalize_version(self.metadata.version)
2023-12-04T14:28:43,966   running bdist_wheel
2023-12-04T14:28:44,095   running build
2023-12-04T14:28:44,096   running build_py
2023-12-04T14:28:44,101   creating build
2023-12-04T14:28:44,102   creating build/lib
2023-12-04T14:28:44,103   creating build/lib/shephard
2023-12-04T14:28:44,104   copying shephard/domain.py -> build/lib/shephard
2023-12-04T14:28:44,107   copying shephard/__init__.py -> build/lib/shephard
2023-12-04T14:28:44,108   copying shephard/protein.py -> build/lib/shephard
2023-12-04T14:28:44,112   copying shephard/track.py -> build/lib/shephard
2023-12-04T14:28:44,114   copying shephard/general_utilities.py -> build/lib/shephard
2023-12-04T14:28:44,116   copying shephard/_version.py -> build/lib/shephard
2023-12-04T14:28:44,117   copying shephard/site.py -> build/lib/shephard
2023-12-04T14:28:44,120   copying shephard/sequence_utilities.py -> build/lib/shephard
2023-12-04T14:28:44,122   copying shephard/proteome.py -> build/lib/shephard
2023-12-04T14:28:44,124   copying shephard/test_domains_sites.py -> build/lib/shephard
2023-12-04T14:28:44,126   copying shephard/exceptions.py -> build/lib/shephard
2023-12-04T14:28:44,128   creating build/lib/shephard/apis
2023-12-04T14:28:44,129   copying shephard/apis/__init__.py -> build/lib/shephard/apis
2023-12-04T14:28:44,131   copying shephard/apis/uniprot.py -> build/lib/shephard/apis
2023-12-04T14:28:44,133   copying shephard/apis/fasta.py -> build/lib/shephard/apis
2023-12-04T14:28:44,135   copying shephard/apis/metapredict.py -> build/lib/shephard/apis
2023-12-04T14:28:44,139   creating build/lib/shephard/tests
2023-12-04T14:28:44,139   copying shephard/tests/test_tracks.py -> build/lib/shephard/tests
2023-12-04T14:28:44,141   copying shephard/tests/test_apis_fasta.py -> build/lib/shephard/tests
2023-12-04T14:28:44,143   copying shephard/tests/test_si_tracks.py -> build/lib/shephard/tests
2023-12-04T14:28:44,145   copying shephard/tests/test_domain_tools.py -> build/lib/shephard/tests
2023-12-04T14:28:44,147   copying shephard/tests/test_si_sites.py -> build/lib/shephard/tests
2023-12-04T14:28:44,149   copying shephard/tests/test_sequence_tools.py -> build/lib/shephard/tests
2023-12-04T14:28:44,151   copying shephard/tests/__init__.py -> build/lib/shephard/tests
2023-12-04T14:28:44,152   copying shephard/tests/test_SiteInterface.py -> build/lib/shephard/tests
2023-12-04T14:28:44,154   copying shephard/tests/conftest.py -> build/lib/shephard/tests
2023-12-04T14:28:44,156   copying shephard/tests/test_protein.py -> build/lib/shephard/tests
2023-12-04T14:28:44,158   copying shephard/tests/test_ProteinAttributesInterface.py -> build/lib/shephard/tests
2023-12-04T14:28:44,160   copying shephard/tests/test_sites.py -> build/lib/shephard/tests
2023-12-04T14:28:44,161   copying shephard/tests/test_proteome.py -> build/lib/shephard/tests
2023-12-04T14:28:44,163   copying shephard/tests/example_test_function.py -> build/lib/shephard/tests
2023-12-04T14:28:44,165   copying shephard/tests/test_logic.py -> build/lib/shephard/tests
2023-12-04T14:28:44,166   copying shephard/tests/test_api_metapredict.py -> build/lib/shephard/tests
2023-12-04T14:28:44,168   copying shephard/tests/test_shephard.py -> build/lib/shephard/tests
2023-12-04T14:28:44,169   copying shephard/tests/test_TrackInterface.py -> build/lib/shephard/tests
2023-12-04T14:28:44,171   copying shephard/tests/test_DomainInterface.py -> build/lib/shephard/tests
2023-12-04T14:28:44,172   copying shephard/tests/test_domains.py -> build/lib/shephard/tests
2023-12-04T14:28:44,174   copying shephard/tests/test_add_remove_annotations.py -> build/lib/shephard/tests
2023-12-04T14:28:44,176   copying shephard/tests/test_track_tools.py -> build/lib/shephard/tests
2023-12-04T14:28:44,177   copying shephard/tests/test_si_domains.py -> build/lib/shephard/tests
2023-12-04T14:28:44,179   copying shephard/tests/test_interfaces.py -> build/lib/shephard/tests
2023-12-04T14:28:44,181   copying shephard/tests/test_ProteinInterface.py -> build/lib/shephard/tests
2023-12-04T14:28:44,182   copying shephard/tests/test_protein_site_functions.py -> build/lib/shephard/tests
2023-12-04T14:28:44,184   creating build/lib/shephard/tools
2023-12-04T14:28:44,185   copying shephard/tools/sequence_tools.py -> build/lib/shephard/tools
2023-12-04T14:28:44,187   copying shephard/tools/site_tools.py -> build/lib/shephard/tools
2023-12-04T14:28:44,189   copying shephard/tools/__init__.py -> build/lib/shephard/tools
2023-12-04T14:28:44,191   copying shephard/tools/domain_tools.py -> build/lib/shephard/tools
2023-12-04T14:28:44,193   copying shephard/tools/track_tools.py -> build/lib/shephard/tools
2023-12-04T14:28:44,195   copying shephard/tools/experimental.py -> build/lib/shephard/tools
2023-12-04T14:28:44,197   creating build/lib/shephard/interfaces
2023-12-04T14:28:44,198   copying shephard/interfaces/si_proteins.py -> build/lib/shephard/interfaces
2023-12-04T14:28:44,200   copying shephard/interfaces/__init__.py -> build/lib/shephard/interfaces
2023-12-04T14:28:44,202   copying shephard/interfaces/interface_tools.py -> build/lib/shephard/interfaces
2023-12-04T14:28:44,204   copying shephard/interfaces/si_domains.py -> build/lib/shephard/interfaces
2023-12-04T14:28:44,207   copying shephard/interfaces/si_protein_attributes.py -> build/lib/shephard/interfaces
2023-12-04T14:28:44,209   copying shephard/interfaces/si_sites.py -> build/lib/shephard/interfaces
2023-12-04T14:28:44,211   copying shephard/interfaces/si_tracks.py -> build/lib/shephard/interfaces
2023-12-04T14:28:44,214   running egg_info
2023-12-04T14:28:44,239   writing shephard.egg-info/PKG-INFO
2023-12-04T14:28:44,242   writing dependency_links to shephard.egg-info/dependency_links.txt
2023-12-04T14:28:44,244   writing requirements to shephard.egg-info/requires.txt
2023-12-04T14:28:44,245   writing top-level names to shephard.egg-info/top_level.txt
2023-12-04T14:28:44,277   reading manifest file 'shephard.egg-info/SOURCES.txt'
2023-12-04T14:28:44,282   reading manifest template 'MANIFEST.in'
2023-12-04T14:28:44,289   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2023-12-04T14:28:44,290   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2023-12-04T14:28:44,291   warning: no previously-included files matching '*.so' found anywhere in distribution
2023-12-04T14:28:44,291   adding license file 'LICENSE'
2023-12-04T14:28:44,298   writing manifest file 'shephard.egg-info/SOURCES.txt'
2023-12-04T14:28:44,301   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'shephard.data' is absent from the `packages` configuration.
2023-12-04T14:28:44,301   !!

2023-12-04T14:28:44,303           ********************************************************************************
2023-12-04T14:28:44,303           ############################
2023-12-04T14:28:44,304           # Package would be ignored #
2023-12-04T14:28:44,304           ############################
2023-12-04T14:28:44,304           Python recognizes 'shephard.data' as an importable package[^1],
2023-12-04T14:28:44,305           but it is absent from setuptools' `packages` configuration.

2023-12-04T14:28:44,305           This leads to an ambiguous overall configuration. If you want to distribute this
2023-12-04T14:28:44,306           package, please make sure that 'shephard.data' is explicitly added
2023-12-04T14:28:44,306           to the `packages` configuration field.

2023-12-04T14:28:44,307           Alternatively, you can also rely on setuptools' discovery methods
2023-12-04T14:28:44,307           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-12-04T14:28:44,308           instead of `find_packages(...)`/`find:`).

2023-12-04T14:28:44,309           You can read more about "package discovery" on setuptools documentation page:

2023-12-04T14:28:44,310           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-12-04T14:28:44,310           If you don't want 'shephard.data' to be distributed and are
2023-12-04T14:28:44,311           already explicitly excluding 'shephard.data' via
2023-12-04T14:28:44,311           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-12-04T14:28:44,312           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-12-04T14:28:44,312           combination with a more fine grained `package-data` configuration.

2023-12-04T14:28:44,313           You can read more about "package data files" on setuptools documentation page:

2023-12-04T14:28:44,314           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-12-04T14:28:44,315           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-12-04T14:28:44,316                 even if it does not contain any `.py` files.
2023-12-04T14:28:44,316                 On the other hand, currently there is no concept of package data
2023-12-04T14:28:44,317                 directory, all directories are treated like packages.
2023-12-04T14:28:44,317           ********************************************************************************

2023-12-04T14:28:44,318   !!
2023-12-04T14:28:44,319     check.warn(importable)
2023-12-04T14:28:44,319   /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.
2023-12-04T14:28:44,320   !!

2023-12-04T14:28:44,321           ********************************************************************************
2023-12-04T14:28:44,321           ############################
2023-12-04T14:28:44,322           # Package would be ignored #
2023-12-04T14:28:44,322           ############################
2023-12-04T14:28:44,323           Python recognizes 'shephard.data.test_data' as an importable package[^1],
2023-12-04T14:28:44,323           but it is absent from setuptools' `packages` configuration.

2023-12-04T14:28:44,324           This leads to an ambiguous overall configuration. If you want to distribute this
2023-12-04T14:28:44,325           package, please make sure that 'shephard.data.test_data' is explicitly added
2023-12-04T14:28:44,325           to the `packages` configuration field.

2023-12-04T14:28:44,326           Alternatively, you can also rely on setuptools' discovery methods
2023-12-04T14:28:44,327           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-12-04T14:28:44,327           instead of `find_packages(...)`/`find:`).

2023-12-04T14:28:44,328           You can read more about "package discovery" on setuptools documentation page:

2023-12-04T14:28:44,329           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-12-04T14:28:44,330           If you don't want 'shephard.data.test_data' to be distributed and are
2023-12-04T14:28:44,331           already explicitly excluding 'shephard.data.test_data' via
2023-12-04T14:28:44,331           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-12-04T14:28:44,331           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-12-04T14:28:44,332           combination with a more fine grained `package-data` configuration.

2023-12-04T14:28:44,332           You can read more about "package data files" on setuptools documentation page:

2023-12-04T14:28:44,333           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-12-04T14:28:44,334           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-12-04T14:28:44,335                 even if it does not contain any `.py` files.
2023-12-04T14:28:44,335                 On the other hand, currently there is no concept of package data
2023-12-04T14:28:44,336                 directory, all directories are treated like packages.
2023-12-04T14:28:44,336           ********************************************************************************

2023-12-04T14:28:44,337   !!
2023-12-04T14:28:44,337     check.warn(importable)
2023-12-04T14:28:44,338   /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.
2023-12-04T14:28:44,338   !!

2023-12-04T14:28:44,339           ********************************************************************************
2023-12-04T14:28:44,340           ############################
2023-12-04T14:28:44,340           # Package would be ignored #
2023-12-04T14:28:44,341           ############################
2023-12-04T14:28:44,341           Python recognizes 'shephard.tests.output_test' as an importable package[^1],
2023-12-04T14:28:44,342           but it is absent from setuptools' `packages` configuration.

2023-12-04T14:28:44,342           This leads to an ambiguous overall configuration. If you want to distribute this
2023-12-04T14:28:44,343           package, please make sure that 'shephard.tests.output_test' is explicitly added
2023-12-04T14:28:44,343           to the `packages` configuration field.

2023-12-04T14:28:44,344           Alternatively, you can also rely on setuptools' discovery methods
2023-12-04T14:28:44,345           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-12-04T14:28:44,345           instead of `find_packages(...)`/`find:`).

2023-12-04T14:28:44,346           You can read more about "package discovery" on setuptools documentation page:

2023-12-04T14:28:44,347           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-12-04T14:28:44,348           If you don't want 'shephard.tests.output_test' to be distributed and are
2023-12-04T14:28:44,349           already explicitly excluding 'shephard.tests.output_test' via
2023-12-04T14:28:44,349           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-12-04T14:28:44,350           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-12-04T14:28:44,350           combination with a more fine grained `package-data` configuration.

2023-12-04T14:28:44,351           You can read more about "package data files" on setuptools documentation page:

2023-12-04T14:28:44,352           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-12-04T14:28:44,354           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-12-04T14:28:44,354                 even if it does not contain any `.py` files.
2023-12-04T14:28:44,355                 On the other hand, currently there is no concept of package data
2023-12-04T14:28:44,355                 directory, all directories are treated like packages.
2023-12-04T14:28:44,356           ********************************************************************************

2023-12-04T14:28:44,357   !!
2023-12-04T14:28:44,357     check.warn(importable)
2023-12-04T14:28:44,358   copying shephard/.DS_Store -> build/lib/shephard
2023-12-04T14:28:44,358   creating build/lib/shephard/data
2023-12-04T14:28:44,358   copying shephard/data/README.md -> build/lib/shephard/data
2023-12-04T14:28:44,359   copying shephard/data/look_and_say.dat -> build/lib/shephard/data
2023-12-04T14:28:44,359   creating build/lib/shephard/data/test_data
2023-12-04T14:28:44,360   copying shephard/data/test_data/TS1_domains_idr.tsv -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,360   copying shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,360   copying shephard/data/test_data/TS1_domains_pscore.tsv -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,361   copying shephard/data/test_data/TS1_protein_attributes.tsv -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,361   copying shephard/data/test_data/TS1_protein_attributes_several.tsv -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,362   copying shephard/data/test_data/TS1_sites.tsv -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,362   copying shephard/data/test_data/TS1_small_proteins.tsv -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,362   copying shephard/data/test_data/TS1_tracks_pscore.tsv -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,363   copying shephard/data/test_data/names.txt -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,363   copying shephard/data/test_data/seqs.fasta -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,364   copying shephard/data/test_data/testset_1.fasta -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,364   copying shephard/data/test_data/testset_1.fasta.fai -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,365   copying shephard/data/test_data/testset_1_ptms.tsv -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,365   copying shephard/data/test_data/ts1_bonus_sites.tsv -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,366   copying shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,366   copying shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,367   copying shephard/data/test_data/tst.py -> build/lib/shephard/data/test_data
2023-12-04T14:28:44,367   copying shephard/tests/test_scratchpad.ipynb -> build/lib/shephard/tests
2023-12-04T14:28:44,368   creating build/lib/shephard/tests/.ipynb_checkpoints
2023-12-04T14:28:44,368   copying shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/lib/shephard/tests/.ipynb_checkpoints
2023-12-04T14:28:44,370   creating build/lib/shephard/tests/output_test
2023-12-04T14:28:44,371   copying shephard/tests/output_test/all_symbols_test.tsv -> build/lib/shephard/tests/output_test
2023-12-04T14:28:44,373   copying shephard/tests/output_test/all_values_test.tsv -> build/lib/shephard/tests/output_test
2023-12-04T14:28:44,376   copying shephard/tests/output_test/all_values_test_from_list.tsv -> build/lib/shephard/tests/output_test
2023-12-04T14:28:44,380   copying shephard/tests/output_test/out_tracks.tsv -> build/lib/shephard/tests/output_test
2023-12-04T14:28:44,383   copying shephard/tests/output_test/readme.md -> build/lib/shephard/tests/output_test
2023-12-04T14:28:44,385   copying shephard/tests/output_test/shephard_track_phosres.tsv -> build/lib/shephard/tests/output_test
2023-12-04T14:28:44,387   copying shephard/tests/output_test/shephard_track_pscore.tsv -> build/lib/shephard/tests/output_test
2023-12-04T14:28:44,390   copying shephard/tests/output_test/test_domains.tsv -> build/lib/shephard/tests/output_test
2023-12-04T14:28:44,392   copying shephard/tests/output_test/test_domains_types.tsv -> build/lib/shephard/tests/output_test
2023-12-04T14:28:44,394   copying shephard/tests/output_test/test_sites.tsv -> build/lib/shephard/tests/output_test
2023-12-04T14:28:44,397   copying shephard/tests/output_test/track_phospho_track.tsv -> build/lib/shephard/tests/output_test
2023-12-04T14:28:44,399   copying shephard/tests/output_test/track_random_vals.tsv -> build/lib/shephard/tests/output_test
2023-12-04T14:28:44,404   UPDATING build/lib/shephard/_version.py
2023-12-04T14:28:44,405   set build/lib/shephard/_version.py to 'v0.1.20'
2023-12-04T14:28:44,431   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2023-12-04T14:28:44,431   !!

2023-12-04T14:28:44,432           ********************************************************************************
2023-12-04T14:28:44,433           Please avoid running ``setup.py`` directly.
2023-12-04T14:28:44,433           Instead, use pypa/build, pypa/installer or other
2023-12-04T14:28:44,433           standards-based tools.

2023-12-04T14:28:44,434           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2023-12-04T14:28:44,435           ********************************************************************************

2023-12-04T14:28:44,436   !!
2023-12-04T14:28:44,436     self.initialize_options()
2023-12-04T14:28:44,456   installing to build/bdist.linux-armv7l/wheel
2023-12-04T14:28:44,456   running install
2023-12-04T14:28:44,480   running install_lib
2023-12-04T14:28:44,505   creating build/bdist.linux-armv7l
2023-12-04T14:28:44,505   creating build/bdist.linux-armv7l/wheel
2023-12-04T14:28:44,506   creating build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,507   copying build/lib/shephard/domain.py -> build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,510   creating build/bdist.linux-armv7l/wheel/shephard/data
2023-12-04T14:28:44,512   creating build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,513   copying build/lib/shephard/data/test_data/tst.py -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,515   copying build/lib/shephard/data/test_data/TS1_protein_attributes.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,516   copying build/lib/shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,518   copying build/lib/shephard/data/test_data/testset_1.fasta -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,520   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,522   copying build/lib/shephard/data/test_data/testset_1.fasta.fai -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,523   copying build/lib/shephard/data/test_data/TS1_domains_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,525   copying build/lib/shephard/data/test_data/TS1_tracks_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,528   copying build/lib/shephard/data/test_data/names.txt -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,529   copying build/lib/shephard/data/test_data/testset_1_ptms.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,531   copying build/lib/shephard/data/test_data/ts1_bonus_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,533   copying build/lib/shephard/data/test_data/seqs.fasta -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,535   copying build/lib/shephard/data/test_data/TS1_protein_attributes_several.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,537   copying build/lib/shephard/data/test_data/TS1_domains_idr.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,538   copying build/lib/shephard/data/test_data/TS1_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,541   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,543   copying build/lib/shephard/data/test_data/TS1_small_proteins.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2023-12-04T14:28:44,544   copying build/lib/shephard/data/look_and_say.dat -> build/bdist.linux-armv7l/wheel/shephard/data
2023-12-04T14:28:44,546   copying build/lib/shephard/data/README.md -> build/bdist.linux-armv7l/wheel/shephard/data
2023-12-04T14:28:44,548   copying build/lib/shephard/__init__.py -> build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,549   copying build/lib/shephard/protein.py -> build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,554   creating build/bdist.linux-armv7l/wheel/shephard/apis
2023-12-04T14:28:44,555   copying build/lib/shephard/apis/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2023-12-04T14:28:44,556   copying build/lib/shephard/apis/uniprot.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2023-12-04T14:28:44,558   copying build/lib/shephard/apis/fasta.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2023-12-04T14:28:44,561   copying build/lib/shephard/apis/metapredict.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2023-12-04T14:28:44,563   copying build/lib/shephard/track.py -> build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,566   creating build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,567   copying build/lib/shephard/tests/test_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,569   copying build/lib/shephard/tests/test_apis_fasta.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,571   copying build/lib/shephard/tests/test_si_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,573   copying build/lib/shephard/tests/test_domain_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,575   copying build/lib/shephard/tests/test_si_sites.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,577   copying build/lib/shephard/tests/test_sequence_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,579   copying build/lib/shephard/tests/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,581   copying build/lib/shephard/tests/test_SiteInterface.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,583   copying build/lib/shephard/tests/conftest.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,585   copying build/lib/shephard/tests/test_protein.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,587   copying build/lib/shephard/tests/test_ProteinAttributesInterface.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,589   copying build/lib/shephard/tests/test_sites.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,591   creating build/bdist.linux-armv7l/wheel/shephard/tests/.ipynb_checkpoints
2023-12-04T14:28:44,592   copying build/lib/shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/bdist.linux-armv7l/wheel/shephard/tests/.ipynb_checkpoints
2023-12-04T14:28:44,597   copying build/lib/shephard/tests/test_proteome.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,601   copying build/lib/shephard/tests/example_test_function.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,605   copying build/lib/shephard/tests/test_logic.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,607   copying build/lib/shephard/tests/test_api_metapredict.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,609   copying build/lib/shephard/tests/test_shephard.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,612   creating build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,613   copying build/lib/shephard/tests/output_test/all_values_test.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,616   copying build/lib/shephard/tests/output_test/all_symbols_test.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,617   copying build/lib/shephard/tests/output_test/track_phospho_track.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,619   copying build/lib/shephard/tests/output_test/shephard_track_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,621   copying build/lib/shephard/tests/output_test/all_values_test_from_list.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,624   copying build/lib/shephard/tests/output_test/test_domains.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,625   copying build/lib/shephard/tests/output_test/track_random_vals.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,627   copying build/lib/shephard/tests/output_test/out_tracks.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,630   copying build/lib/shephard/tests/output_test/shephard_track_phosres.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,631   copying build/lib/shephard/tests/output_test/test_domains_types.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,633   copying build/lib/shephard/tests/output_test/readme.md -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,635   copying build/lib/shephard/tests/output_test/test_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2023-12-04T14:28:44,638   copying build/lib/shephard/tests/test_TrackInterface.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,640   copying build/lib/shephard/tests/test_DomainInterface.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,642   copying build/lib/shephard/tests/test_domains.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,644   copying build/lib/shephard/tests/test_add_remove_annotations.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,646   copying build/lib/shephard/tests/test_track_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,648   copying build/lib/shephard/tests/test_si_domains.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,650   copying build/lib/shephard/tests/test_scratchpad.ipynb -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,652   copying build/lib/shephard/tests/test_interfaces.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,654   copying build/lib/shephard/tests/test_ProteinInterface.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,656   copying build/lib/shephard/tests/test_protein_site_functions.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2023-12-04T14:28:44,658   copying build/lib/shephard/general_utilities.py -> build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,660   copying build/lib/shephard/_version.py -> build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,661   copying build/lib/shephard/site.py -> build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,664   copying build/lib/shephard/sequence_utilities.py -> build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,666   copying build/lib/shephard/proteome.py -> build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,669   creating build/bdist.linux-armv7l/wheel/shephard/tools
2023-12-04T14:28:44,671   copying build/lib/shephard/tools/sequence_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2023-12-04T14:28:44,673   copying build/lib/shephard/tools/site_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2023-12-04T14:28:44,675   copying build/lib/shephard/tools/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2023-12-04T14:28:44,676   copying build/lib/shephard/tools/domain_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2023-12-04T14:28:44,679   copying build/lib/shephard/tools/track_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2023-12-04T14:28:44,681   copying build/lib/shephard/tools/experimental.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2023-12-04T14:28:44,683   creating build/bdist.linux-armv7l/wheel/shephard/interfaces
2023-12-04T14:28:44,684   copying build/lib/shephard/interfaces/si_proteins.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2023-12-04T14:28:44,686   copying build/lib/shephard/interfaces/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2023-12-04T14:28:44,688   copying build/lib/shephard/interfaces/interface_tools.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2023-12-04T14:28:44,690   copying build/lib/shephard/interfaces/si_domains.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2023-12-04T14:28:44,693   copying build/lib/shephard/interfaces/si_protein_attributes.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2023-12-04T14:28:44,695   copying build/lib/shephard/interfaces/si_sites.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2023-12-04T14:28:44,697   copying build/lib/shephard/interfaces/si_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2023-12-04T14:28:44,700   copying build/lib/shephard/test_domains_sites.py -> build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,702   copying build/lib/shephard/exceptions.py -> build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,704   copying build/lib/shephard/.DS_Store -> build/bdist.linux-armv7l/wheel/shephard
2023-12-04T14:28:44,706   running install_egg_info
2023-12-04T14:28:44,738   Copying shephard.egg-info to build/bdist.linux-armv7l/wheel/shephard-0.1.20-py3.11.egg-info
2023-12-04T14:28:44,747   running install_scripts
2023-12-04T14:28:44,761   creating build/bdist.linux-armv7l/wheel/shephard-0.1.20.dist-info/WHEEL
2023-12-04T14:28:44,763   creating '/tmp/pip-wheel-wgkrqk_y/shephard-0.1.20-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-12-04T14:28:44,766   adding 'shephard/.DS_Store'
2023-12-04T14:28:44,769   adding 'shephard/__init__.py'
2023-12-04T14:28:44,770   adding 'shephard/_version.py'
2023-12-04T14:28:44,773   adding 'shephard/domain.py'
2023-12-04T14:28:44,774   adding 'shephard/exceptions.py'
2023-12-04T14:28:44,776   adding 'shephard/general_utilities.py'
2023-12-04T14:28:44,785   adding 'shephard/protein.py'
2023-12-04T14:28:44,791   adding 'shephard/proteome.py'
2023-12-04T14:28:44,793   adding 'shephard/sequence_utilities.py'
2023-12-04T14:28:44,795   adding 'shephard/site.py'
2023-12-04T14:28:44,796   adding 'shephard/test_domains_sites.py'
2023-12-04T14:28:44,799   adding 'shephard/track.py'
2023-12-04T14:28:44,800   adding 'shephard/apis/__init__.py'
2023-12-04T14:28:44,803   adding 'shephard/apis/fasta.py'
2023-12-04T14:28:44,805   adding 'shephard/apis/metapredict.py'
2023-12-04T14:28:44,807   adding 'shephard/apis/uniprot.py'
2023-12-04T14:28:44,808   adding 'shephard/data/README.md'
2023-12-04T14:28:44,810   adding 'shephard/data/look_and_say.dat'
2023-12-04T14:28:44,811   adding 'shephard/data/test_data/TS1_domains_idr.tsv'
2023-12-04T14:28:44,813   adding 'shephard/data/test_data/TS1_domains_idr_and_others.tsv'
2023-12-04T14:28:44,814   adding 'shephard/data/test_data/TS1_domains_pscore.tsv'
2023-12-04T14:28:44,815   adding 'shephard/data/test_data/TS1_protein_attributes.tsv'
2023-12-04T14:28:44,816   adding 'shephard/data/test_data/TS1_protein_attributes_several.tsv'
2023-12-04T14:28:44,817   adding 'shephard/data/test_data/TS1_sites.tsv'
2023-12-04T14:28:44,819   adding 'shephard/data/test_data/TS1_small_proteins.tsv'
2023-12-04T14:28:44,827   adding 'shephard/data/test_data/TS1_tracks_pscore.tsv'
2023-12-04T14:28:44,829   adding 'shephard/data/test_data/names.txt'
2023-12-04T14:28:44,830   adding 'shephard/data/test_data/seqs.fasta'
2023-12-04T14:28:44,832   adding 'shephard/data/test_data/testset_1.fasta'
2023-12-04T14:28:44,833   adding 'shephard/data/test_data/testset_1.fasta.fai'
2023-12-04T14:28:44,834   adding 'shephard/data/test_data/testset_1_ptms.tsv'
2023-12-04T14:28:44,835   adding 'shephard/data/test_data/ts1_bonus_sites.tsv'
2023-12-04T14:28:44,836   adding 'shephard/data/test_data/ts1_bonus_sites_bad.tsv'
2023-12-04T14:28:44,837   adding 'shephard/data/test_data/ts1_bonus_sites_bad2.tsv'
2023-12-04T14:28:44,838   adding 'shephard/data/test_data/tst.py'
2023-12-04T14:28:44,840   adding 'shephard/interfaces/__init__.py'
2023-12-04T14:28:44,842   adding 'shephard/interfaces/interface_tools.py'
2023-12-04T14:28:44,845   adding 'shephard/interfaces/si_domains.py'
2023-12-04T14:28:44,848   adding 'shephard/interfaces/si_protein_attributes.py'
2023-12-04T14:28:44,850   adding 'shephard/interfaces/si_proteins.py'
2023-12-04T14:28:44,853   adding 'shephard/interfaces/si_sites.py'
2023-12-04T14:28:44,856   adding 'shephard/interfaces/si_tracks.py'
2023-12-04T14:28:44,859   adding 'shephard/tests/__init__.py'
2023-12-04T14:28:44,860   adding 'shephard/tests/conftest.py'
2023-12-04T14:28:44,861   adding 'shephard/tests/example_test_function.py'
2023-12-04T14:28:44,863   adding 'shephard/tests/test_DomainInterface.py'
2023-12-04T14:28:44,864   adding 'shephard/tests/test_ProteinAttributesInterface.py'
2023-12-04T14:28:44,865   adding 'shephard/tests/test_ProteinInterface.py'
2023-12-04T14:28:44,866   adding 'shephard/tests/test_SiteInterface.py'
2023-12-04T14:28:44,868   adding 'shephard/tests/test_TrackInterface.py'
2023-12-04T14:28:44,869   adding 'shephard/tests/test_add_remove_annotations.py'
2023-12-04T14:28:44,871   adding 'shephard/tests/test_api_metapredict.py'
2023-12-04T14:28:44,873   adding 'shephard/tests/test_apis_fasta.py'
2023-12-04T14:28:44,874   adding 'shephard/tests/test_domain_tools.py'
2023-12-04T14:28:44,876   adding 'shephard/tests/test_domains.py'
2023-12-04T14:28:44,877   adding 'shephard/tests/test_interfaces.py'
2023-12-04T14:28:44,878   adding 'shephard/tests/test_logic.py'
2023-12-04T14:28:44,880   adding 'shephard/tests/test_protein.py'
2023-12-04T14:28:44,882   adding 'shephard/tests/test_protein_site_functions.py'
2023-12-04T14:28:44,883   adding 'shephard/tests/test_proteome.py'
2023-12-04T14:28:44,885   adding 'shephard/tests/test_scratchpad.ipynb'
2023-12-04T14:28:44,887   adding 'shephard/tests/test_sequence_tools.py'
2023-12-04T14:28:44,888   adding 'shephard/tests/test_shephard.py'
2023-12-04T14:28:44,889   adding 'shephard/tests/test_si_domains.py'
2023-12-04T14:28:44,891   adding 'shephard/tests/test_si_sites.py'
2023-12-04T14:28:44,893   adding 'shephard/tests/test_si_tracks.py'
2023-12-04T14:28:44,894   adding 'shephard/tests/test_sites.py'
2023-12-04T14:28:44,896   adding 'shephard/tests/test_track_tools.py'
2023-12-04T14:28:44,897   adding 'shephard/tests/test_tracks.py'
2023-12-04T14:28:44,898   adding 'shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb'
2023-12-04T14:28:44,900   adding 'shephard/tests/output_test/all_symbols_test.tsv'
2023-12-04T14:28:44,902   adding 'shephard/tests/output_test/all_values_test.tsv'
2023-12-04T14:28:44,905   adding 'shephard/tests/output_test/all_values_test_from_list.tsv'
2023-12-04T14:28:44,914   adding 'shephard/tests/output_test/out_tracks.tsv'
2023-12-04T14:28:44,915   adding 'shephard/tests/output_test/readme.md'
2023-12-04T14:28:44,917   adding 'shephard/tests/output_test/shephard_track_phosres.tsv'
2023-12-04T14:28:44,925   adding 'shephard/tests/output_test/shephard_track_pscore.tsv'
2023-12-04T14:28:44,926   adding 'shephard/tests/output_test/test_domains.tsv'
2023-12-04T14:28:44,928   adding 'shephard/tests/output_test/test_domains_types.tsv'
2023-12-04T14:28:44,931   adding 'shephard/tests/output_test/test_sites.tsv'
2023-12-04T14:28:44,932   adding 'shephard/tests/output_test/track_phospho_track.tsv'
2023-12-04T14:28:44,934   adding 'shephard/tests/output_test/track_random_vals.tsv'
2023-12-04T14:28:44,935   adding 'shephard/tools/__init__.py'
2023-12-04T14:28:44,939   adding 'shephard/tools/domain_tools.py'
2023-12-04T14:28:44,940   adding 'shephard/tools/experimental.py'
2023-12-04T14:28:44,941   adding 'shephard/tools/sequence_tools.py'
2023-12-04T14:28:44,943   adding 'shephard/tools/site_tools.py'
2023-12-04T14:28:44,944   adding 'shephard/tools/track_tools.py'
2023-12-04T14:28:44,946   adding 'shephard-0.1.20.dist-info/LICENSE'
2023-12-04T14:28:44,948   adding 'shephard-0.1.20.dist-info/METADATA'
2023-12-04T14:28:44,949   adding 'shephard-0.1.20.dist-info/WHEEL'
2023-12-04T14:28:44,950   adding 'shephard-0.1.20.dist-info/top_level.txt'
2023-12-04T14:28:44,951   adding 'shephard-0.1.20.dist-info/RECORD'
2023-12-04T14:28:44,955   removing build/bdist.linux-armv7l/wheel
2023-12-04T14:28:45,077   Building wheel for shephard (setup.py): finished with status 'done'
2023-12-04T14:28:45,081   Created wheel for shephard: filename=shephard-0.1.20-py3-none-any.whl size=198463 sha256=24e0e6400e28f09571d88701fe01ae333e945fde39dac06662db18acf07102f7
2023-12-04T14:28:45,082   Stored in directory: /tmp/pip-ephem-wheel-cache-118bdnap/wheels/65/b3/d6/11ac2ead7870d787fb4ca5fcb798942af84f9eefd5d0153e1d
2023-12-04T14:28:45,095 Successfully built shephard
2023-12-04T14:28:45,102 Removed build tracker: '/tmp/pip-build-tracker-8boimf4g'