2022-09-04T18:40:12,747 Created temporary directory: /tmp/pip-ephem-wheel-cache-vata44l5
2022-09-04T18:40:12,752 Created temporary directory: /tmp/pip-build-tracker-16qs57dl
2022-09-04T18:40:12,753 Initialized build tracking at /tmp/pip-build-tracker-16qs57dl
2022-09-04T18:40:12,753 Created build tracker: /tmp/pip-build-tracker-16qs57dl
2022-09-04T18:40:12,754 Entered build tracker: /tmp/pip-build-tracker-16qs57dl
2022-09-04T18:40:12,755 Created temporary directory: /tmp/pip-wheel-ogy_q3s3
2022-09-04T18:40:12,820 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2022-09-04T18:40:12,828 2 location(s) to search for versions of shephard:
2022-09-04T18:40:12,828 * https://pypi.org/simple/shephard/
2022-09-04T18:40:12,828 * https://www.piwheels.org/simple/shephard/
2022-09-04T18:40:12,829 Fetching project page and analyzing links: https://pypi.org/simple/shephard/
2022-09-04T18:40:12,830 Getting page https://pypi.org/simple/shephard/
2022-09-04T18:40:12,833 Found index url https://pypi.org/simple
2022-09-04T18:40:13,021   Found link https://files.pythonhosted.org/packages/a9/95/cbdbdeb72c0c4970872dc8b61c9df622274cc80602640b478e234c921234/shephard-0.1.5.tar.gz#sha256=dde3b1d4760dff0a87253ea62b9cf0762efd76c4c6aaeae254017e7dd58de730 (from https://pypi.org/simple/shephard/), version: 0.1.5
2022-09-04T18:40:13,022   Found link https://files.pythonhosted.org/packages/e9/11/69a637d6d4e0cb3a2addc9c06587e781747dfee014076fdaab76d466c46f/shephard-0.1.7.tar.gz#sha256=fc335190dca3e216cdfb474656b171b519c914c1a0907613f0e452e72e902c37 (from https://pypi.org/simple/shephard/), version: 0.1.7
2022-09-04T18:40:13,023   Found link https://files.pythonhosted.org/packages/b7/90/ea0b27088b3586d48ecaaae9743f8289d28c8e602c4aee5bb4e342b06fc5/shephard-0.1.8.tar.gz#sha256=ef741c657dac4ce44f5e94f73fe3721b4e8873e7b9f5c4b998567936db232335 (from https://pypi.org/simple/shephard/), version: 0.1.8
2022-09-04T18:40:13,024   Found link https://files.pythonhosted.org/packages/2d/0b/2c408626a7f199cb04f61d0fffb3372420ad5564e6bffb942646d140232a/shephard-0.1.12.tar.gz#sha256=5a73342bb93a0837965ee85f744ac04d2a7a7c14abfcc295da6fa1ff9e18fbaa (from https://pypi.org/simple/shephard/), version: 0.1.12
2022-09-04T18:40:13,025   Found link https://files.pythonhosted.org/packages/60/78/e58f5c608c7cc8363648b8466f262582a7de95a0331f7b3e87085cf31179/shephard-0.1.14.tar.gz#sha256=5ffd758fee0e494acbba492caf00b6e5755044b9187458ee97868843dffb767f (from https://pypi.org/simple/shephard/), version: 0.1.14
2022-09-04T18:40:13,025   Found link https://files.pythonhosted.org/packages/78/01/9fc9805f42e59bdf8a00197d349471405e1f27c254562ef81a79f0c67a18/shephard-0.1.15.tar.gz#sha256=43e9987b88dd017d24f0b8e91cf7b3a508662abbfd66cb4236d121ad5682b049 (from https://pypi.org/simple/shephard/), version: 0.1.15
2022-09-04T18:40:13,026   Found link https://files.pythonhosted.org/packages/c6/9c/5920ae7fe8ea8af0aa79d7d2554018f6408462d68ac30b501933c9870bc9/shephard-0.1.16.tar.gz#sha256=5de16f3b45c62dcd9997b0b31fe1551a442a4ea0b3c0efb04c615b6e987f179e (from https://pypi.org/simple/shephard/), version: 0.1.16
2022-09-04T18:40:13,027 Fetching project page and analyzing links: https://www.piwheels.org/simple/shephard/
2022-09-04T18:40:13,028 Getting page https://www.piwheels.org/simple/shephard/
2022-09-04T18:40:13,030 Found index url https://www.piwheels.org/simple
2022-09-04T18:40:13,248   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/)
2022-09-04T18:40:13,248   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/)
2022-09-04T18:40:13,249   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/)
2022-09-04T18:40:13,250   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/)
2022-09-04T18:40:13,250   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/)
2022-09-04T18:40:13,251   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/)
2022-09-04T18:40:13,251 Skipping link: not a file: https://www.piwheels.org/simple/shephard/
2022-09-04T18:40:13,252 Skipping link: not a file: https://pypi.org/simple/shephard/
2022-09-04T18:40:13,288 Given no hashes to check 1 links for project 'shephard': discarding no candidates
2022-09-04T18:40:13,319 Collecting shephard==0.1.16
2022-09-04T18:40:13,323   Created temporary directory: /tmp/pip-unpack-chdsocoe
2022-09-04T18:40:13,995   Downloading shephard-0.1.16.tar.gz (185 kB)
2022-09-04T18:40:14,643   Added shephard==0.1.16 from https://files.pythonhosted.org/packages/c6/9c/5920ae7fe8ea8af0aa79d7d2554018f6408462d68ac30b501933c9870bc9/shephard-0.1.16.tar.gz#sha256=5de16f3b45c62dcd9997b0b31fe1551a442a4ea0b3c0efb04c615b6e987f179e to build tracker '/tmp/pip-build-tracker-16qs57dl'
2022-09-04T18:40:14,646   Running setup.py (path:/tmp/pip-wheel-ogy_q3s3/shephard_91423ddc54734c79b28c8b7e044504a6/setup.py) egg_info for package shephard
2022-09-04T18:40:14,647   Created temporary directory: /tmp/pip-pip-egg-info-c0pirr2a
2022-09-04T18:40:14,648   Preparing metadata (setup.py): started
2022-09-04T18:40:14,650   Running command python setup.py egg_info
2022-09-04T18:40:22,158   running egg_info
2022-09-04T18:40:22,166   creating /tmp/pip-pip-egg-info-c0pirr2a/shephard.egg-info
2022-09-04T18:40:22,869   writing /tmp/pip-pip-egg-info-c0pirr2a/shephard.egg-info/PKG-INFO
2022-09-04T18:40:23,463   writing dependency_links to /tmp/pip-pip-egg-info-c0pirr2a/shephard.egg-info/dependency_links.txt
2022-09-04T18:40:26,415   writing requirements to /tmp/pip-pip-egg-info-c0pirr2a/shephard.egg-info/requires.txt
2022-09-04T18:40:27,005   writing top-level names to /tmp/pip-pip-egg-info-c0pirr2a/shephard.egg-info/top_level.txt
2022-09-04T18:40:27,008   writing manifest file '/tmp/pip-pip-egg-info-c0pirr2a/shephard.egg-info/SOURCES.txt'
2022-09-04T18:40:27,271   reading manifest file '/tmp/pip-pip-egg-info-c0pirr2a/shephard.egg-info/SOURCES.txt'
2022-09-04T18:40:27,275   reading manifest template 'MANIFEST.in'
2022-09-04T18:40:27,297   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:531: UserWarning: Normalizing 'v0.1.16' to '0.1.16'
2022-09-04T18:40:27,297     warnings.warn(tmpl.format(**locals()))
2022-09-04T18:40:27,297   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2022-09-04T18:40:27,300   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2022-09-04T18:40:27,302   warning: no previously-included files matching '*.so' found anywhere in distribution
2022-09-04T18:40:27,303   adding license file 'LICENSE'
2022-09-04T18:40:27,315   writing manifest file '/tmp/pip-pip-egg-info-c0pirr2a/shephard.egg-info/SOURCES.txt'
2022-09-04T18:40:27,533   Preparing metadata (setup.py): finished with status 'done'
2022-09-04T18:40:27,545   Source in /tmp/pip-wheel-ogy_q3s3/shephard_91423ddc54734c79b28c8b7e044504a6 has version 0.1.16, which satisfies requirement shephard==0.1.16 from https://files.pythonhosted.org/packages/c6/9c/5920ae7fe8ea8af0aa79d7d2554018f6408462d68ac30b501933c9870bc9/shephard-0.1.16.tar.gz#sha256=5de16f3b45c62dcd9997b0b31fe1551a442a4ea0b3c0efb04c615b6e987f179e
2022-09-04T18:40:27,547   Removed shephard==0.1.16 from https://files.pythonhosted.org/packages/c6/9c/5920ae7fe8ea8af0aa79d7d2554018f6408462d68ac30b501933c9870bc9/shephard-0.1.16.tar.gz#sha256=5de16f3b45c62dcd9997b0b31fe1551a442a4ea0b3c0efb04c615b6e987f179e from build tracker '/tmp/pip-build-tracker-16qs57dl'
2022-09-04T18:40:27,556 Created temporary directory: /tmp/pip-unpack-f37z084g
2022-09-04T18:40:27,558 Building wheels for collected packages: shephard
2022-09-04T18:40:27,568   Created temporary directory: /tmp/pip-wheel-5v92c2oq
2022-09-04T18:40:27,569   Building wheel for shephard (setup.py): started
2022-09-04T18:40:27,571   Destination directory: /tmp/pip-wheel-5v92c2oq
2022-09-04T18:40:27,572   Running command python setup.py bdist_wheel
2022-09-04T18:40:34,192   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:531: UserWarning: Normalizing 'v0.1.16' to '0.1.16'
2022-09-04T18:40:34,193     warnings.warn(tmpl.format(**locals()))
2022-09-04T18:40:34,491   running bdist_wheel
2022-09-04T18:40:34,828   running build
2022-09-04T18:40:34,828   running build_py
2022-09-04T18:40:34,842   creating build
2022-09-04T18:40:34,843   creating build/lib
2022-09-04T18:40:34,844   creating build/lib/shephard
2022-09-04T18:40:34,846   copying shephard/test_domains_sites.py -> build/lib/shephard
2022-09-04T18:40:34,850   copying shephard/__init__.py -> build/lib/shephard
2022-09-04T18:40:34,853   copying shephard/site.py -> build/lib/shephard
2022-09-04T18:40:34,859   copying shephard/track.py -> build/lib/shephard
2022-09-04T18:40:34,863   copying shephard/exceptions.py -> build/lib/shephard
2022-09-04T18:40:34,867   copying shephard/general_utilities.py -> build/lib/shephard
2022-09-04T18:40:34,870   copying shephard/sequence_utilities.py -> build/lib/shephard
2022-09-04T18:40:34,873   copying shephard/proteome.py -> build/lib/shephard
2022-09-04T18:40:34,879   copying shephard/domain.py -> build/lib/shephard
2022-09-04T18:40:34,883   copying shephard/protein.py -> build/lib/shephard
2022-09-04T18:40:34,891   copying shephard/_version.py -> build/lib/shephard
2022-09-04T18:40:34,897   creating build/lib/shephard/tests
2022-09-04T18:40:34,898   copying shephard/tests/test_add_remove_annotations.py -> build/lib/shephard/tests
2022-09-04T18:40:34,902   copying shephard/tests/test_si_domains.py -> build/lib/shephard/tests
2022-09-04T18:40:34,906   copying shephard/tests/test_logic.py -> build/lib/shephard/tests
2022-09-04T18:40:34,908   copying shephard/tests/__init__.py -> build/lib/shephard/tests
2022-09-04T18:40:34,911   copying shephard/tests/test_shephard.py -> build/lib/shephard/tests
2022-09-04T18:40:34,914   copying shephard/tests/test_interfaces.py -> build/lib/shephard/tests
2022-09-04T18:40:34,917   copying shephard/tests/test_domains.py -> build/lib/shephard/tests
2022-09-04T18:40:34,922   copying shephard/tests/test_si_sites.py -> build/lib/shephard/tests
2022-09-04T18:40:34,925   copying shephard/tests/test_protein_site_functions.py -> build/lib/shephard/tests
2022-09-04T18:40:34,929   copying shephard/tests/conftest.py -> build/lib/shephard/tests
2022-09-04T18:40:34,932   copying shephard/tests/test_tracks.py -> build/lib/shephard/tests
2022-09-04T18:40:34,935   copying shephard/tests/test_apis_fasta.py -> build/lib/shephard/tests
2022-09-04T18:40:34,939   copying shephard/tests/example_test_function.py -> build/lib/shephard/tests
2022-09-04T18:40:34,943   copying shephard/tests/test_sequence_tools.py -> build/lib/shephard/tests
2022-09-04T18:40:34,946   copying shephard/tests/test_proteome.py -> build/lib/shephard/tests
2022-09-04T18:40:34,949   copying shephard/tests/test_protein.py -> build/lib/shephard/tests
2022-09-04T18:40:34,954   copying shephard/tests/test_sites.py -> build/lib/shephard/tests
2022-09-04T18:40:34,957   copying shephard/tests/test_track_tools.py -> build/lib/shephard/tests
2022-09-04T18:40:34,961   copying shephard/tests/test_domain_tools.py -> build/lib/shephard/tests
2022-09-04T18:40:34,965   copying shephard/tests/test_si_tracks.py -> build/lib/shephard/tests
2022-09-04T18:40:34,970   creating build/lib/shephard/apis
2022-09-04T18:40:34,972   copying shephard/apis/__init__.py -> build/lib/shephard/apis
2022-09-04T18:40:34,975   copying shephard/apis/uniprot.py -> build/lib/shephard/apis
2022-09-04T18:40:34,979   copying shephard/apis/fasta.py -> build/lib/shephard/apis
2022-09-04T18:40:34,985   creating build/lib/shephard/interfaces
2022-09-04T18:40:34,987   copying shephard/interfaces/si_sites.py -> build/lib/shephard/interfaces
2022-09-04T18:40:34,992   copying shephard/interfaces/__init__.py -> build/lib/shephard/interfaces
2022-09-04T18:40:34,995   copying shephard/interfaces/interface_tools.py -> build/lib/shephard/interfaces
2022-09-04T18:40:35,000   copying shephard/interfaces/si_domains.py -> build/lib/shephard/interfaces
2022-09-04T18:40:35,005   copying shephard/interfaces/si_protein_attributes.py -> build/lib/shephard/interfaces
2022-09-04T18:40:35,010   copying shephard/interfaces/si_proteins.py -> build/lib/shephard/interfaces
2022-09-04T18:40:35,014   copying shephard/interfaces/si_tracks.py -> build/lib/shephard/interfaces
2022-09-04T18:40:35,021   creating build/lib/shephard/tools
2022-09-04T18:40:35,022   copying shephard/tools/__init__.py -> build/lib/shephard/tools
2022-09-04T18:40:35,026   copying shephard/tools/sequence_tools.py -> build/lib/shephard/tools
2022-09-04T18:40:35,029   copying shephard/tools/experimental.py -> build/lib/shephard/tools
2022-09-04T18:40:35,033   copying shephard/tools/domain_tools.py -> build/lib/shephard/tools
2022-09-04T18:40:35,037   copying shephard/tools/site_tools.py -> build/lib/shephard/tools
2022-09-04T18:40:35,041   copying shephard/tools/track_tools.py -> build/lib/shephard/tools
2022-09-04T18:40:35,043   running egg_info
2022-09-04T18:40:36,445   writing shephard.egg-info/PKG-INFO
2022-09-04T18:40:37,029   writing dependency_links to shephard.egg-info/dependency_links.txt
2022-09-04T18:40:39,939   writing requirements to shephard.egg-info/requires.txt
2022-09-04T18:40:40,523   writing top-level names to shephard.egg-info/top_level.txt
2022-09-04T18:40:40,649   reading manifest file 'shephard.egg-info/SOURCES.txt'
2022-09-04T18:40:40,672   reading manifest template 'MANIFEST.in'
2022-09-04T18:40:40,688   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2022-09-04T18:40:40,690   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2022-09-04T18:40:40,692   warning: no previously-included files matching '*.so' found anywhere in distribution
2022-09-04T18:40:40,692   adding license file 'LICENSE'
2022-09-04T18:40:40,709   writing manifest file 'shephard.egg-info/SOURCES.txt'
2022-09-04T18:40:40,715   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning:     !!


2022-09-04T18:40:40,716       ############################
2022-09-04T18:40:40,716       # Package would be ignored #
2022-09-04T18:40:40,716       ############################
2022-09-04T18:40:40,717       Python recognizes 'shephard.data' as an importable package, however it is
2022-09-04T18:40:40,717       included in the distribution as "data".
2022-09-04T18:40:40,717       This behavior is likely to change in future versions of setuptools (and
2022-09-04T18:40:40,718       therefore is considered deprecated).

2022-09-04T18:40:40,718       Please make sure that 'shephard.data' is included as a package by using
2022-09-04T18:40:40,719       setuptools' `packages` configuration field or the proper discovery methods.

2022-09-04T18:40:40,719       You can read more about "package discovery" and "data files" on setuptools
2022-09-04T18:40:40,720       documentation page.


2022-09-04T18:40:40,720   !!

2022-09-04T18:40:40,721     check.warn(importable)
2022-09-04T18:40:40,721   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning:     !!


2022-09-04T18:40:40,722       ############################
2022-09-04T18:40:40,723       # Package would be ignored #
2022-09-04T18:40:40,723       ############################
2022-09-04T18:40:40,723       Python recognizes 'shephard.data.test_data' as an importable package, however it is
2022-09-04T18:40:40,724       included in the distribution as "data".
2022-09-04T18:40:40,724       This behavior is likely to change in future versions of setuptools (and
2022-09-04T18:40:40,724       therefore is considered deprecated).

2022-09-04T18:40:40,725       Please make sure that 'shephard.data.test_data' is included as a package by using
2022-09-04T18:40:40,725       setuptools' `packages` configuration field or the proper discovery methods.

2022-09-04T18:40:40,726       You can read more about "package discovery" and "data files" on setuptools
2022-09-04T18:40:40,726       documentation page.


2022-09-04T18:40:40,727   !!

2022-09-04T18:40:40,727     check.warn(importable)
2022-09-04T18:40:40,728   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning:     !!


2022-09-04T18:40:40,729       ############################
2022-09-04T18:40:40,729       # Package would be ignored #
2022-09-04T18:40:40,729       ############################
2022-09-04T18:40:40,730       Python recognizes 'shephard.tests.output_test' as an importable package, however it is
2022-09-04T18:40:40,730       included in the distribution as "data".
2022-09-04T18:40:40,730       This behavior is likely to change in future versions of setuptools (and
2022-09-04T18:40:40,731       therefore is considered deprecated).

2022-09-04T18:40:40,731       Please make sure that 'shephard.tests.output_test' is included as a package by using
2022-09-04T18:40:40,732       setuptools' `packages` configuration field or the proper discovery methods.

2022-09-04T18:40:40,732       You can read more about "package discovery" and "data files" on setuptools
2022-09-04T18:40:40,733       documentation page.


2022-09-04T18:40:40,734   !!

2022-09-04T18:40:40,734     check.warn(importable)
2022-09-04T18:40:40,735   creating build/lib/shephard/data
2022-09-04T18:40:40,735   copying shephard/data/README.md -> build/lib/shephard/data
2022-09-04T18:40:40,735   copying shephard/data/look_and_say.dat -> build/lib/shephard/data
2022-09-04T18:40:40,739   creating build/lib/shephard/data/test_data
2022-09-04T18:40:40,740   copying shephard/data/test_data/TS1_domains_idr.tsv -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,744   copying shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,748   copying shephard/data/test_data/TS1_domains_pscore.tsv -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,752   copying shephard/data/test_data/TS1_protein_attributes.tsv -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,756   copying shephard/data/test_data/TS1_sites.tsv -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,760   copying shephard/data/test_data/TS1_tracks_pscore.tsv -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,766   copying shephard/data/test_data/names.txt -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,770   copying shephard/data/test_data/seqs.fasta -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,775   copying shephard/data/test_data/testset_1.fasta -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,780   copying shephard/data/test_data/testset_1.fasta.fai -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,784   copying shephard/data/test_data/testset_1_ptms.tsv -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,788   copying shephard/data/test_data/ts1_bonus_sites.tsv -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,792   copying shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,796   copying shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,800   copying shephard/data/test_data/tst.py -> build/lib/shephard/data/test_data
2022-09-04T18:40:40,805   copying shephard/tests/test_protein_site_functions.py~ -> build/lib/shephard/tests
2022-09-04T18:40:40,810   copying shephard/tests/test_scratchpad.ipynb -> build/lib/shephard/tests
2022-09-04T18:40:40,814   creating build/lib/shephard/tests/.ipynb_checkpoints
2022-09-04T18:40:40,816   copying shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/lib/shephard/tests/.ipynb_checkpoints
2022-09-04T18:40:40,820   creating build/lib/shephard/tests/output_test
2022-09-04T18:40:40,822   copying shephard/tests/output_test/all_symbols_test.tsv -> build/lib/shephard/tests/output_test
2022-09-04T18:40:40,826   copying shephard/tests/output_test/all_values_test.tsv -> build/lib/shephard/tests/output_test
2022-09-04T18:40:40,832   copying shephard/tests/output_test/all_values_test_from_list.tsv -> build/lib/shephard/tests/output_test
2022-09-04T18:40:40,839   copying shephard/tests/output_test/out_tracks.tsv -> build/lib/shephard/tests/output_test
2022-09-04T18:40:40,844   copying shephard/tests/output_test/readme.md -> build/lib/shephard/tests/output_test
2022-09-04T18:40:40,848   copying shephard/tests/output_test/shephard_track_phosres.tsv -> build/lib/shephard/tests/output_test
2022-09-04T18:40:40,853   copying shephard/tests/output_test/shephard_track_pscore.tsv -> build/lib/shephard/tests/output_test
2022-09-04T18:40:40,859   copying shephard/tests/output_test/test_domains.tsv -> build/lib/shephard/tests/output_test
2022-09-04T18:40:40,863   copying shephard/tests/output_test/test_sites.tsv -> build/lib/shephard/tests/output_test
2022-09-04T18:40:40,871   copying shephard/tests/output_test/track_phospho_track.tsv -> build/lib/shephard/tests/output_test
2022-09-04T18:40:40,875   copying shephard/tests/output_test/track_random_vals.tsv -> build/lib/shephard/tests/output_test
2022-09-04T18:40:40,890   UPDATING build/lib/shephard/_version.py
2022-09-04T18:40:40,893   set build/lib/shephard/_version.py to 'v0.1.16'
2022-09-04T18:40:41,595   /usr/local/lib/python3.7/dist-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
2022-09-04T18:40:41,596     setuptools.SetuptoolsDeprecationWarning,
2022-09-04T18:40:42,295   installing to build/bdist.linux-armv7l/wheel
2022-09-04T18:40:42,296   running install
2022-09-04T18:40:42,357   running install_lib
2022-09-04T18:40:43,072   creating build/bdist.linux-armv7l
2022-09-04T18:40:43,073   creating build/bdist.linux-armv7l/wheel
2022-09-04T18:40:43,077   creating build/bdist.linux-armv7l/wheel/shephard
2022-09-04T18:40:43,080   creating build/bdist.linux-armv7l/wheel/shephard/data
2022-09-04T18:40:43,084   creating build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,086   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,091   copying build/lib/shephard/data/test_data/TS1_protein_attributes.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,094   copying build/lib/shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,098   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,101   copying build/lib/shephard/data/test_data/TS1_tracks_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,107   copying build/lib/shephard/data/test_data/TS1_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,111   copying build/lib/shephard/data/test_data/ts1_bonus_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,114   copying build/lib/shephard/data/test_data/tst.py -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,118   copying build/lib/shephard/data/test_data/seqs.fasta -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,122   copying build/lib/shephard/data/test_data/names.txt -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,125   copying build/lib/shephard/data/test_data/testset_1_ptms.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,129   copying build/lib/shephard/data/test_data/testset_1.fasta -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,133   copying build/lib/shephard/data/test_data/TS1_domains_idr.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,136   copying build/lib/shephard/data/test_data/TS1_domains_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,139   copying build/lib/shephard/data/test_data/testset_1.fasta.fai -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T18:40:43,143   copying build/lib/shephard/data/look_and_say.dat -> build/bdist.linux-armv7l/wheel/shephard/data
2022-09-04T18:40:43,146   copying build/lib/shephard/data/README.md -> build/bdist.linux-armv7l/wheel/shephard/data
2022-09-04T18:40:43,150   copying build/lib/shephard/test_domains_sites.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T18:40:43,153   copying build/lib/shephard/__init__.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T18:40:43,158   creating build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,161   creating build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T18:40:43,163   copying build/lib/shephard/tests/output_test/track_phospho_track.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T18:40:43,167   copying build/lib/shephard/tests/output_test/out_tracks.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T18:40:43,173   copying build/lib/shephard/tests/output_test/all_symbols_test.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T18:40:43,177   copying build/lib/shephard/tests/output_test/all_values_test_from_list.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T18:40:43,182   copying build/lib/shephard/tests/output_test/all_values_test.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T18:40:43,189   copying build/lib/shephard/tests/output_test/test_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T18:40:43,196   copying build/lib/shephard/tests/output_test/test_domains.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T18:40:43,201   copying build/lib/shephard/tests/output_test/shephard_track_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T18:40:43,207   copying build/lib/shephard/tests/output_test/readme.md -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T18:40:43,211   copying build/lib/shephard/tests/output_test/shephard_track_phosres.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T18:40:43,215   copying build/lib/shephard/tests/output_test/track_random_vals.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T18:40:43,219   copying build/lib/shephard/tests/test_add_remove_annotations.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,223   copying build/lib/shephard/tests/test_si_domains.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,228   copying build/lib/shephard/tests/test_logic.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,231   copying build/lib/shephard/tests/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,235   copying build/lib/shephard/tests/test_shephard.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,239   copying build/lib/shephard/tests/test_interfaces.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,243   copying build/lib/shephard/tests/test_domains.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,250   creating build/bdist.linux-armv7l/wheel/shephard/tests/.ipynb_checkpoints
2022-09-04T18:40:43,252   copying build/lib/shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/bdist.linux-armv7l/wheel/shephard/tests/.ipynb_checkpoints
2022-09-04T18:40:43,256   copying build/lib/shephard/tests/test_si_sites.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,260   copying build/lib/shephard/tests/test_protein_site_functions.py~ -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,266   copying build/lib/shephard/tests/test_protein_site_functions.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,270   copying build/lib/shephard/tests/test_scratchpad.ipynb -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,275   copying build/lib/shephard/tests/conftest.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,279   copying build/lib/shephard/tests/test_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,283   copying build/lib/shephard/tests/test_apis_fasta.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,288   copying build/lib/shephard/tests/example_test_function.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,292   copying build/lib/shephard/tests/test_sequence_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,295   copying build/lib/shephard/tests/test_proteome.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,299   copying build/lib/shephard/tests/test_protein.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,304   copying build/lib/shephard/tests/test_sites.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,309   copying build/lib/shephard/tests/test_track_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,312   copying build/lib/shephard/tests/test_domain_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,317   copying build/lib/shephard/tests/test_si_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T18:40:43,323   copying build/lib/shephard/site.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T18:40:43,328   copying build/lib/shephard/track.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T18:40:43,333   copying build/lib/shephard/exceptions.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T18:40:43,338   creating build/bdist.linux-armv7l/wheel/shephard/apis
2022-09-04T18:40:43,340   copying build/lib/shephard/apis/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2022-09-04T18:40:43,344   copying build/lib/shephard/apis/uniprot.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2022-09-04T18:40:43,349   copying build/lib/shephard/apis/fasta.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2022-09-04T18:40:43,354   copying build/lib/shephard/general_utilities.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T18:40:43,358   copying build/lib/shephard/sequence_utilities.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T18:40:43,363   creating build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T18:40:43,365   copying build/lib/shephard/interfaces/si_sites.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T18:40:43,371   copying build/lib/shephard/interfaces/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T18:40:43,375   copying build/lib/shephard/interfaces/interface_tools.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T18:40:43,380   copying build/lib/shephard/interfaces/si_domains.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T18:40:43,386   copying build/lib/shephard/interfaces/si_protein_attributes.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T18:40:43,390   copying build/lib/shephard/interfaces/si_proteins.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T18:40:43,395   copying build/lib/shephard/interfaces/si_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T18:40:43,401   copying build/lib/shephard/proteome.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T18:40:43,408   copying build/lib/shephard/domain.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T18:40:43,414   creating build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T18:40:43,415   copying build/lib/shephard/tools/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T18:40:43,419   copying build/lib/shephard/tools/sequence_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T18:40:43,422   copying build/lib/shephard/tools/experimental.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T18:40:43,426   copying build/lib/shephard/tools/domain_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T18:40:43,430   copying build/lib/shephard/tools/site_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T18:40:43,434   copying build/lib/shephard/tools/track_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T18:40:43,437   copying build/lib/shephard/protein.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T18:40:43,447   copying build/lib/shephard/_version.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T18:40:43,449   running install_egg_info
2022-09-04T18:40:44,161   Copying shephard.egg-info to build/bdist.linux-armv7l/wheel/shephard-0.1.16-py3.7.egg-info
2022-09-04T18:40:44,181   running install_scripts
2022-09-04T18:40:44,322   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2022-09-04T18:40:44,331   creating build/bdist.linux-armv7l/wheel/shephard-0.1.16.dist-info/WHEEL
2022-09-04T18:40:44,335   creating '/tmp/pip-wheel-5v92c2oq/shephard-0.1.16-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2022-09-04T18:40:44,340   adding 'shephard/__init__.py'
2022-09-04T18:40:44,342   adding 'shephard/_version.py'
2022-09-04T18:40:44,348   adding 'shephard/domain.py'
2022-09-04T18:40:44,351   adding 'shephard/exceptions.py'
2022-09-04T18:40:44,354   adding 'shephard/general_utilities.py'
2022-09-04T18:40:44,378   adding 'shephard/protein.py'
2022-09-04T18:40:44,392   adding 'shephard/proteome.py'
2022-09-04T18:40:44,396   adding 'shephard/sequence_utilities.py'
2022-09-04T18:40:44,401   adding 'shephard/site.py'
2022-09-04T18:40:44,404   adding 'shephard/test_domains_sites.py'
2022-09-04T18:40:44,408   adding 'shephard/track.py'
2022-09-04T18:40:44,412   adding 'shephard/apis/__init__.py'
2022-09-04T18:40:44,417   adding 'shephard/apis/fasta.py'
2022-09-04T18:40:44,421   adding 'shephard/apis/uniprot.py'
2022-09-04T18:40:44,425   adding 'shephard/data/README.md'
2022-09-04T18:40:44,427   adding 'shephard/data/look_and_say.dat'
2022-09-04T18:40:44,431   adding 'shephard/data/test_data/TS1_domains_idr.tsv'
2022-09-04T18:40:44,433   adding 'shephard/data/test_data/TS1_domains_idr_and_others.tsv'
2022-09-04T18:40:44,435   adding 'shephard/data/test_data/TS1_domains_pscore.tsv'
2022-09-04T18:40:44,437   adding 'shephard/data/test_data/TS1_protein_attributes.tsv'
2022-09-04T18:40:44,440   adding 'shephard/data/test_data/TS1_sites.tsv'
2022-09-04T18:40:44,462   adding 'shephard/data/test_data/TS1_tracks_pscore.tsv'
2022-09-04T18:40:44,464   adding 'shephard/data/test_data/names.txt'
2022-09-04T18:40:44,468   adding 'shephard/data/test_data/seqs.fasta'
2022-09-04T18:40:44,471   adding 'shephard/data/test_data/testset_1.fasta'
2022-09-04T18:40:44,473   adding 'shephard/data/test_data/testset_1.fasta.fai'
2022-09-04T18:40:44,475   adding 'shephard/data/test_data/testset_1_ptms.tsv'
2022-09-04T18:40:44,477   adding 'shephard/data/test_data/ts1_bonus_sites.tsv'
2022-09-04T18:40:44,479   adding 'shephard/data/test_data/ts1_bonus_sites_bad.tsv'
2022-09-04T18:40:44,481   adding 'shephard/data/test_data/ts1_bonus_sites_bad2.tsv'
2022-09-04T18:40:44,484   adding 'shephard/data/test_data/tst.py'
2022-09-04T18:40:44,487   adding 'shephard/interfaces/__init__.py'
2022-09-04T18:40:44,491   adding 'shephard/interfaces/interface_tools.py'
2022-09-04T18:40:44,498   adding 'shephard/interfaces/si_domains.py'
2022-09-04T18:40:44,503   adding 'shephard/interfaces/si_protein_attributes.py'
2022-09-04T18:40:44,508   adding 'shephard/interfaces/si_proteins.py'
2022-09-04T18:40:44,513   adding 'shephard/interfaces/si_sites.py'
2022-09-04T18:40:44,521   adding 'shephard/interfaces/si_tracks.py'
2022-09-04T18:40:44,526   adding 'shephard/tests/__init__.py'
2022-09-04T18:40:44,529   adding 'shephard/tests/conftest.py'
2022-09-04T18:40:44,531   adding 'shephard/tests/example_test_function.py'
2022-09-04T18:40:44,533   adding 'shephard/tests/test_add_remove_annotations.py'
2022-09-04T18:40:44,536   adding 'shephard/tests/test_apis_fasta.py'
2022-09-04T18:40:44,539   adding 'shephard/tests/test_domain_tools.py'
2022-09-04T18:40:44,543   adding 'shephard/tests/test_domains.py'
2022-09-04T18:40:44,545   adding 'shephard/tests/test_interfaces.py'
2022-09-04T18:40:44,547   adding 'shephard/tests/test_logic.py'
2022-09-04T18:40:44,551   adding 'shephard/tests/test_protein.py'
2022-09-04T18:40:44,554   adding 'shephard/tests/test_protein_site_functions.py'
2022-09-04T18:40:44,558   adding 'shephard/tests/test_protein_site_functions.py~'
2022-09-04T18:40:44,561   adding 'shephard/tests/test_proteome.py'
2022-09-04T18:40:44,564   adding 'shephard/tests/test_scratchpad.ipynb'
2022-09-04T18:40:44,567   adding 'shephard/tests/test_sequence_tools.py'
2022-09-04T18:40:44,569   adding 'shephard/tests/test_shephard.py'
2022-09-04T18:40:44,571   adding 'shephard/tests/test_si_domains.py'
2022-09-04T18:40:44,574   adding 'shephard/tests/test_si_sites.py'
2022-09-04T18:40:44,578   adding 'shephard/tests/test_si_tracks.py'
2022-09-04T18:40:44,581   adding 'shephard/tests/test_sites.py'
2022-09-04T18:40:44,583   adding 'shephard/tests/test_track_tools.py'
2022-09-04T18:40:44,585   adding 'shephard/tests/test_tracks.py'
2022-09-04T18:40:44,589   adding 'shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb'
2022-09-04T18:40:44,592   adding 'shephard/tests/output_test/all_symbols_test.tsv'
2022-09-04T18:40:44,597   adding 'shephard/tests/output_test/all_values_test.tsv'
2022-09-04T18:40:44,604   adding 'shephard/tests/output_test/all_values_test_from_list.tsv'
2022-09-04T18:40:44,626   adding 'shephard/tests/output_test/out_tracks.tsv'
2022-09-04T18:40:44,629   adding 'shephard/tests/output_test/readme.md'
2022-09-04T18:40:44,631   adding 'shephard/tests/output_test/shephard_track_phosres.tsv'
2022-09-04T18:40:44,652   adding 'shephard/tests/output_test/shephard_track_pscore.tsv'
2022-09-04T18:40:44,655   adding 'shephard/tests/output_test/test_domains.tsv'
2022-09-04T18:40:44,662   adding 'shephard/tests/output_test/test_sites.tsv'
2022-09-04T18:40:44,665   adding 'shephard/tests/output_test/track_phospho_track.tsv'
2022-09-04T18:40:44,668   adding 'shephard/tests/output_test/track_random_vals.tsv'
2022-09-04T18:40:44,671   adding 'shephard/tools/__init__.py'
2022-09-04T18:40:44,678   adding 'shephard/tools/domain_tools.py'
2022-09-04T18:40:44,681   adding 'shephard/tools/experimental.py'
2022-09-04T18:40:44,684   adding 'shephard/tools/sequence_tools.py'
2022-09-04T18:40:44,686   adding 'shephard/tools/site_tools.py'
2022-09-04T18:40:44,689   adding 'shephard/tools/track_tools.py'
2022-09-04T18:40:44,694   adding 'shephard-0.1.16.dist-info/LICENSE'
2022-09-04T18:40:44,697   adding 'shephard-0.1.16.dist-info/METADATA'
2022-09-04T18:40:44,699   adding 'shephard-0.1.16.dist-info/WHEEL'
2022-09-04T18:40:44,700   adding 'shephard-0.1.16.dist-info/top_level.txt'
2022-09-04T18:40:44,703   adding 'shephard-0.1.16.dist-info/RECORD'
2022-09-04T18:40:44,714   removing build/bdist.linux-armv7l/wheel
2022-09-04T18:40:45,003   Building wheel for shephard (setup.py): finished with status 'done'
2022-09-04T18:40:45,015   Created wheel for shephard: filename=shephard-0.1.16-py3-none-any.whl size=182440 sha256=f8e78c819d4b0150399cc6bb2176f78cba05e409f65559ce80fd765577c27f81
2022-09-04T18:40:45,017   Stored in directory: /tmp/pip-ephem-wheel-cache-vata44l5/wheels/67/25/53/32813f6b863312b2dd7313839976af02570570a26e2ad562ff
2022-09-04T18:40:45,046 Successfully built shephard
2022-09-04T18:40:45,066 Removed build tracker: '/tmp/pip-build-tracker-16qs57dl'