2022-09-04T00:44:08,525 Created temporary directory: /tmp/pip-ephem-wheel-cache-z4_xeq4d
2022-09-04T00:44:08,531 Created temporary directory: /tmp/pip-build-tracker-xwzw9qub
2022-09-04T00:44:08,532 Initialized build tracking at /tmp/pip-build-tracker-xwzw9qub
2022-09-04T00:44:08,532 Created build tracker: /tmp/pip-build-tracker-xwzw9qub
2022-09-04T00:44:08,532 Entered build tracker: /tmp/pip-build-tracker-xwzw9qub
2022-09-04T00:44:08,534 Created temporary directory: /tmp/pip-wheel-n1wsj416
2022-09-04T00:44:08,604 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2022-09-04T00:44:08,612 2 location(s) to search for versions of shephard:
2022-09-04T00:44:08,612 * https://pypi.org/simple/shephard/
2022-09-04T00:44:08,612 * https://www.piwheels.org/simple/shephard/
2022-09-04T00:44:08,613 Fetching project page and analyzing links: https://pypi.org/simple/shephard/
2022-09-04T00:44:08,614 Getting page https://pypi.org/simple/shephard/
2022-09-04T00:44:08,618 Found index url https://pypi.org/simple
2022-09-04T00:44:08,752   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
2022-09-04T00:44:08,753   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
2022-09-04T00:44:08,754   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
2022-09-04T00:44:08,755   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
2022-09-04T00:44:08,755   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
2022-09-04T00:44:08,756   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
2022-09-04T00:44:08,757 Fetching project page and analyzing links: https://www.piwheels.org/simple/shephard/
2022-09-04T00:44:08,758 Getting page https://www.piwheels.org/simple/shephard/
2022-09-04T00:44:08,760 Found index url https://www.piwheels.org/simple
2022-09-04T00:44:08,972   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/)
2022-09-04T00:44:08,973   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/)
2022-09-04T00:44:08,973   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/)
2022-09-04T00:44:08,974   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/)
2022-09-04T00:44:08,974 Skipping link: not a file: https://www.piwheels.org/simple/shephard/
2022-09-04T00:44:08,975 Skipping link: not a file: https://pypi.org/simple/shephard/
2022-09-04T00:44:09,010 Given no hashes to check 1 links for project 'shephard': discarding no candidates
2022-09-04T00:44:09,041 Collecting shephard==0.1.15
2022-09-04T00:44:09,046   Created temporary directory: /tmp/pip-unpack-mbtukrr8
2022-09-04T00:44:09,446   Downloading shephard-0.1.15.tar.gz (183 kB)
2022-09-04T00:44:10,085   Added shephard==0.1.15 from https://files.pythonhosted.org/packages/78/01/9fc9805f42e59bdf8a00197d349471405e1f27c254562ef81a79f0c67a18/shephard-0.1.15.tar.gz#sha256=43e9987b88dd017d24f0b8e91cf7b3a508662abbfd66cb4236d121ad5682b049 to build tracker '/tmp/pip-build-tracker-xwzw9qub'
2022-09-04T00:44:10,088   Running setup.py (path:/tmp/pip-wheel-n1wsj416/shephard_9606ad763f6a4ca29377378f864ebab7/setup.py) egg_info for package shephard
2022-09-04T00:44:10,089   Created temporary directory: /tmp/pip-pip-egg-info-46nhyf6z
2022-09-04T00:44:10,090   Preparing metadata (setup.py): started
2022-09-04T00:44:10,092   Running command python setup.py egg_info
2022-09-04T00:44:18,084   running egg_info
2022-09-04T00:44:18,089   creating /tmp/pip-pip-egg-info-46nhyf6z/shephard.egg-info
2022-09-04T00:44:18,839   writing /tmp/pip-pip-egg-info-46nhyf6z/shephard.egg-info/PKG-INFO
2022-09-04T00:44:19,446   writing dependency_links to /tmp/pip-pip-egg-info-46nhyf6z/shephard.egg-info/dependency_links.txt
2022-09-04T00:44:22,478   writing requirements to /tmp/pip-pip-egg-info-46nhyf6z/shephard.egg-info/requires.txt
2022-09-04T00:44:23,086   writing top-level names to /tmp/pip-pip-egg-info-46nhyf6z/shephard.egg-info/top_level.txt
2022-09-04T00:44:23,088   writing manifest file '/tmp/pip-pip-egg-info-46nhyf6z/shephard.egg-info/SOURCES.txt'
2022-09-04T00:44:23,416   reading manifest file '/tmp/pip-pip-egg-info-46nhyf6z/shephard.egg-info/SOURCES.txt'
2022-09-04T00:44:23,419   reading manifest template 'MANIFEST.in'
2022-09-04T00:44:23,439   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:531: UserWarning: Normalizing 'v0.1.15' to '0.1.15'
2022-09-04T00:44:23,439     warnings.warn(tmpl.format(**locals()))
2022-09-04T00:44:23,440   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2022-09-04T00:44:23,440   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2022-09-04T00:44:23,442   warning: no previously-included files matching '*.so' found anywhere in distribution
2022-09-04T00:44:23,442   adding license file 'LICENSE'
2022-09-04T00:44:23,454   writing manifest file '/tmp/pip-pip-egg-info-46nhyf6z/shephard.egg-info/SOURCES.txt'
2022-09-04T00:44:23,673   Preparing metadata (setup.py): finished with status 'done'
2022-09-04T00:44:23,684   Source in /tmp/pip-wheel-n1wsj416/shephard_9606ad763f6a4ca29377378f864ebab7 has version 0.1.15, which satisfies requirement shephard==0.1.15 from https://files.pythonhosted.org/packages/78/01/9fc9805f42e59bdf8a00197d349471405e1f27c254562ef81a79f0c67a18/shephard-0.1.15.tar.gz#sha256=43e9987b88dd017d24f0b8e91cf7b3a508662abbfd66cb4236d121ad5682b049
2022-09-04T00:44:23,686   Removed shephard==0.1.15 from https://files.pythonhosted.org/packages/78/01/9fc9805f42e59bdf8a00197d349471405e1f27c254562ef81a79f0c67a18/shephard-0.1.15.tar.gz#sha256=43e9987b88dd017d24f0b8e91cf7b3a508662abbfd66cb4236d121ad5682b049 from build tracker '/tmp/pip-build-tracker-xwzw9qub'
2022-09-04T00:44:23,696 Created temporary directory: /tmp/pip-unpack-_3eyeqr7
2022-09-04T00:44:23,697 Building wheels for collected packages: shephard
2022-09-04T00:44:23,707   Created temporary directory: /tmp/pip-wheel-ad79q153
2022-09-04T00:44:23,708   Building wheel for shephard (setup.py): started
2022-09-04T00:44:23,710   Destination directory: /tmp/pip-wheel-ad79q153
2022-09-04T00:44:23,710   Running command python setup.py bdist_wheel
2022-09-04T00:44:30,649   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:531: UserWarning: Normalizing 'v0.1.15' to '0.1.15'
2022-09-04T00:44:30,651     warnings.warn(tmpl.format(**locals()))
2022-09-04T00:44:30,978   running bdist_wheel
2022-09-04T00:44:31,408   running build
2022-09-04T00:44:31,409   running build_py
2022-09-04T00:44:31,422   creating build
2022-09-04T00:44:31,423   creating build/lib
2022-09-04T00:44:31,424   creating build/lib/shephard
2022-09-04T00:44:31,426   copying shephard/test_domains_sites.py -> build/lib/shephard
2022-09-04T00:44:31,430   copying shephard/protein.py -> build/lib/shephard
2022-09-04T00:44:31,438   copying shephard/__init__.py -> build/lib/shephard
2022-09-04T00:44:31,441   copying shephard/domain.py -> build/lib/shephard
2022-09-04T00:44:31,446   copying shephard/proteome.py -> build/lib/shephard
2022-09-04T00:44:31,452   copying shephard/_version.py -> build/lib/shephard
2022-09-04T00:44:31,456   copying shephard/general_utilities.py -> build/lib/shephard
2022-09-04T00:44:31,459   copying shephard/site.py -> build/lib/shephard
2022-09-04T00:44:31,464   copying shephard/track.py -> build/lib/shephard
2022-09-04T00:44:31,469   copying shephard/sequence_utilities.py -> build/lib/shephard
2022-09-04T00:44:31,472   copying shephard/exceptions.py -> build/lib/shephard
2022-09-04T00:44:31,477   creating build/lib/shephard/tools
2022-09-04T00:44:31,479   copying shephard/tools/__init__.py -> build/lib/shephard/tools
2022-09-04T00:44:31,483   copying shephard/tools/domain_tools.py -> build/lib/shephard/tools
2022-09-04T00:44:31,487   copying shephard/tools/sequence_tools.py -> build/lib/shephard/tools
2022-09-04T00:44:31,491   copying shephard/tools/experimental.py -> build/lib/shephard/tools
2022-09-04T00:44:31,494   copying shephard/tools/track_tools.py -> build/lib/shephard/tools
2022-09-04T00:44:31,498   copying shephard/tools/site_tools.py -> build/lib/shephard/tools
2022-09-04T00:44:31,505   creating build/lib/shephard/tests
2022-09-04T00:44:31,506   copying shephard/tests/test_si_domains.py -> build/lib/shephard/tests
2022-09-04T00:44:31,511   copying shephard/tests/test_si_sites.py -> build/lib/shephard/tests
2022-09-04T00:44:31,514   copying shephard/tests/test_shephard.py -> build/lib/shephard/tests
2022-09-04T00:44:31,517   copying shephard/tests/__init__.py -> build/lib/shephard/tests
2022-09-04T00:44:31,521   copying shephard/tests/example_test_function.py -> build/lib/shephard/tests
2022-09-04T00:44:31,525   copying shephard/tests/test_sites.py -> build/lib/shephard/tests
2022-09-04T00:44:31,528   copying shephard/tests/conftest.py -> build/lib/shephard/tests
2022-09-04T00:44:31,531   copying shephard/tests/test_domains.py -> build/lib/shephard/tests
2022-09-04T00:44:31,536   copying shephard/tests/test_add_remove_annotations.py -> build/lib/shephard/tests
2022-09-04T00:44:31,539   copying shephard/tests/test_si_tracks.py -> build/lib/shephard/tests
2022-09-04T00:44:31,544   copying shephard/tests/test_domain_tools.py -> build/lib/shephard/tests
2022-09-04T00:44:31,549   copying shephard/tests/test_apis_fasta.py -> build/lib/shephard/tests
2022-09-04T00:44:31,552   copying shephard/tests/test_logic.py -> build/lib/shephard/tests
2022-09-04T00:44:31,555   copying shephard/tests/test_sequence_tools.py -> build/lib/shephard/tests
2022-09-04T00:44:31,559   copying shephard/tests/test_track_tools.py -> build/lib/shephard/tests
2022-09-04T00:44:31,562   copying shephard/tests/test_interfaces.py -> build/lib/shephard/tests
2022-09-04T00:44:31,565   copying shephard/tests/test_protein.py -> build/lib/shephard/tests
2022-09-04T00:44:31,570   copying shephard/tests/test_proteome.py -> build/lib/shephard/tests
2022-09-04T00:44:31,574   copying shephard/tests/test_tracks.py -> build/lib/shephard/tests
2022-09-04T00:44:31,578   creating build/lib/shephard/apis
2022-09-04T00:44:31,580   copying shephard/apis/__init__.py -> build/lib/shephard/apis
2022-09-04T00:44:31,583   copying shephard/apis/fasta.py -> build/lib/shephard/apis
2022-09-04T00:44:31,588   copying shephard/apis/uniprot.py -> build/lib/shephard/apis
2022-09-04T00:44:31,593   creating build/lib/shephard/interfaces
2022-09-04T00:44:31,595   copying shephard/interfaces/interface_tools.py -> build/lib/shephard/interfaces
2022-09-04T00:44:31,600   copying shephard/interfaces/__init__.py -> build/lib/shephard/interfaces
2022-09-04T00:44:31,603   copying shephard/interfaces/si_sites.py -> build/lib/shephard/interfaces
2022-09-04T00:44:31,608   copying shephard/interfaces/si_tracks.py -> build/lib/shephard/interfaces
2022-09-04T00:44:31,613   copying shephard/interfaces/si_protein_attributes.py -> build/lib/shephard/interfaces
2022-09-04T00:44:31,617   copying shephard/interfaces/si_proteins.py -> build/lib/shephard/interfaces
2022-09-04T00:44:31,622   copying shephard/interfaces/si_domains.py -> build/lib/shephard/interfaces
2022-09-04T00:44:31,626   running egg_info
2022-09-04T00:44:33,105   writing shephard.egg-info/PKG-INFO
2022-09-04T00:44:33,690   writing dependency_links to shephard.egg-info/dependency_links.txt
2022-09-04T00:44:36,623   writing requirements to shephard.egg-info/requires.txt
2022-09-04T00:44:37,211   writing top-level names to shephard.egg-info/top_level.txt
2022-09-04T00:44:37,368   reading manifest file 'shephard.egg-info/SOURCES.txt'
2022-09-04T00:44:37,390   reading manifest template 'MANIFEST.in'
2022-09-04T00:44:37,406   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2022-09-04T00:44:37,408   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2022-09-04T00:44:37,410   warning: no previously-included files matching '*.so' found anywhere in distribution
2022-09-04T00:44:37,410   adding license file 'LICENSE'
2022-09-04T00:44:37,427   writing manifest file 'shephard.egg-info/SOURCES.txt'
2022-09-04T00:44:37,433   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning:     !!


2022-09-04T00:44:37,434       ############################
2022-09-04T00:44:37,434       # Package would be ignored #
2022-09-04T00:44:37,434       ############################
2022-09-04T00:44:37,435       Python recognizes 'shephard.data' as an importable package, however it is
2022-09-04T00:44:37,435       included in the distribution as "data".
2022-09-04T00:44:37,435       This behavior is likely to change in future versions of setuptools (and
2022-09-04T00:44:37,436       therefore is considered deprecated).

2022-09-04T00:44:37,436       Please make sure that 'shephard.data' is included as a package by using
2022-09-04T00:44:37,437       setuptools' `packages` configuration field or the proper discovery methods.

2022-09-04T00:44:37,437       You can read more about "package discovery" and "data files" on setuptools
2022-09-04T00:44:37,437       documentation page.


2022-09-04T00:44:37,438   !!

2022-09-04T00:44:37,439     check.warn(importable)
2022-09-04T00:44:37,439   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning:     !!


2022-09-04T00:44:37,440       ############################
2022-09-04T00:44:37,441       # Package would be ignored #
2022-09-04T00:44:37,441       ############################
2022-09-04T00:44:37,441       Python recognizes 'shephard.data.test_data' as an importable package, however it is
2022-09-04T00:44:37,441       included in the distribution as "data".
2022-09-04T00:44:37,442       This behavior is likely to change in future versions of setuptools (and
2022-09-04T00:44:37,442       therefore is considered deprecated).

2022-09-04T00:44:37,443       Please make sure that 'shephard.data.test_data' is included as a package by using
2022-09-04T00:44:37,443       setuptools' `packages` configuration field or the proper discovery methods.

2022-09-04T00:44:37,443       You can read more about "package discovery" and "data files" on setuptools
2022-09-04T00:44:37,444       documentation page.


2022-09-04T00:44:37,445   !!

2022-09-04T00:44:37,445     check.warn(importable)
2022-09-04T00:44:37,446   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning:     !!


2022-09-04T00:44:37,447       ############################
2022-09-04T00:44:37,447       # Package would be ignored #
2022-09-04T00:44:37,447       ############################
2022-09-04T00:44:37,448       Python recognizes 'shephard.tests.output_test' as an importable package, however it is
2022-09-04T00:44:37,448       included in the distribution as "data".
2022-09-04T00:44:37,448       This behavior is likely to change in future versions of setuptools (and
2022-09-04T00:44:37,449       therefore is considered deprecated).

2022-09-04T00:44:37,449       Please make sure that 'shephard.tests.output_test' is included as a package by using
2022-09-04T00:44:37,450       setuptools' `packages` configuration field or the proper discovery methods.

2022-09-04T00:44:37,451       You can read more about "package discovery" and "data files" on setuptools
2022-09-04T00:44:37,451       documentation page.


2022-09-04T00:44:37,452   !!

2022-09-04T00:44:37,453     check.warn(importable)
2022-09-04T00:44:37,453   creating build/lib/shephard/data
2022-09-04T00:44:37,453   copying shephard/data/README.md -> build/lib/shephard/data
2022-09-04T00:44:37,454   copying shephard/data/look_and_say.dat -> build/lib/shephard/data
2022-09-04T00:44:37,456   creating build/lib/shephard/data/test_data
2022-09-04T00:44:37,457   copying shephard/data/test_data/TS1_domains_idr.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,462   copying shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,465   copying shephard/data/test_data/TS1_domains_pscore.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,469   copying shephard/data/test_data/TS1_protein_attributes.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,472   copying shephard/data/test_data/TS1_sites.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,477   copying shephard/data/test_data/TS1_tracks_pscore.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,482   copying shephard/data/test_data/names.txt -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,486   copying shephard/data/test_data/seqs.fasta -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,491   copying shephard/data/test_data/testset_1.fasta -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,495   copying shephard/data/test_data/testset_1.fasta.fai -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,499   copying shephard/data/test_data/testset_1_ptms.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,503   copying shephard/data/test_data/ts1_bonus_sites.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,506   copying shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,510   copying shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,514   copying shephard/data/test_data/tst.py -> build/lib/shephard/data/test_data
2022-09-04T00:44:37,518   copying shephard/tests/test_scratchpad.ipynb -> build/lib/shephard/tests
2022-09-04T00:44:37,522   creating build/lib/shephard/tests/.ipynb_checkpoints
2022-09-04T00:44:37,524   copying shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/lib/shephard/tests/.ipynb_checkpoints
2022-09-04T00:44:37,527   creating build/lib/shephard/tests/output_test
2022-09-04T00:44:37,529   copying shephard/tests/output_test/all_symbols_test.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:37,533   copying shephard/tests/output_test/all_values_test.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:37,539   copying shephard/tests/output_test/all_values_test_from_list.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:37,544   copying shephard/tests/output_test/out_tracks.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:37,550   copying shephard/tests/output_test/readme.md -> build/lib/shephard/tests/output_test
2022-09-04T00:44:37,554   copying shephard/tests/output_test/shephard_track_phosres.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:37,558   copying shephard/tests/output_test/shephard_track_pscore.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:37,563   copying shephard/tests/output_test/test_domains.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:37,567   copying shephard/tests/output_test/test_sites.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:37,574   copying shephard/tests/output_test/track_phospho_track.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:37,578   copying shephard/tests/output_test/track_random_vals.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:37,592   UPDATING build/lib/shephard/_version.py
2022-09-04T00:44:37,594   set build/lib/shephard/_version.py to 'v0.1.15'
2022-09-04T00:44:38,332   /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.
2022-09-04T00:44:38,333     setuptools.SetuptoolsDeprecationWarning,
2022-09-04T00:44:39,068   installing to build/bdist.linux-armv7l/wheel
2022-09-04T00:44:39,068   running install
2022-09-04T00:44:39,128   running install_lib
2022-09-04T00:44:39,863   creating build/bdist.linux-armv7l
2022-09-04T00:44:39,864   creating build/bdist.linux-armv7l/wheel
2022-09-04T00:44:39,868   creating build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:39,870   copying build/lib/shephard/test_domains_sites.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:39,874   copying build/lib/shephard/protein.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:39,883   creating build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,884   copying build/lib/shephard/tools/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,888   copying build/lib/shephard/tools/domain_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,893   copying build/lib/shephard/tools/sequence_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,897   copying build/lib/shephard/tools/experimental.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,900   copying build/lib/shephard/tools/track_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,904   copying build/lib/shephard/tools/site_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,907   copying build/lib/shephard/__init__.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:39,911   copying build/lib/shephard/domain.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:39,917   creating build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,918   copying build/lib/shephard/tests/test_si_domains.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,923   copying build/lib/shephard/tests/test_si_sites.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,927   copying build/lib/shephard/tests/test_shephard.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,930   copying build/lib/shephard/tests/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,935   creating build/bdist.linux-armv7l/wheel/shephard/tests/.ipynb_checkpoints
2022-09-04T00:44:39,936   copying build/lib/shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/bdist.linux-armv7l/wheel/shephard/tests/.ipynb_checkpoints
2022-09-04T00:44:39,940   copying build/lib/shephard/tests/example_test_function.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,943   copying build/lib/shephard/tests/test_sites.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,947   copying build/lib/shephard/tests/conftest.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,951   copying build/lib/shephard/tests/test_domains.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,955   copying build/lib/shephard/tests/test_add_remove_annotations.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,958   copying build/lib/shephard/tests/test_si_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,963   copying build/lib/shephard/tests/test_domain_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,967   copying build/lib/shephard/tests/test_apis_fasta.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:39,972   creating build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:39,974   copying build/lib/shephard/tests/output_test/out_tracks.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:39,979   copying build/lib/shephard/tests/output_test/all_symbols_test.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:39,983   copying build/lib/shephard/tests/output_test/shephard_track_phosres.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:39,986   copying build/lib/shephard/tests/output_test/readme.md -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:39,990   copying build/lib/shephard/tests/output_test/track_random_vals.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:39,994   copying build/lib/shephard/tests/output_test/all_values_test.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:39,999   copying build/lib/shephard/tests/output_test/test_domains.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:40,002   copying build/lib/shephard/tests/output_test/all_values_test_from_list.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:40,007   copying build/lib/shephard/tests/output_test/shephard_track_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:40,013   copying build/lib/shephard/tests/output_test/track_phospho_track.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:40,016   copying build/lib/shephard/tests/output_test/test_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:40,024   copying build/lib/shephard/tests/test_logic.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:40,026   copying build/lib/shephard/tests/test_sequence_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:40,030   copying build/lib/shephard/tests/test_scratchpad.ipynb -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:40,034   copying build/lib/shephard/tests/test_track_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:40,037   copying build/lib/shephard/tests/test_interfaces.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:40,041   copying build/lib/shephard/tests/test_protein.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:40,045   copying build/lib/shephard/tests/test_proteome.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:40,049   copying build/lib/shephard/tests/test_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:40,052   copying build/lib/shephard/proteome.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:40,059   copying build/lib/shephard/_version.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:40,062   copying build/lib/shephard/general_utilities.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:40,066   copying build/lib/shephard/site.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:40,071   creating build/bdist.linux-armv7l/wheel/shephard/data
2022-09-04T00:44:40,073   copying build/lib/shephard/data/README.md -> build/bdist.linux-armv7l/wheel/shephard/data
2022-09-04T00:44:40,076   copying build/lib/shephard/data/look_and_say.dat -> build/bdist.linux-armv7l/wheel/shephard/data
2022-09-04T00:44:40,081   creating build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,083   copying build/lib/shephard/data/test_data/TS1_tracks_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,088   copying build/lib/shephard/data/test_data/TS1_domains_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,091   copying build/lib/shephard/data/test_data/TS1_protein_attributes.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,095   copying build/lib/shephard/data/test_data/TS1_domains_idr.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,098   copying build/lib/shephard/data/test_data/testset_1.fasta.fai -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,102   copying build/lib/shephard/data/test_data/testset_1.fasta -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,106   copying build/lib/shephard/data/test_data/names.txt -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,110   copying build/lib/shephard/data/test_data/ts1_bonus_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,113   copying build/lib/shephard/data/test_data/testset_1_ptms.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,116   copying build/lib/shephard/data/test_data/seqs.fasta -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,120   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,124   copying build/lib/shephard/data/test_data/TS1_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,128   copying build/lib/shephard/data/test_data/tst.py -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,131   copying build/lib/shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,135   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:40,138   copying build/lib/shephard/track.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:40,143   copying build/lib/shephard/sequence_utilities.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:40,146   copying build/lib/shephard/exceptions.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:40,151   creating build/bdist.linux-armv7l/wheel/shephard/apis
2022-09-04T00:44:40,153   copying build/lib/shephard/apis/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2022-09-04T00:44:40,156   copying build/lib/shephard/apis/fasta.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2022-09-04T00:44:40,161   copying build/lib/shephard/apis/uniprot.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2022-09-04T00:44:40,166   creating build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:40,168   copying build/lib/shephard/interfaces/interface_tools.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:40,173   copying build/lib/shephard/interfaces/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:40,176   copying build/lib/shephard/interfaces/si_sites.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:40,181   copying build/lib/shephard/interfaces/si_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:40,186   copying build/lib/shephard/interfaces/si_protein_attributes.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:40,190   copying build/lib/shephard/interfaces/si_proteins.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:40,194   copying build/lib/shephard/interfaces/si_domains.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:40,199   running install_egg_info
2022-09-04T00:44:40,941   Copying shephard.egg-info to build/bdist.linux-armv7l/wheel/shephard-0.1.15-py3.7.egg-info
2022-09-04T00:44:40,963   running install_scripts
2022-09-04T00:44:41,105   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2022-09-04T00:44:41,114   creating build/bdist.linux-armv7l/wheel/shephard-0.1.15.dist-info/WHEEL
2022-09-04T00:44:41,119   creating '/tmp/pip-wheel-ad79q153/shephard-0.1.15-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2022-09-04T00:44:41,124   adding 'shephard/__init__.py'
2022-09-04T00:44:41,127   adding 'shephard/_version.py'
2022-09-04T00:44:41,132   adding 'shephard/domain.py'
2022-09-04T00:44:41,135   adding 'shephard/exceptions.py'
2022-09-04T00:44:41,137   adding 'shephard/general_utilities.py'
2022-09-04T00:44:41,161   adding 'shephard/protein.py'
2022-09-04T00:44:41,176   adding 'shephard/proteome.py'
2022-09-04T00:44:41,180   adding 'shephard/sequence_utilities.py'
2022-09-04T00:44:41,185   adding 'shephard/site.py'
2022-09-04T00:44:41,187   adding 'shephard/test_domains_sites.py'
2022-09-04T00:44:41,193   adding 'shephard/track.py'
2022-09-04T00:44:41,196   adding 'shephard/apis/__init__.py'
2022-09-04T00:44:41,202   adding 'shephard/apis/fasta.py'
2022-09-04T00:44:41,206   adding 'shephard/apis/uniprot.py'
2022-09-04T00:44:41,209   adding 'shephard/data/README.md'
2022-09-04T00:44:41,211   adding 'shephard/data/look_and_say.dat'
2022-09-04T00:44:41,216   adding 'shephard/data/test_data/TS1_domains_idr.tsv'
2022-09-04T00:44:41,218   adding 'shephard/data/test_data/TS1_domains_idr_and_others.tsv'
2022-09-04T00:44:41,220   adding 'shephard/data/test_data/TS1_domains_pscore.tsv'
2022-09-04T00:44:41,222   adding 'shephard/data/test_data/TS1_protein_attributes.tsv'
2022-09-04T00:44:41,225   adding 'shephard/data/test_data/TS1_sites.tsv'
2022-09-04T00:44:41,246   adding 'shephard/data/test_data/TS1_tracks_pscore.tsv'
2022-09-04T00:44:41,249   adding 'shephard/data/test_data/names.txt'
2022-09-04T00:44:41,252   adding 'shephard/data/test_data/seqs.fasta'
2022-09-04T00:44:41,255   adding 'shephard/data/test_data/testset_1.fasta'
2022-09-04T00:44:41,257   adding 'shephard/data/test_data/testset_1.fasta.fai'
2022-09-04T00:44:41,259   adding 'shephard/data/test_data/testset_1_ptms.tsv'
2022-09-04T00:44:41,262   adding 'shephard/data/test_data/ts1_bonus_sites.tsv'
2022-09-04T00:44:41,264   adding 'shephard/data/test_data/ts1_bonus_sites_bad.tsv'
2022-09-04T00:44:41,266   adding 'shephard/data/test_data/ts1_bonus_sites_bad2.tsv'
2022-09-04T00:44:41,268   adding 'shephard/data/test_data/tst.py'
2022-09-04T00:44:41,271   adding 'shephard/interfaces/__init__.py'
2022-09-04T00:44:41,275   adding 'shephard/interfaces/interface_tools.py'
2022-09-04T00:44:41,282   adding 'shephard/interfaces/si_domains.py'
2022-09-04T00:44:41,287   adding 'shephard/interfaces/si_protein_attributes.py'
2022-09-04T00:44:41,292   adding 'shephard/interfaces/si_proteins.py'
2022-09-04T00:44:41,298   adding 'shephard/interfaces/si_sites.py'
2022-09-04T00:44:41,306   adding 'shephard/interfaces/si_tracks.py'
2022-09-04T00:44:41,310   adding 'shephard/tests/__init__.py'
2022-09-04T00:44:41,313   adding 'shephard/tests/conftest.py'
2022-09-04T00:44:41,315   adding 'shephard/tests/example_test_function.py'
2022-09-04T00:44:41,317   adding 'shephard/tests/test_add_remove_annotations.py'
2022-09-04T00:44:41,320   adding 'shephard/tests/test_apis_fasta.py'
2022-09-04T00:44:41,323   adding 'shephard/tests/test_domain_tools.py'
2022-09-04T00:44:41,327   adding 'shephard/tests/test_domains.py'
2022-09-04T00:44:41,329   adding 'shephard/tests/test_interfaces.py'
2022-09-04T00:44:41,331   adding 'shephard/tests/test_logic.py'
2022-09-04T00:44:41,335   adding 'shephard/tests/test_protein.py'
2022-09-04T00:44:41,338   adding 'shephard/tests/test_proteome.py'
2022-09-04T00:44:41,341   adding 'shephard/tests/test_scratchpad.ipynb'
2022-09-04T00:44:41,344   adding 'shephard/tests/test_sequence_tools.py'
2022-09-04T00:44:41,353   adding 'shephard/tests/test_shephard.py'
2022-09-04T00:44:41,356   adding 'shephard/tests/test_si_domains.py'
2022-09-04T00:44:41,359   adding 'shephard/tests/test_si_sites.py'
2022-09-04T00:44:41,363   adding 'shephard/tests/test_si_tracks.py'
2022-09-04T00:44:41,365   adding 'shephard/tests/test_sites.py'
2022-09-04T00:44:41,368   adding 'shephard/tests/test_track_tools.py'
2022-09-04T00:44:41,370   adding 'shephard/tests/test_tracks.py'
2022-09-04T00:44:41,373   adding 'shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb'
2022-09-04T00:44:41,377   adding 'shephard/tests/output_test/all_symbols_test.tsv'
2022-09-04T00:44:41,382   adding 'shephard/tests/output_test/all_values_test.tsv'
2022-09-04T00:44:41,387   adding 'shephard/tests/output_test/all_values_test_from_list.tsv'
2022-09-04T00:44:41,408   adding 'shephard/tests/output_test/out_tracks.tsv'
2022-09-04T00:44:41,411   adding 'shephard/tests/output_test/readme.md'
2022-09-04T00:44:41,413   adding 'shephard/tests/output_test/shephard_track_phosres.tsv'
2022-09-04T00:44:41,434   adding 'shephard/tests/output_test/shephard_track_pscore.tsv'
2022-09-04T00:44:41,436   adding 'shephard/tests/output_test/test_domains.tsv'
2022-09-04T00:44:41,443   adding 'shephard/tests/output_test/test_sites.tsv'
2022-09-04T00:44:41,446   adding 'shephard/tests/output_test/track_phospho_track.tsv'
2022-09-04T00:44:41,450   adding 'shephard/tests/output_test/track_random_vals.tsv'
2022-09-04T00:44:41,453   adding 'shephard/tools/__init__.py'
2022-09-04T00:44:41,459   adding 'shephard/tools/domain_tools.py'
2022-09-04T00:44:41,462   adding 'shephard/tools/experimental.py'
2022-09-04T00:44:41,465   adding 'shephard/tools/sequence_tools.py'
2022-09-04T00:44:41,468   adding 'shephard/tools/site_tools.py'
2022-09-04T00:44:41,471   adding 'shephard/tools/track_tools.py'
2022-09-04T00:44:41,476   adding 'shephard-0.1.15.dist-info/LICENSE'
2022-09-04T00:44:41,479   adding 'shephard-0.1.15.dist-info/METADATA'
2022-09-04T00:44:41,481   adding 'shephard-0.1.15.dist-info/WHEEL'
2022-09-04T00:44:41,482   adding 'shephard-0.1.15.dist-info/top_level.txt'
2022-09-04T00:44:41,485   adding 'shephard-0.1.15.dist-info/RECORD'
2022-09-04T00:44:41,495   removing build/bdist.linux-armv7l/wheel
2022-09-04T00:44:41,787   Building wheel for shephard (setup.py): finished with status 'done'
2022-09-04T00:44:41,799   Created wheel for shephard: filename=shephard-0.1.15-py3-none-any.whl size=178026 sha256=79ddd35e1cf2c5fc12afbbb7ccd13a338a58db5b7af8b2777c70a6ec6c6a5e6f
2022-09-04T00:44:41,801   Stored in directory: /tmp/pip-ephem-wheel-cache-z4_xeq4d/wheels/f3/78/fd/32ba46c1ef8608088c8ee7e363210b7b37afd001fc1a0075f6
2022-09-04T00:44:41,831 Successfully built shephard
2022-09-04T00:44:41,852 Removed build tracker: '/tmp/pip-build-tracker-xwzw9qub'