2022-09-04T00:44:05,472 Created temporary directory: /tmp/pip-ephem-wheel-cache-o7ckkr0y
2022-09-04T00:44:05,478 Created temporary directory: /tmp/pip-build-tracker-y3mp0bw6
2022-09-04T00:44:05,478 Initialized build tracking at /tmp/pip-build-tracker-y3mp0bw6
2022-09-04T00:44:05,479 Created build tracker: /tmp/pip-build-tracker-y3mp0bw6
2022-09-04T00:44:05,479 Entered build tracker: /tmp/pip-build-tracker-y3mp0bw6
2022-09-04T00:44:05,480 Created temporary directory: /tmp/pip-wheel-o3y_si99
2022-09-04T00:44:05,550 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2022-09-04T00:44:05,558 2 location(s) to search for versions of shephard:
2022-09-04T00:44:05,558 * https://pypi.org/simple/shephard/
2022-09-04T00:44:05,558 * https://www.piwheels.org/simple/shephard/
2022-09-04T00:44:05,559 Fetching project page and analyzing links: https://pypi.org/simple/shephard/
2022-09-04T00:44:05,560 Getting page https://pypi.org/simple/shephard/
2022-09-04T00:44:05,564 Found index url https://pypi.org/simple
2022-09-04T00:44:05,750   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
2022-09-04T00:44:05,751   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
2022-09-04T00:44:05,751   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
2022-09-04T00:44:05,752   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
2022-09-04T00:44:05,753   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
2022-09-04T00:44:05,753   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
2022-09-04T00:44:05,754 Fetching project page and analyzing links: https://www.piwheels.org/simple/shephard/
2022-09-04T00:44:05,755 Getting page https://www.piwheels.org/simple/shephard/
2022-09-04T00:44:05,757 Found index url https://www.piwheels.org/simple
2022-09-04T00:44:05,960   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/)
2022-09-04T00:44:05,961   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/)
2022-09-04T00:44:05,961   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/)
2022-09-04T00:44:05,962   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/)
2022-09-04T00:44:05,962 Skipping link: not a file: https://www.piwheels.org/simple/shephard/
2022-09-04T00:44:05,963 Skipping link: not a file: https://pypi.org/simple/shephard/
2022-09-04T00:44:05,999 Given no hashes to check 1 links for project 'shephard': discarding no candidates
2022-09-04T00:44:06,029 Collecting shephard==0.1.14
2022-09-04T00:44:06,034   Created temporary directory: /tmp/pip-unpack-mwvhww5d
2022-09-04T00:44:06,697   Downloading shephard-0.1.14.tar.gz (183 kB)
2022-09-04T00:44:07,334   Added shephard==0.1.14 from https://files.pythonhosted.org/packages/60/78/e58f5c608c7cc8363648b8466f262582a7de95a0331f7b3e87085cf31179/shephard-0.1.14.tar.gz#sha256=5ffd758fee0e494acbba492caf00b6e5755044b9187458ee97868843dffb767f to build tracker '/tmp/pip-build-tracker-y3mp0bw6'
2022-09-04T00:44:07,338   Running setup.py (path:/tmp/pip-wheel-o3y_si99/shephard_429af6ce6c004f55888babf721ceb3d7/setup.py) egg_info for package shephard
2022-09-04T00:44:07,339   Created temporary directory: /tmp/pip-pip-egg-info-errgslzf
2022-09-04T00:44:07,340   Preparing metadata (setup.py): started
2022-09-04T00:44:07,342   Running command python setup.py egg_info
2022-09-04T00:44:15,485   running egg_info
2022-09-04T00:44:15,489   creating /tmp/pip-pip-egg-info-errgslzf/shephard.egg-info
2022-09-04T00:44:16,225   writing /tmp/pip-pip-egg-info-errgslzf/shephard.egg-info/PKG-INFO
2022-09-04T00:44:16,816   writing dependency_links to /tmp/pip-pip-egg-info-errgslzf/shephard.egg-info/dependency_links.txt
2022-09-04T00:44:19,757   writing requirements to /tmp/pip-pip-egg-info-errgslzf/shephard.egg-info/requires.txt
2022-09-04T00:44:20,348   writing top-level names to /tmp/pip-pip-egg-info-errgslzf/shephard.egg-info/top_level.txt
2022-09-04T00:44:20,350   writing manifest file '/tmp/pip-pip-egg-info-errgslzf/shephard.egg-info/SOURCES.txt'
2022-09-04T00:44:20,683   reading manifest file '/tmp/pip-pip-egg-info-errgslzf/shephard.egg-info/SOURCES.txt'
2022-09-04T00:44:20,687   reading manifest template 'MANIFEST.in'
2022-09-04T00:44:20,707   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:531: UserWarning: Normalizing 'v0.1.14' to '0.1.14'
2022-09-04T00:44:20,707     warnings.warn(tmpl.format(**locals()))
2022-09-04T00:44:20,708   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2022-09-04T00:44:20,710   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2022-09-04T00:44:20,712   warning: no previously-included files matching '*.so' found anywhere in distribution
2022-09-04T00:44:20,713   adding license file 'LICENSE'
2022-09-04T00:44:20,726   writing manifest file '/tmp/pip-pip-egg-info-errgslzf/shephard.egg-info/SOURCES.txt'
2022-09-04T00:44:20,947   Preparing metadata (setup.py): finished with status 'done'
2022-09-04T00:44:20,959   Source in /tmp/pip-wheel-o3y_si99/shephard_429af6ce6c004f55888babf721ceb3d7 has version 0.1.14, which satisfies requirement shephard==0.1.14 from https://files.pythonhosted.org/packages/60/78/e58f5c608c7cc8363648b8466f262582a7de95a0331f7b3e87085cf31179/shephard-0.1.14.tar.gz#sha256=5ffd758fee0e494acbba492caf00b6e5755044b9187458ee97868843dffb767f
2022-09-04T00:44:20,961   Removed shephard==0.1.14 from https://files.pythonhosted.org/packages/60/78/e58f5c608c7cc8363648b8466f262582a7de95a0331f7b3e87085cf31179/shephard-0.1.14.tar.gz#sha256=5ffd758fee0e494acbba492caf00b6e5755044b9187458ee97868843dffb767f from build tracker '/tmp/pip-build-tracker-y3mp0bw6'
2022-09-04T00:44:20,970 Created temporary directory: /tmp/pip-unpack-t177e2hv
2022-09-04T00:44:20,971 Building wheels for collected packages: shephard
2022-09-04T00:44:20,981   Created temporary directory: /tmp/pip-wheel-u_v7gqoe
2022-09-04T00:44:20,982   Building wheel for shephard (setup.py): started
2022-09-04T00:44:20,984   Destination directory: /tmp/pip-wheel-u_v7gqoe
2022-09-04T00:44:20,984   Running command python setup.py bdist_wheel
2022-09-04T00:44:28,125   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:531: UserWarning: Normalizing 'v0.1.14' to '0.1.14'
2022-09-04T00:44:28,126     warnings.warn(tmpl.format(**locals()))
2022-09-04T00:44:28,467   running bdist_wheel
2022-09-04T00:44:30,159   running build
2022-09-04T00:44:30,160   running build_py
2022-09-04T00:44:30,174   creating build
2022-09-04T00:44:30,175   creating build/lib
2022-09-04T00:44:30,176   creating build/lib/shephard
2022-09-04T00:44:30,178   copying shephard/protein.py -> build/lib/shephard
2022-09-04T00:44:30,187   copying shephard/site.py -> build/lib/shephard
2022-09-04T00:44:30,192   copying shephard/exceptions.py -> build/lib/shephard
2022-09-04T00:44:30,195   copying shephard/track.py -> build/lib/shephard
2022-09-04T00:44:30,199   copying shephard/general_utilities.py -> build/lib/shephard
2022-09-04T00:44:30,202   copying shephard/__init__.py -> build/lib/shephard
2022-09-04T00:44:30,205   copying shephard/domain.py -> build/lib/shephard
2022-09-04T00:44:30,209   copying shephard/test_domains_sites.py -> build/lib/shephard
2022-09-04T00:44:30,212   copying shephard/_version.py -> build/lib/shephard
2022-09-04T00:44:30,215   copying shephard/proteome.py -> build/lib/shephard
2022-09-04T00:44:30,220   copying shephard/sequence_utilities.py -> build/lib/shephard
2022-09-04T00:44:30,225   creating build/lib/shephard/interfaces
2022-09-04T00:44:30,226   copying shephard/interfaces/__init__.py -> build/lib/shephard/interfaces
2022-09-04T00:44:30,230   copying shephard/interfaces/si_protein_attributes.py -> build/lib/shephard/interfaces
2022-09-04T00:44:30,234   copying shephard/interfaces/si_sites.py -> build/lib/shephard/interfaces
2022-09-04T00:44:30,238   copying shephard/interfaces/si_tracks.py -> build/lib/shephard/interfaces
2022-09-04T00:44:30,243   copying shephard/interfaces/interface_tools.py -> build/lib/shephard/interfaces
2022-09-04T00:44:30,247   copying shephard/interfaces/si_proteins.py -> build/lib/shephard/interfaces
2022-09-04T00:44:30,251   copying shephard/interfaces/si_domains.py -> build/lib/shephard/interfaces
2022-09-04T00:44:30,257   creating build/lib/shephard/apis
2022-09-04T00:44:30,259   copying shephard/apis/uniprot.py -> build/lib/shephard/apis
2022-09-04T00:44:30,263   copying shephard/apis/__init__.py -> build/lib/shephard/apis
2022-09-04T00:44:30,266   copying shephard/apis/fasta.py -> build/lib/shephard/apis
2022-09-04T00:44:30,273   creating build/lib/shephard/tests
2022-09-04T00:44:30,274   copying shephard/tests/test_sequence_tools.py -> build/lib/shephard/tests
2022-09-04T00:44:30,278   copying shephard/tests/test_si_domains.py -> build/lib/shephard/tests
2022-09-04T00:44:30,281   copying shephard/tests/test_tracks.py -> build/lib/shephard/tests
2022-09-04T00:44:30,285   copying shephard/tests/test_shephard.py -> build/lib/shephard/tests
2022-09-04T00:44:30,288   copying shephard/tests/test_si_tracks.py -> build/lib/shephard/tests
2022-09-04T00:44:30,293   copying shephard/tests/__init__.py -> build/lib/shephard/tests
2022-09-04T00:44:30,296   copying shephard/tests/test_si_sites.py -> build/lib/shephard/tests
2022-09-04T00:44:30,300   copying shephard/tests/test_track_tools.py -> build/lib/shephard/tests
2022-09-04T00:44:30,303   copying shephard/tests/test_proteome.py -> build/lib/shephard/tests
2022-09-04T00:44:30,306   copying shephard/tests/test_logic.py -> build/lib/shephard/tests
2022-09-04T00:44:30,309   copying shephard/tests/test_interfaces.py -> build/lib/shephard/tests
2022-09-04T00:44:30,312   copying shephard/tests/test_apis_fasta.py -> build/lib/shephard/tests
2022-09-04T00:44:30,315   copying shephard/tests/conftest.py -> build/lib/shephard/tests
2022-09-04T00:44:30,318   copying shephard/tests/test_protein.py -> build/lib/shephard/tests
2022-09-04T00:44:30,323   copying shephard/tests/test_sites.py -> build/lib/shephard/tests
2022-09-04T00:44:30,326   copying shephard/tests/test_domain_tools.py -> build/lib/shephard/tests
2022-09-04T00:44:30,329   copying shephard/tests/test_add_remove_annotations.py -> build/lib/shephard/tests
2022-09-04T00:44:30,332   copying shephard/tests/example_test_function.py -> build/lib/shephard/tests
2022-09-04T00:44:30,335   copying shephard/tests/test_domains.py -> build/lib/shephard/tests
2022-09-04T00:44:30,341   creating build/lib/shephard/tools
2022-09-04T00:44:30,342   copying shephard/tools/track_tools.py -> build/lib/shephard/tools
2022-09-04T00:44:30,346   copying shephard/tools/experimental.py -> build/lib/shephard/tools
2022-09-04T00:44:30,349   copying shephard/tools/sequence_tools.py -> build/lib/shephard/tools
2022-09-04T00:44:30,352   copying shephard/tools/__init__.py -> build/lib/shephard/tools
2022-09-04T00:44:30,355   copying shephard/tools/domain_tools.py -> build/lib/shephard/tools
2022-09-04T00:44:30,359   copying shephard/tools/site_tools.py -> build/lib/shephard/tools
2022-09-04T00:44:30,362   running egg_info
2022-09-04T00:44:31,899   writing shephard.egg-info/PKG-INFO
2022-09-04T00:44:32,486   writing dependency_links to shephard.egg-info/dependency_links.txt
2022-09-04T00:44:35,425   writing requirements to shephard.egg-info/requires.txt
2022-09-04T00:44:36,014   writing top-level names to shephard.egg-info/top_level.txt
2022-09-04T00:44:36,180   reading manifest file 'shephard.egg-info/SOURCES.txt'
2022-09-04T00:44:36,205   reading manifest template 'MANIFEST.in'
2022-09-04T00:44:36,221   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2022-09-04T00:44:36,223   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2022-09-04T00:44:36,225   warning: no previously-included files matching '*.so' found anywhere in distribution
2022-09-04T00:44:36,225   adding license file 'LICENSE'
2022-09-04T00:44:36,242   writing manifest file 'shephard.egg-info/SOURCES.txt'
2022-09-04T00:44:36,248   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning:     !!


2022-09-04T00:44:36,249       ############################
2022-09-04T00:44:36,249       # Package would be ignored #
2022-09-04T00:44:36,249       ############################
2022-09-04T00:44:36,250       Python recognizes 'shephard.data' as an importable package, however it is
2022-09-04T00:44:36,250       included in the distribution as "data".
2022-09-04T00:44:36,250       This behavior is likely to change in future versions of setuptools (and
2022-09-04T00:44:36,251       therefore is considered deprecated).

2022-09-04T00:44:36,251       Please make sure that 'shephard.data' is included as a package by using
2022-09-04T00:44:36,252       setuptools' `packages` configuration field or the proper discovery methods.

2022-09-04T00:44:36,252       You can read more about "package discovery" and "data files" on setuptools
2022-09-04T00:44:36,252       documentation page.


2022-09-04T00:44:36,253   !!

2022-09-04T00:44:36,254     check.warn(importable)
2022-09-04T00:44:36,254   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning:     !!


2022-09-04T00:44:36,255       ############################
2022-09-04T00:44:36,255       # Package would be ignored #
2022-09-04T00:44:36,256       ############################
2022-09-04T00:44:36,256       Python recognizes 'shephard.data.test_data' as an importable package, however it is
2022-09-04T00:44:36,256       included in the distribution as "data".
2022-09-04T00:44:36,256       This behavior is likely to change in future versions of setuptools (and
2022-09-04T00:44:36,257       therefore is considered deprecated).

2022-09-04T00:44:36,257       Please make sure that 'shephard.data.test_data' is included as a package by using
2022-09-04T00:44:36,258       setuptools' `packages` configuration field or the proper discovery methods.

2022-09-04T00:44:36,258       You can read more about "package discovery" and "data files" on setuptools
2022-09-04T00:44:36,258       documentation page.


2022-09-04T00:44:36,259   !!

2022-09-04T00:44:36,260     check.warn(importable)
2022-09-04T00:44:36,260   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning:     !!


2022-09-04T00:44:36,261       ############################
2022-09-04T00:44:36,262       # Package would be ignored #
2022-09-04T00:44:36,263       ############################
2022-09-04T00:44:36,263       Python recognizes 'shephard.tests.output_test' as an importable package, however it is
2022-09-04T00:44:36,263       included in the distribution as "data".
2022-09-04T00:44:36,264       This behavior is likely to change in future versions of setuptools (and
2022-09-04T00:44:36,264       therefore is considered deprecated).

2022-09-04T00:44:36,266       Please make sure that 'shephard.tests.output_test' is included as a package by using
2022-09-04T00:44:36,266       setuptools' `packages` configuration field or the proper discovery methods.

2022-09-04T00:44:36,267       You can read more about "package discovery" and "data files" on setuptools
2022-09-04T00:44:36,268       documentation page.


2022-09-04T00:44:36,269   !!

2022-09-04T00:44:36,270     check.warn(importable)
2022-09-04T00:44:36,270   creating build/lib/shephard/data
2022-09-04T00:44:36,271   copying shephard/data/README.md -> build/lib/shephard/data
2022-09-04T00:44:36,271   copying shephard/data/look_and_say.dat -> build/lib/shephard/data
2022-09-04T00:44:36,272   creating build/lib/shephard/data/test_data
2022-09-04T00:44:36,273   copying shephard/data/test_data/TS1_domains_idr.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,278   copying shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,281   copying shephard/data/test_data/TS1_domains_pscore.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,285   copying shephard/data/test_data/TS1_protein_attributes.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,289   copying shephard/data/test_data/TS1_sites.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,294   copying shephard/data/test_data/TS1_tracks_pscore.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,300   copying shephard/data/test_data/names.txt -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,304   copying shephard/data/test_data/seqs.fasta -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,309   copying shephard/data/test_data/testset_1.fasta -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,314   copying shephard/data/test_data/testset_1.fasta.fai -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,318   copying shephard/data/test_data/testset_1_ptms.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,322   copying shephard/data/test_data/ts1_bonus_sites.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,326   copying shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,330   copying shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,335   copying shephard/data/test_data/tst.py -> build/lib/shephard/data/test_data
2022-09-04T00:44:36,339   copying shephard/tests/test_scratchpad.ipynb -> build/lib/shephard/tests
2022-09-04T00:44:36,344   creating build/lib/shephard/tests/.ipynb_checkpoints
2022-09-04T00:44:36,345   copying shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/lib/shephard/tests/.ipynb_checkpoints
2022-09-04T00:44:36,350   creating build/lib/shephard/tests/output_test
2022-09-04T00:44:36,351   copying shephard/tests/output_test/all_symbols_test.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:36,356   copying shephard/tests/output_test/all_values_test.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:36,362   copying shephard/tests/output_test/all_values_test_from_list.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:36,368   copying shephard/tests/output_test/out_tracks.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:36,375   copying shephard/tests/output_test/readme.md -> build/lib/shephard/tests/output_test
2022-09-04T00:44:36,379   copying shephard/tests/output_test/shephard_track_phosres.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:36,383   copying shephard/tests/output_test/shephard_track_pscore.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:36,390   copying shephard/tests/output_test/test_domains.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:36,394   copying shephard/tests/output_test/test_sites.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:36,403   copying shephard/tests/output_test/track_phospho_track.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:36,407   copying shephard/tests/output_test/track_random_vals.tsv -> build/lib/shephard/tests/output_test
2022-09-04T00:44:36,421   UPDATING build/lib/shephard/_version.py
2022-09-04T00:44:36,424   set build/lib/shephard/_version.py to 'v0.1.14'
2022-09-04T00:44:37,176   /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.
2022-09-04T00:44:37,177     setuptools.SetuptoolsDeprecationWarning,
2022-09-04T00:44:37,919   installing to build/bdist.linux-armv7l/wheel
2022-09-04T00:44:37,920   running install
2022-09-04T00:44:37,980   running install_lib
2022-09-04T00:44:38,731   creating build/bdist.linux-armv7l
2022-09-04T00:44:38,732   creating build/bdist.linux-armv7l/wheel
2022-09-04T00:44:38,735   creating build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:38,737   copying build/lib/shephard/protein.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:38,746   copying build/lib/shephard/site.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:38,751   copying build/lib/shephard/exceptions.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:38,756   creating build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:38,758   copying build/lib/shephard/interfaces/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:38,761   copying build/lib/shephard/interfaces/si_protein_attributes.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:38,766   copying build/lib/shephard/interfaces/si_sites.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:38,771   copying build/lib/shephard/interfaces/si_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:38,776   copying build/lib/shephard/interfaces/interface_tools.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:38,780   copying build/lib/shephard/interfaces/si_proteins.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:38,785   copying build/lib/shephard/interfaces/si_domains.py -> build/bdist.linux-armv7l/wheel/shephard/interfaces
2022-09-04T00:44:38,790   copying build/lib/shephard/track.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:38,795   copying build/lib/shephard/general_utilities.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:38,798   copying build/lib/shephard/__init__.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:38,802   copying build/lib/shephard/domain.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:38,806   copying build/lib/shephard/test_domains_sites.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:38,811   creating build/bdist.linux-armv7l/wheel/shephard/apis
2022-09-04T00:44:38,812   copying build/lib/shephard/apis/uniprot.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2022-09-04T00:44:38,817   copying build/lib/shephard/apis/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2022-09-04T00:44:38,821   copying build/lib/shephard/apis/fasta.py -> build/bdist.linux-armv7l/wheel/shephard/apis
2022-09-04T00:44:38,826   copying build/lib/shephard/_version.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:38,831   creating build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,832   copying build/lib/shephard/tests/test_sequence_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,836   copying build/lib/shephard/tests/test_si_domains.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,840   copying build/lib/shephard/tests/test_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,843   copying build/lib/shephard/tests/test_shephard.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,846   copying build/lib/shephard/tests/test_si_tracks.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,851   copying build/lib/shephard/tests/test_scratchpad.ipynb -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,856   creating build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:38,858   copying build/lib/shephard/tests/output_test/readme.md -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:38,861   copying build/lib/shephard/tests/output_test/test_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:38,869   copying build/lib/shephard/tests/output_test/all_symbols_test.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:38,873   copying build/lib/shephard/tests/output_test/test_domains.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:38,876   copying build/lib/shephard/tests/output_test/all_values_test.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:38,883   copying build/lib/shephard/tests/output_test/shephard_track_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:38,890   copying build/lib/shephard/tests/output_test/track_phospho_track.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:38,894   copying build/lib/shephard/tests/output_test/all_values_test_from_list.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:38,901   copying build/lib/shephard/tests/output_test/shephard_track_phosres.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:38,905   copying build/lib/shephard/tests/output_test/out_tracks.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:38,912   copying build/lib/shephard/tests/output_test/track_random_vals.tsv -> build/bdist.linux-armv7l/wheel/shephard/tests/output_test
2022-09-04T00:44:38,916   copying build/lib/shephard/tests/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,920   copying build/lib/shephard/tests/test_si_sites.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,924   copying build/lib/shephard/tests/test_track_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,928   copying build/lib/shephard/tests/test_proteome.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,933   copying build/lib/shephard/tests/test_logic.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,936   copying build/lib/shephard/tests/test_interfaces.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,940   copying build/lib/shephard/tests/test_apis_fasta.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,944   copying build/lib/shephard/tests/conftest.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,948   copying build/lib/shephard/tests/test_protein.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,954   copying build/lib/shephard/tests/test_sites.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,958   copying build/lib/shephard/tests/test_domain_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,963   copying build/lib/shephard/tests/test_add_remove_annotations.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,968   creating build/bdist.linux-armv7l/wheel/shephard/tests/.ipynb_checkpoints
2022-09-04T00:44:38,970   copying build/lib/shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb -> build/bdist.linux-armv7l/wheel/shephard/tests/.ipynb_checkpoints
2022-09-04T00:44:38,975   copying build/lib/shephard/tests/example_test_function.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,979   copying build/lib/shephard/tests/test_domains.py -> build/bdist.linux-armv7l/wheel/shephard/tests
2022-09-04T00:44:38,984   copying build/lib/shephard/proteome.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:38,992   copying build/lib/shephard/sequence_utilities.py -> build/bdist.linux-armv7l/wheel/shephard
2022-09-04T00:44:38,997   creating build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,000   copying build/lib/shephard/tools/track_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,004   copying build/lib/shephard/tools/experimental.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,008   copying build/lib/shephard/tools/sequence_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,012   copying build/lib/shephard/tools/__init__.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,016   copying build/lib/shephard/tools/domain_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,022   copying build/lib/shephard/tools/site_tools.py -> build/bdist.linux-armv7l/wheel/shephard/tools
2022-09-04T00:44:39,027   creating build/bdist.linux-armv7l/wheel/shephard/data
2022-09-04T00:44:39,029   copying build/lib/shephard/data/README.md -> build/bdist.linux-armv7l/wheel/shephard/data
2022-09-04T00:44:39,034   creating build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,037   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,041   copying build/lib/shephard/data/test_data/testset_1.fasta -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,045   copying build/lib/shephard/data/test_data/tst.py -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,049   copying build/lib/shephard/data/test_data/TS1_protein_attributes.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,052   copying build/lib/shephard/data/test_data/TS1_domains_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,055   copying build/lib/shephard/data/test_data/testset_1.fasta.fai -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,059   copying build/lib/shephard/data/test_data/names.txt -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,062   copying build/lib/shephard/data/test_data/testset_1_ptms.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,065   copying build/lib/shephard/data/test_data/TS1_domains_idr_and_others.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,068   copying build/lib/shephard/data/test_data/TS1_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,072   copying build/lib/shephard/data/test_data/ts1_bonus_sites.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,076   copying build/lib/shephard/data/test_data/TS1_domains_idr.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,079   copying build/lib/shephard/data/test_data/ts1_bonus_sites_bad2.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,082   copying build/lib/shephard/data/test_data/seqs.fasta -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,086   copying build/lib/shephard/data/test_data/TS1_tracks_pscore.tsv -> build/bdist.linux-armv7l/wheel/shephard/data/test_data
2022-09-04T00:44:39,092   copying build/lib/shephard/data/look_and_say.dat -> build/bdist.linux-armv7l/wheel/shephard/data
2022-09-04T00:44:39,094   running install_egg_info
2022-09-04T00:44:39,843   Copying shephard.egg-info to build/bdist.linux-armv7l/wheel/shephard-0.1.14-py3.7.egg-info
2022-09-04T00:44:39,864   running install_scripts
2022-09-04T00:44:40,005   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2022-09-04T00:44:40,014   creating build/bdist.linux-armv7l/wheel/shephard-0.1.14.dist-info/WHEEL
2022-09-04T00:44:40,018   creating '/tmp/pip-wheel-u_v7gqoe/shephard-0.1.14-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2022-09-04T00:44:40,023   adding 'shephard/__init__.py'
2022-09-04T00:44:40,026   adding 'shephard/_version.py'
2022-09-04T00:44:40,031   adding 'shephard/domain.py'
2022-09-04T00:44:40,034   adding 'shephard/exceptions.py'
2022-09-04T00:44:40,037   adding 'shephard/general_utilities.py'
2022-09-04T00:44:40,060   adding 'shephard/protein.py'
2022-09-04T00:44:40,074   adding 'shephard/proteome.py'
2022-09-04T00:44:40,078   adding 'shephard/sequence_utilities.py'
2022-09-04T00:44:40,083   adding 'shephard/site.py'
2022-09-04T00:44:40,086   adding 'shephard/test_domains_sites.py'
2022-09-04T00:44:40,091   adding 'shephard/track.py'
2022-09-04T00:44:40,095   adding 'shephard/apis/__init__.py'
2022-09-04T00:44:40,100   adding 'shephard/apis/fasta.py'
2022-09-04T00:44:40,104   adding 'shephard/apis/uniprot.py'
2022-09-04T00:44:40,108   adding 'shephard/data/README.md'
2022-09-04T00:44:40,110   adding 'shephard/data/look_and_say.dat'
2022-09-04T00:44:40,114   adding 'shephard/data/test_data/TS1_domains_idr.tsv'
2022-09-04T00:44:40,116   adding 'shephard/data/test_data/TS1_domains_idr_and_others.tsv'
2022-09-04T00:44:40,118   adding 'shephard/data/test_data/TS1_domains_pscore.tsv'
2022-09-04T00:44:40,120   adding 'shephard/data/test_data/TS1_protein_attributes.tsv'
2022-09-04T00:44:40,123   adding 'shephard/data/test_data/TS1_sites.tsv'
2022-09-04T00:44:40,144   adding 'shephard/data/test_data/TS1_tracks_pscore.tsv'
2022-09-04T00:44:40,147   adding 'shephard/data/test_data/names.txt'
2022-09-04T00:44:40,150   adding 'shephard/data/test_data/seqs.fasta'
2022-09-04T00:44:40,154   adding 'shephard/data/test_data/testset_1.fasta'
2022-09-04T00:44:40,156   adding 'shephard/data/test_data/testset_1.fasta.fai'
2022-09-04T00:44:40,158   adding 'shephard/data/test_data/testset_1_ptms.tsv'
2022-09-04T00:44:40,160   adding 'shephard/data/test_data/ts1_bonus_sites.tsv'
2022-09-04T00:44:40,162   adding 'shephard/data/test_data/ts1_bonus_sites_bad.tsv'
2022-09-04T00:44:40,165   adding 'shephard/data/test_data/ts1_bonus_sites_bad2.tsv'
2022-09-04T00:44:40,167   adding 'shephard/data/test_data/tst.py'
2022-09-04T00:44:40,170   adding 'shephard/interfaces/__init__.py'
2022-09-04T00:44:40,174   adding 'shephard/interfaces/interface_tools.py'
2022-09-04T00:44:40,182   adding 'shephard/interfaces/si_domains.py'
2022-09-04T00:44:40,187   adding 'shephard/interfaces/si_protein_attributes.py'
2022-09-04T00:44:40,191   adding 'shephard/interfaces/si_proteins.py'
2022-09-04T00:44:40,197   adding 'shephard/interfaces/si_sites.py'
2022-09-04T00:44:40,205   adding 'shephard/interfaces/si_tracks.py'
2022-09-04T00:44:40,209   adding 'shephard/tests/__init__.py'
2022-09-04T00:44:40,211   adding 'shephard/tests/conftest.py'
2022-09-04T00:44:40,214   adding 'shephard/tests/example_test_function.py'
2022-09-04T00:44:40,216   adding 'shephard/tests/test_add_remove_annotations.py'
2022-09-04T00:44:40,219   adding 'shephard/tests/test_apis_fasta.py'
2022-09-04T00:44:40,222   adding 'shephard/tests/test_domain_tools.py'
2022-09-04T00:44:40,226   adding 'shephard/tests/test_domains.py'
2022-09-04T00:44:40,228   adding 'shephard/tests/test_interfaces.py'
2022-09-04T00:44:40,230   adding 'shephard/tests/test_logic.py'
2022-09-04T00:44:40,234   adding 'shephard/tests/test_protein.py'
2022-09-04T00:44:40,238   adding 'shephard/tests/test_proteome.py'
2022-09-04T00:44:40,241   adding 'shephard/tests/test_scratchpad.ipynb'
2022-09-04T00:44:40,243   adding 'shephard/tests/test_sequence_tools.py'
2022-09-04T00:44:40,245   adding 'shephard/tests/test_shephard.py'
2022-09-04T00:44:40,248   adding 'shephard/tests/test_si_domains.py'
2022-09-04T00:44:40,251   adding 'shephard/tests/test_si_sites.py'
2022-09-04T00:44:40,255   adding 'shephard/tests/test_si_tracks.py'
2022-09-04T00:44:40,258   adding 'shephard/tests/test_sites.py'
2022-09-04T00:44:40,260   adding 'shephard/tests/test_track_tools.py'
2022-09-04T00:44:40,263   adding 'shephard/tests/test_tracks.py'
2022-09-04T00:44:40,266   adding 'shephard/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb'
2022-09-04T00:44:40,270   adding 'shephard/tests/output_test/all_symbols_test.tsv'
2022-09-04T00:44:40,275   adding 'shephard/tests/output_test/all_values_test.tsv'
2022-09-04T00:44:40,280   adding 'shephard/tests/output_test/all_values_test_from_list.tsv'
2022-09-04T00:44:40,301   adding 'shephard/tests/output_test/out_tracks.tsv'
2022-09-04T00:44:40,304   adding 'shephard/tests/output_test/readme.md'
2022-09-04T00:44:40,306   adding 'shephard/tests/output_test/shephard_track_phosres.tsv'
2022-09-04T00:44:40,327   adding 'shephard/tests/output_test/shephard_track_pscore.tsv'
2022-09-04T00:44:40,330   adding 'shephard/tests/output_test/test_domains.tsv'
2022-09-04T00:44:40,337   adding 'shephard/tests/output_test/test_sites.tsv'
2022-09-04T00:44:40,341   adding 'shephard/tests/output_test/track_phospho_track.tsv'
2022-09-04T00:44:40,344   adding 'shephard/tests/output_test/track_random_vals.tsv'
2022-09-04T00:44:40,347   adding 'shephard/tools/__init__.py'
2022-09-04T00:44:40,354   adding 'shephard/tools/domain_tools.py'
2022-09-04T00:44:40,357   adding 'shephard/tools/experimental.py'
2022-09-04T00:44:40,360   adding 'shephard/tools/sequence_tools.py'
2022-09-04T00:44:40,363   adding 'shephard/tools/site_tools.py'
2022-09-04T00:44:40,366   adding 'shephard/tools/track_tools.py'
2022-09-04T00:44:40,371   adding 'shephard-0.1.14.dist-info/LICENSE'
2022-09-04T00:44:40,374   adding 'shephard-0.1.14.dist-info/METADATA'
2022-09-04T00:44:40,376   adding 'shephard-0.1.14.dist-info/WHEEL'
2022-09-04T00:44:40,378   adding 'shephard-0.1.14.dist-info/top_level.txt'
2022-09-04T00:44:40,382   adding 'shephard-0.1.14.dist-info/RECORD'
2022-09-04T00:44:40,393   removing build/bdist.linux-armv7l/wheel
2022-09-04T00:44:40,700   Building wheel for shephard (setup.py): finished with status 'done'
2022-09-04T00:44:40,712   Created wheel for shephard: filename=shephard-0.1.14-py3-none-any.whl size=178032 sha256=475a3c0e8212f4d337f0f1dc4abe953595d119c3b46c8cc25fcc63502c39ac2d
2022-09-04T00:44:40,714   Stored in directory: /tmp/pip-ephem-wheel-cache-o7ckkr0y/wheels/b7/6a/e4/d51840ba3e2ae8c05898ce0105024465c666a5f0261f911e7e
2022-09-04T00:44:40,744 Successfully built shephard
2022-09-04T00:44:40,765 Removed build tracker: '/tmp/pip-build-tracker-y3mp0bw6'