2025-06-10T23:42:07,569 Created temporary directory: /tmp/pip-build-tracker-86v6_0o0 2025-06-10T23:42:07,570 Initialized build tracking at /tmp/pip-build-tracker-86v6_0o0 2025-06-10T23:42:07,571 Created build tracker: /tmp/pip-build-tracker-86v6_0o0 2025-06-10T23:42:07,572 Entered build tracker: /tmp/pip-build-tracker-86v6_0o0 2025-06-10T23:42:07,572 Created temporary directory: /tmp/pip-wheel-ai7b6pro 2025-06-10T23:42:07,577 Created temporary directory: /tmp/pip-ephem-wheel-cache-f6etm6l7 2025-06-10T23:42:07,625 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-10T23:42:07,627 2 location(s) to search for versions of pub-worm: 2025-06-10T23:42:07,627 * https://pypi.org/simple/pub-worm/ 2025-06-10T23:42:07,627 * https://www.piwheels.org/simple/pub-worm/ 2025-06-10T23:42:07,628 Fetching project page and analyzing links: https://pypi.org/simple/pub-worm/ 2025-06-10T23:42:07,629 Getting page https://pypi.org/simple/pub-worm/ 2025-06-10T23:42:07,631 Found index url https://pypi.org/simple/ 2025-06-10T23:42:07,858 Fetched page https://pypi.org/simple/pub-worm/ as application/vnd.pypi.simple.v1+json 2025-06-10T23:42:07,862 Found link https://files.pythonhosted.org/packages/b8/f0/9bb3afc5b9c0aba5ffc3e0530f85826c7d472bd722f814015247c340fb9f/pub_worm-0.0.1.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.0.1 2025-06-10T23:42:07,863 Found link https://files.pythonhosted.org/packages/d8/da/df592d4da97e43ba80b8d21977686643e2fe53863198e8636d52f8385c43/pub_worm-0.1.1.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.1.1 2025-06-10T23:42:07,864 Found link https://files.pythonhosted.org/packages/6f/b8/c578681405080946ef981f7d8ffca920a824488067c8d71585d3ed6a579d/pub_worm-0.1.2.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.1.2 2025-06-10T23:42:07,864 Found link https://files.pythonhosted.org/packages/95/ea/f0d51e75f6a6bc592da883218d988cf193bf319166fa473a9b9b88e8d264/pub_worm-0.1.3.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.1.3 2025-06-10T23:42:07,865 Found link https://files.pythonhosted.org/packages/75/a9/79c8f5eedf2bb7efb9da2d0fe145f73a38f517eb8598c34ee7c96cde0708/pub_worm-0.1.4.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.1.4 2025-06-10T23:42:07,866 Found link https://files.pythonhosted.org/packages/49/b1/562faa427fd1ff40c449f87cda75c7c1df17d70bb5190dd9acaa36d175b1/pub_worm-0.1.5.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.1.5 2025-06-10T23:42:07,867 Found link https://files.pythonhosted.org/packages/80/a0/1ce94f51ef16d83a09dea4f1985b068452c7880801597bd3eb82efd056fc/pub_worm-0.1.6.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.1.6 2025-06-10T23:42:07,868 Found link https://files.pythonhosted.org/packages/a3/21/a1cd9d1377b513ca7bb426346eb849aa4c84f3b3a3e1d80c0c7b05585d92/pub_worm-0.1.7.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.1.7 2025-06-10T23:42:07,868 Found link https://files.pythonhosted.org/packages/8f/fc/a0c2da18b286317e2843459c01336317cfeaa46efe28b278201968d1176d/pub_worm-0.1.8.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.1.8 2025-06-10T23:42:07,869 Found link https://files.pythonhosted.org/packages/05/8b/338f3714f1fa9c96e6eb4161453ee1686e7e852c3e568f53de43d9181cba/pub_worm-0.1.9.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.1.9 2025-06-10T23:42:07,870 Found link https://files.pythonhosted.org/packages/97/77/c5713bb989282f6cc978673a6444be453c991049862f200a583aae8061de/pub_worm-0.2.0.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.2.0 2025-06-10T23:42:07,871 Found link https://files.pythonhosted.org/packages/ba/54/2d9a593a5d99fea472983a809a8764698e89d7e9336eb4dece805bb685d1/pub_worm-0.2.1.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.2.1 2025-06-10T23:42:07,871 Found link https://files.pythonhosted.org/packages/da/24/bc0ded99393b36c2a10169df8df556b1ffa4efbcb6cc88c6d0d1245a4490/pub_worm-0.2.2.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.2.2 2025-06-10T23:42:07,872 Found link https://files.pythonhosted.org/packages/33/30/9561212f51f111d9449c44d81a0be28a5cf0c3b0b074539017aaf0d3630c/pub_worm-0.2.3.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.2.3 2025-06-10T23:42:07,873 Found link https://files.pythonhosted.org/packages/6c/a1/cf793b17a67838982ea4ec3ad482fcb8a43a35ccf82d0ac3271755dd778c/pub_worm-0.2.4.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.2.4 2025-06-10T23:42:07,874 Found link https://files.pythonhosted.org/packages/43/11/631571482818adc400afa644ca4fb69ab1c3380d266d34f0112877514a49/pub_worm-0.2.5.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.2.5 2025-06-10T23:42:07,874 Found link https://files.pythonhosted.org/packages/7d/07/f0b969d2ecfe9daa5682c4565ed168d28aa1e45dff044a102bdb549c2cba/pub_worm-0.2.6.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.2.6 2025-06-10T23:42:07,875 Found link https://files.pythonhosted.org/packages/f5/e4/6c2a317ea14ff7acce17ad7087f4937e860cb48d28976812e19191e544e5/pub_worm-0.2.7.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.2.7 2025-06-10T23:42:07,876 Found link https://files.pythonhosted.org/packages/51/40/51943d1557acd97d0bd3c5e4ea9131e52649895cce775d41150299780858/pub_worm-0.2.8.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.2.8 2025-06-10T23:42:07,876 Found link https://files.pythonhosted.org/packages/96/9b/59b37b2341e80821c39f248138f73e554aa06b6ab437d44aca25ec803725/pub_worm-0.2.9.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.2.9 2025-06-10T23:42:07,877 Found link https://files.pythonhosted.org/packages/6a/ca/c5f05833b54c4ddb2b8d70e1c3e9631b195d28c7dc92cfbbd22d539d9f0e/pub_worm-0.3.0.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.0 2025-06-10T23:42:07,877 Found link https://files.pythonhosted.org/packages/85/d9/83a18281c7792db68fb6f9af515e5a50b5235c2d9816586d522060be97a7/pub_worm-0.3.1.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.1 2025-06-10T23:42:07,878 Found link https://files.pythonhosted.org/packages/d6/ea/750af1e220e8ea7ca825e574c5f8485c82cebc05826882f736e492d11d4a/pub_worm-0.3.2.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.2 2025-06-10T23:42:07,879 Found link https://files.pythonhosted.org/packages/8a/b9/75cdcce68e88b56c29aacadd8cc4229c649b54f1e2ec77582527997599ce/pub_worm-0.3.3.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.3 2025-06-10T23:42:07,879 Found link https://files.pythonhosted.org/packages/4e/3c/d7b15b0ca8d9ef436dd08e08a40d7b1e039c3a9e786a5e9dfa8101d02dd7/pub_worm-0.3.4.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.4 2025-06-10T23:42:07,880 Found link https://files.pythonhosted.org/packages/a0/0f/b34482f11648e05a16204f290f64ff41a798e896121355059e8b5f039c47/pub_worm-0.3.5.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.5 2025-06-10T23:42:07,881 Found link https://files.pythonhosted.org/packages/53/5c/99090a17cc43030da42e4951e37a6b81a1ea98a54f4b7e12db9e4a35c6f2/pub_worm-0.3.6.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.6 2025-06-10T23:42:07,882 Found link https://files.pythonhosted.org/packages/6f/48/015e25d3a60e7e8234cb2c2edd8b45d742fcd70992e06041d71c543b7200/pub_worm-0.3.7.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.7 2025-06-10T23:42:07,883 Found link https://files.pythonhosted.org/packages/1a/78/e345c49eee5b968f3766c1bd34690a53fdad25695df6d793ebb3879bb715/pub_worm-0.3.8.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.8 2025-06-10T23:42:07,883 Found link https://files.pythonhosted.org/packages/60/1a/b9e6351cdffb27c2ed342a6fcd2fa8f18e3a22a7ca93ca0f8dc0d535941b/pub_worm-0.3.9.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.9 2025-06-10T23:42:07,884 Found link https://files.pythonhosted.org/packages/0d/db/ae6735152a6ae0d0b25538316ac438c74875242907bd6b0053c6fa2173b4/pub_worm-0.3.10.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.10 2025-06-10T23:42:07,885 Found link https://files.pythonhosted.org/packages/c9/7c/8ac6631b74eb781a27c88eed56ff3e592945f74bb73bc525319702534162/pub_worm-0.3.11.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.11 2025-06-10T23:42:07,886 Found link https://files.pythonhosted.org/packages/ab/bb/4a6eb4bf7849059ff077a76690d91a44d4aa67fbfc2dca814c640da0a30f/pub_worm-0.3.12.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.12 2025-06-10T23:42:07,887 Found link https://files.pythonhosted.org/packages/49/9a/b32f9d8d361b31f47f630f14ef510ade5abad9b93fc6c441686fb96d9fc6/pub_worm-0.3.13.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.13 2025-06-10T23:42:07,887 Found link https://files.pythonhosted.org/packages/7f/88/9b6c038faacd7806ec013840d180c8428a718c9fd72ef87e600dfa8cff5c/pub_worm-0.3.14.tar.gz (from https://pypi.org/simple/pub-worm/), version: 0.3.14 2025-06-10T23:42:07,888 Fetching project page and analyzing links: https://www.piwheels.org/simple/pub-worm/ 2025-06-10T23:42:07,888 Getting page https://www.piwheels.org/simple/pub-worm/ 2025-06-10T23:42:07,890 Found index url https://www.piwheels.org/simple/ 2025-06-10T23:42:08,050 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pub-worm/ 2025-06-10T23:42:08,703 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pub-worm/ 2025-06-10T23:42:09,867 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pub-worm/ 2025-06-10T23:42:12,024 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pub-worm/ 2025-06-10T23:42:16,180 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/pub-worm/ 2025-06-10T23:42:16,338 Could not fetch URL https://www.piwheels.org/simple/pub-worm/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/pub-worm/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping 2025-06-10T23:42:16,339 Skipping link: not a file: https://www.piwheels.org/simple/pub-worm/ 2025-06-10T23:42:16,340 Skipping link: not a file: https://pypi.org/simple/pub-worm/ 2025-06-10T23:42:16,362 Given no hashes to check 1 links for project 'pub-worm': discarding no candidates 2025-06-10T23:42:16,364 Collecting pub-worm==0.3.10 2025-06-10T23:42:16,366 Created temporary directory: /tmp/pip-unpack-qin7cs1t 2025-06-10T23:42:16,611 Downloading pub_worm-0.3.10.tar.gz (396 kB) 2025-06-10T23:42:16,822 Added pub-worm==0.3.10 from https://files.pythonhosted.org/packages/0d/db/ae6735152a6ae0d0b25538316ac438c74875242907bd6b0053c6fa2173b4/pub_worm-0.3.10.tar.gz to build tracker '/tmp/pip-build-tracker-86v6_0o0' 2025-06-10T23:42:16,825 Running setup.py (path:/tmp/pip-wheel-ai7b6pro/pub-worm_5da4a22b2c444681832186da256f8b79/setup.py) egg_info for package pub-worm 2025-06-10T23:42:16,826 Created temporary directory: /tmp/pip-pip-egg-info-_9xly999 2025-06-10T23:42:16,826 Preparing metadata (setup.py): started 2025-06-10T23:42:16,828 Running command python setup.py egg_info 2025-06-10T23:42:17,770 running egg_info 2025-06-10T23:42:17,798 creating /tmp/pip-pip-egg-info-_9xly999/pub_worm.egg-info 2025-06-10T23:42:17,799 writing /tmp/pip-pip-egg-info-_9xly999/pub_worm.egg-info/PKG-INFO 2025-06-10T23:42:17,803 writing dependency_links to /tmp/pip-pip-egg-info-_9xly999/pub_worm.egg-info/dependency_links.txt 2025-06-10T23:42:17,805 writing requirements to /tmp/pip-pip-egg-info-_9xly999/pub_worm.egg-info/requires.txt 2025-06-10T23:42:17,806 writing top-level names to /tmp/pip-pip-egg-info-_9xly999/pub_worm.egg-info/top_level.txt 2025-06-10T23:42:17,808 writing manifest file '/tmp/pip-pip-egg-info-_9xly999/pub_worm.egg-info/SOURCES.txt' 2025-06-10T23:42:17,908 reading manifest file '/tmp/pip-pip-egg-info-_9xly999/pub_worm.egg-info/SOURCES.txt' 2025-06-10T23:42:17,910 reading manifest template 'MANIFEST.in' 2025-06-10T23:42:17,912 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json' 2025-06-10T23:42:17,913 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json' 2025-06-10T23:42:17,913 warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json' 2025-06-10T23:42:17,916 writing manifest file '/tmp/pip-pip-egg-info-_9xly999/pub_worm.egg-info/SOURCES.txt' 2025-06-10T23:42:18,027 Preparing metadata (setup.py): finished with status 'done' 2025-06-10T23:42:18,031 Source in /tmp/pip-wheel-ai7b6pro/pub-worm_5da4a22b2c444681832186da256f8b79 has version 0.3.10, which satisfies requirement pub-worm==0.3.10 from https://files.pythonhosted.org/packages/0d/db/ae6735152a6ae0d0b25538316ac438c74875242907bd6b0053c6fa2173b4/pub_worm-0.3.10.tar.gz 2025-06-10T23:42:18,032 Removed pub-worm==0.3.10 from https://files.pythonhosted.org/packages/0d/db/ae6735152a6ae0d0b25538316ac438c74875242907bd6b0053c6fa2173b4/pub_worm-0.3.10.tar.gz from build tracker '/tmp/pip-build-tracker-86v6_0o0' 2025-06-10T23:42:18,039 Created temporary directory: /tmp/pip-unpack-eowefj5j 2025-06-10T23:42:18,040 Created temporary directory: /tmp/pip-unpack-fnspw6k4 2025-06-10T23:42:18,040 Building wheels for collected packages: pub-worm 2025-06-10T23:42:18,045 Created temporary directory: /tmp/pip-wheel-2vf3thty 2025-06-10T23:42:18,045 DEPRECATION: Building 'pub-worm' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pub-worm'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-06-10T23:42:18,047 Building wheel for pub-worm (setup.py): started 2025-06-10T23:42:18,048 Destination directory: /tmp/pip-wheel-2vf3thty 2025-06-10T23:42:18,048 Running command python setup.py bdist_wheel 2025-06-10T23:42:18,903 running bdist_wheel 2025-06-10T23:42:19,041 running build 2025-06-10T23:42:19,041 running build_py 2025-06-10T23:42:19,073 creating build/lib/tests 2025-06-10T23:42:19,075 copying tests/__init__.py -> build/lib/tests 2025-06-10T23:42:19,078 creating build/lib/pub_worm 2025-06-10T23:42:19,079 copying pub_worm/__init__.py -> build/lib/pub_worm 2025-06-10T23:42:19,081 creating build/lib/tests/ncbi 2025-06-10T23:42:19,082 copying tests/ncbi/__init__.py -> build/lib/tests/ncbi 2025-06-10T23:42:19,084 copying tests/ncbi/test_entreze_api.py -> build/lib/tests/ncbi 2025-06-10T23:42:19,087 creating build/lib/tests/wormbase 2025-06-10T23:42:19,088 copying tests/wormbase/__init__.py -> build/lib/tests/wormbase 2025-06-10T23:42:19,090 copying tests/wormbase/test_wormbase_api.py -> build/lib/tests/wormbase 2025-06-10T23:42:19,092 creating build/lib/tests/orcid 2025-06-10T23:42:19,094 copying tests/orcid/__init__.py -> build/lib/tests/orcid 2025-06-10T23:42:19,096 copying tests/orcid/test_orcid_api.py -> build/lib/tests/orcid 2025-06-10T23:42:19,098 creating build/lib/tests/impact_factor 2025-06-10T23:42:19,099 copying tests/impact_factor/__init__.py -> build/lib/tests/impact_factor 2025-06-10T23:42:19,101 copying tests/impact_factor/test_get_impact_factor.py -> build/lib/tests/impact_factor 2025-06-10T23:42:19,104 creating build/lib/pub_worm/biorxiv 2025-06-10T23:42:19,105 copying pub_worm/biorxiv/__init__.py -> build/lib/pub_worm/biorxiv 2025-06-10T23:42:19,107 copying pub_worm/biorxiv/biorxiv_api.py -> build/lib/pub_worm/biorxiv 2025-06-10T23:42:19,109 creating build/lib/pub_worm/ncbi 2025-06-10T23:42:19,110 copying pub_worm/ncbi/__init__.py -> build/lib/pub_worm/ncbi 2025-06-10T23:42:19,112 copying pub_worm/ncbi/entreze_api.py -> build/lib/pub_worm/ncbi 2025-06-10T23:42:19,115 creating build/lib/pub_worm/ensembl 2025-06-10T23:42:19,116 copying pub_worm/ensembl/ensembl_api.py -> build/lib/pub_worm/ensembl 2025-06-10T23:42:19,118 copying pub_worm/ensembl/__init__.py -> build/lib/pub_worm/ensembl 2025-06-10T23:42:19,120 creating build/lib/pub_worm/wormbase 2025-06-10T23:42:19,120 copying pub_worm/wormbase/__init__.py -> build/lib/pub_worm/wormbase 2025-06-10T23:42:19,122 copying pub_worm/wormbase/wormbase_util.py -> build/lib/pub_worm/wormbase 2025-06-10T23:42:19,125 copying pub_worm/wormbase/to_csv_helpers.py -> build/lib/pub_worm/wormbase 2025-06-10T23:42:19,127 copying pub_worm/wormbase/wormbase_api.py -> build/lib/pub_worm/wormbase 2025-06-10T23:42:19,129 creating build/lib/pub_worm/orcid 2025-06-10T23:42:19,130 copying pub_worm/orcid/__init__.py -> build/lib/pub_worm/orcid 2025-06-10T23:42:19,132 copying pub_worm/orcid/orcid_api.py -> build/lib/pub_worm/orcid 2025-06-10T23:42:19,135 creating build/lib/pub_worm/impact_factor 2025-06-10T23:42:19,136 copying pub_worm/impact_factor/__init__.py -> build/lib/pub_worm/impact_factor 2025-06-10T23:42:19,138 copying pub_worm/impact_factor/impact_factor_lookup.py -> build/lib/pub_worm/impact_factor 2025-06-10T23:42:19,139 running egg_info 2025-06-10T23:42:19,168 writing pub_worm.egg-info/PKG-INFO 2025-06-10T23:42:19,171 writing dependency_links to pub_worm.egg-info/dependency_links.txt 2025-06-10T23:42:19,173 writing requirements to pub_worm.egg-info/requires.txt 2025-06-10T23:42:19,175 writing top-level names to pub_worm.egg-info/top_level.txt 2025-06-10T23:42:19,216 reading manifest file 'pub_worm.egg-info/SOURCES.txt' 2025-06-10T23:42:19,220 reading manifest template 'MANIFEST.in' 2025-06-10T23:42:19,221 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json' 2025-06-10T23:42:19,222 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json' 2025-06-10T23:42:19,222 warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json' 2025-06-10T23:42:19,226 writing manifest file 'pub_worm.egg-info/SOURCES.txt' 2025-06-10T23:42:19,228 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pub_worm.impact_factor.data' is absent from the `packages` configuration. 2025-06-10T23:42:19,229 !! 2025-06-10T23:42:19,230 ******************************************************************************** 2025-06-10T23:42:19,231 ############################ 2025-06-10T23:42:19,231 # Package would be ignored # 2025-06-10T23:42:19,232 ############################ 2025-06-10T23:42:19,233 Python recognizes 'pub_worm.impact_factor.data' as an importable package[^1], 2025-06-10T23:42:19,233 but it is absent from setuptools' `packages` configuration. 2025-06-10T23:42:19,234 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-10T23:42:19,235 package, please make sure that 'pub_worm.impact_factor.data' is explicitly added 2025-06-10T23:42:19,235 to the `packages` configuration field. 2025-06-10T23:42:19,237 Alternatively, you can also rely on setuptools' discovery methods 2025-06-10T23:42:19,237 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-10T23:42:19,238 instead of `find_packages(...)`/`find:`). 2025-06-10T23:42:19,239 You can read more about "package discovery" on setuptools documentation page: 2025-06-10T23:42:19,240 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-10T23:42:19,241 If you don't want 'pub_worm.impact_factor.data' to be distributed and are 2025-06-10T23:42:19,242 already explicitly excluding 'pub_worm.impact_factor.data' via 2025-06-10T23:42:19,242 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-10T23:42:19,243 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-10T23:42:19,243 combination with a more fine grained `package-data` configuration. 2025-06-10T23:42:19,244 You can read more about "package data files" on setuptools documentation page: 2025-06-10T23:42:19,245 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-10T23:42:19,246 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-10T23:42:19,247 even if it does not contain any `.py` files. 2025-06-10T23:42:19,247 On the other hand, currently there is no concept of package data 2025-06-10T23:42:19,247 directory, all directories are treated like packages. 2025-06-10T23:42:19,248 ******************************************************************************** 2025-06-10T23:42:19,249 !! 2025-06-10T23:42:19,249 check.warn(importable) 2025-06-10T23:42:19,250 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pub_worm.wormbase.data' is absent from the `packages` configuration. 2025-06-10T23:42:19,250 !! 2025-06-10T23:42:19,252 ******************************************************************************** 2025-06-10T23:42:19,252 ############################ 2025-06-10T23:42:19,253 # Package would be ignored # 2025-06-10T23:42:19,254 ############################ 2025-06-10T23:42:19,254 Python recognizes 'pub_worm.wormbase.data' as an importable package[^1], 2025-06-10T23:42:19,255 but it is absent from setuptools' `packages` configuration. 2025-06-10T23:42:19,264 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-10T23:42:19,266 package, please make sure that 'pub_worm.wormbase.data' is explicitly added 2025-06-10T23:42:19,270 to the `packages` configuration field. 2025-06-10T23:42:19,275 Alternatively, you can also rely on setuptools' discovery methods 2025-06-10T23:42:19,275 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-10T23:42:19,276 instead of `find_packages(...)`/`find:`). 2025-06-10T23:42:19,277 You can read more about "package discovery" on setuptools documentation page: 2025-06-10T23:42:19,278 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-10T23:42:19,279 If you don't want 'pub_worm.wormbase.data' to be distributed and are 2025-06-10T23:42:19,280 already explicitly excluding 'pub_worm.wormbase.data' via 2025-06-10T23:42:19,280 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-10T23:42:19,281 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-10T23:42:19,282 combination with a more fine grained `package-data` configuration. 2025-06-10T23:42:19,283 You can read more about "package data files" on setuptools documentation page: 2025-06-10T23:42:19,284 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-10T23:42:19,286 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-10T23:42:19,287 even if it does not contain any `.py` files. 2025-06-10T23:42:19,287 On the other hand, currently there is no concept of package data 2025-06-10T23:42:19,288 directory, all directories are treated like packages. 2025-06-10T23:42:19,289 ******************************************************************************** 2025-06-10T23:42:19,290 !! 2025-06-10T23:42:19,290 check.warn(importable) 2025-06-10T23:42:19,291 creating build/lib/pub_worm/wormbase/data 2025-06-10T23:42:19,291 copying pub_worm/wormbase/data/wormbase_field_gene.json -> build/lib/pub_worm/wormbase/data 2025-06-10T23:42:19,292 copying pub_worm/wormbase/data/wormbase_field_paper.json -> build/lib/pub_worm/wormbase/data 2025-06-10T23:42:19,292 copying pub_worm/wormbase/data/wormbase_widget_gene.json -> build/lib/pub_worm/wormbase/data 2025-06-10T23:42:19,293 creating build/lib/pub_worm/impact_factor/data 2025-06-10T23:42:19,293 copying pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/lib/pub_worm/impact_factor/data 2025-06-10T23:42:19,313 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-10T23:42:19,314 !! 2025-06-10T23:42:19,315 ******************************************************************************** 2025-06-10T23:42:19,315 Please avoid running ``setup.py`` directly. 2025-06-10T23:42:19,316 Instead, use pypa/build, pypa/installer or other 2025-06-10T23:42:19,317 standards-based tools. 2025-06-10T23:42:19,318 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-10T23:42:19,318 or your builds will no longer be supported. 2025-06-10T23:42:19,319 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-10T23:42:19,320 ******************************************************************************** 2025-06-10T23:42:19,321 !! 2025-06-10T23:42:19,321 self.initialize_options() 2025-06-10T23:42:19,343 installing to build/bdist.linux-armv7l/wheel 2025-06-10T23:42:19,343 running install 2025-06-10T23:42:19,367 running install_lib 2025-06-10T23:42:19,396 creating build/bdist.linux-armv7l/wheel 2025-06-10T23:42:19,398 creating build/bdist.linux-armv7l/wheel/tests 2025-06-10T23:42:19,400 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2025-06-10T23:42:19,402 creating build/bdist.linux-armv7l/wheel/tests/ncbi 2025-06-10T23:42:19,403 copying build/lib/tests/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi 2025-06-10T23:42:19,405 copying build/lib/tests/ncbi/test_entreze_api.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi 2025-06-10T23:42:19,408 creating build/bdist.linux-armv7l/wheel/tests/wormbase 2025-06-10T23:42:19,409 copying build/lib/tests/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase 2025-06-10T23:42:19,410 copying build/lib/tests/wormbase/test_wormbase_api.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase 2025-06-10T23:42:19,413 creating build/bdist.linux-armv7l/wheel/tests/orcid 2025-06-10T23:42:19,414 copying build/lib/tests/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/orcid 2025-06-10T23:42:19,416 copying build/lib/tests/orcid/test_orcid_api.py -> build/bdist.linux-armv7l/wheel/./tests/orcid 2025-06-10T23:42:19,418 creating build/bdist.linux-armv7l/wheel/tests/impact_factor 2025-06-10T23:42:19,419 copying build/lib/tests/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor 2025-06-10T23:42:19,421 copying build/lib/tests/impact_factor/test_get_impact_factor.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor 2025-06-10T23:42:19,424 creating build/bdist.linux-armv7l/wheel/pub_worm 2025-06-10T23:42:19,425 creating build/bdist.linux-armv7l/wheel/pub_worm/biorxiv 2025-06-10T23:42:19,427 copying build/lib/pub_worm/biorxiv/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv 2025-06-10T23:42:19,428 copying build/lib/pub_worm/biorxiv/biorxiv_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv 2025-06-10T23:42:19,430 copying build/lib/pub_worm/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm 2025-06-10T23:42:19,433 creating build/bdist.linux-armv7l/wheel/pub_worm/ncbi 2025-06-10T23:42:19,434 copying build/lib/pub_worm/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi 2025-06-10T23:42:19,436 copying build/lib/pub_worm/ncbi/entreze_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi 2025-06-10T23:42:19,439 creating build/bdist.linux-armv7l/wheel/pub_worm/ensembl 2025-06-10T23:42:19,440 copying build/lib/pub_worm/ensembl/ensembl_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl 2025-06-10T23:42:19,442 copying build/lib/pub_worm/ensembl/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl 2025-06-10T23:42:19,444 creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase 2025-06-10T23:42:19,445 copying build/lib/pub_worm/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-10T23:42:19,447 copying build/lib/pub_worm/wormbase/wormbase_util.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-10T23:42:19,449 copying build/lib/pub_worm/wormbase/to_csv_helpers.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-10T23:42:19,451 copying build/lib/pub_worm/wormbase/wormbase_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-10T23:42:19,454 creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase/data 2025-06-10T23:42:19,455 copying build/lib/pub_worm/wormbase/data/wormbase_field_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data 2025-06-10T23:42:19,457 copying build/lib/pub_worm/wormbase/data/wormbase_field_paper.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data 2025-06-10T23:42:19,459 copying build/lib/pub_worm/wormbase/data/wormbase_widget_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data 2025-06-10T23:42:19,462 creating build/bdist.linux-armv7l/wheel/pub_worm/orcid 2025-06-10T23:42:19,463 copying build/lib/pub_worm/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid 2025-06-10T23:42:19,464 copying build/lib/pub_worm/orcid/orcid_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid 2025-06-10T23:42:19,467 creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor 2025-06-10T23:42:19,468 copying build/lib/pub_worm/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor 2025-06-10T23:42:19,470 copying build/lib/pub_worm/impact_factor/impact_factor_lookup.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor 2025-06-10T23:42:19,473 creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor/data 2025-06-10T23:42:19,474 copying build/lib/pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor/data 2025-06-10T23:42:19,500 running install_egg_info 2025-06-10T23:42:19,538 Copying pub_worm.egg-info to build/bdist.linux-armv7l/wheel/./pub_worm-0.3.10-py3.11.egg-info 2025-06-10T23:42:19,551 running install_scripts 2025-06-10T23:42:19,562 creating build/bdist.linux-armv7l/wheel/pub_worm-0.3.10.dist-info/WHEEL 2025-06-10T23:42:19,565 creating '/tmp/pip-wheel-2vf3thty/pub_worm-0.3.10-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-10T23:42:19,567 adding 'pub_worm/__init__.py' 2025-06-10T23:42:19,569 adding 'pub_worm/biorxiv/__init__.py' 2025-06-10T23:42:19,571 adding 'pub_worm/biorxiv/biorxiv_api.py' 2025-06-10T23:42:19,572 adding 'pub_worm/ensembl/__init__.py' 2025-06-10T23:42:19,574 adding 'pub_worm/ensembl/ensembl_api.py' 2025-06-10T23:42:19,576 adding 'pub_worm/impact_factor/__init__.py' 2025-06-10T23:42:19,578 adding 'pub_worm/impact_factor/impact_factor_lookup.py' 2025-06-10T23:42:19,748 adding 'pub_worm/impact_factor/data/2022_JCR_IF.csv' 2025-06-10T23:42:19,758 adding 'pub_worm/ncbi/__init__.py' 2025-06-10T23:42:19,761 adding 'pub_worm/ncbi/entreze_api.py' 2025-06-10T23:42:19,763 adding 'pub_worm/orcid/__init__.py' 2025-06-10T23:42:19,765 adding 'pub_worm/orcid/orcid_api.py' 2025-06-10T23:42:19,766 adding 'pub_worm/wormbase/__init__.py' 2025-06-10T23:42:19,768 adding 'pub_worm/wormbase/to_csv_helpers.py' 2025-06-10T23:42:19,770 adding 'pub_worm/wormbase/wormbase_api.py' 2025-06-10T23:42:19,771 adding 'pub_worm/wormbase/wormbase_util.py' 2025-06-10T23:42:19,773 adding 'pub_worm/wormbase/data/wormbase_field_gene.json' 2025-06-10T23:42:19,774 adding 'pub_worm/wormbase/data/wormbase_field_paper.json' 2025-06-10T23:42:19,775 adding 'pub_worm/wormbase/data/wormbase_widget_gene.json' 2025-06-10T23:42:19,778 adding 'tests/__init__.py' 2025-06-10T23:42:19,779 adding 'tests/impact_factor/__init__.py' 2025-06-10T23:42:19,781 adding 'tests/impact_factor/test_get_impact_factor.py' 2025-06-10T23:42:19,782 adding 'tests/ncbi/__init__.py' 2025-06-10T23:42:19,784 adding 'tests/ncbi/test_entreze_api.py' 2025-06-10T23:42:19,786 adding 'tests/orcid/__init__.py' 2025-06-10T23:42:19,787 adding 'tests/orcid/test_orcid_api.py' 2025-06-10T23:42:19,789 adding 'tests/wormbase/__init__.py' 2025-06-10T23:42:19,790 adding 'tests/wormbase/test_wormbase_api.py' 2025-06-10T23:42:19,791 adding 'pub_worm-0.3.10.dist-info/METADATA' 2025-06-10T23:42:19,792 adding 'pub_worm-0.3.10.dist-info/WHEEL' 2025-06-10T23:42:19,793 adding 'pub_worm-0.3.10.dist-info/top_level.txt' 2025-06-10T23:42:19,794 adding 'pub_worm-0.3.10.dist-info/RECORD' 2025-06-10T23:42:19,801 removing build/bdist.linux-armv7l/wheel 2025-06-10T23:42:19,931 Building wheel for pub-worm (setup.py): finished with status 'done' 2025-06-10T23:42:19,937 Created wheel for pub-worm: filename=pub_worm-0.3.10-py3-none-any.whl size=402803 sha256=458c269f2f076dbbc993893ac98aada106f56b2edb2d190e27db848a53ed9547 2025-06-10T23:42:19,938 Stored in directory: /tmp/pip-ephem-wheel-cache-f6etm6l7/wheels/77/2d/f0/319265b3996c16924ec2fa95cf8e9f5f87271cc381bc01731b 2025-06-10T23:42:19,950 Successfully built pub-worm 2025-06-10T23:42:19,970 Removed build tracker: '/tmp/pip-build-tracker-86v6_0o0'