2025-06-11T15:12:44,557 Created temporary directory: /tmp/pip-build-tracker-2njpu1a9 2025-06-11T15:12:44,559 Initialized build tracking at /tmp/pip-build-tracker-2njpu1a9 2025-06-11T15:12:44,559 Created build tracker: /tmp/pip-build-tracker-2njpu1a9 2025-06-11T15:12:44,560 Entered build tracker: /tmp/pip-build-tracker-2njpu1a9 2025-06-11T15:12:44,561 Created temporary directory: /tmp/pip-wheel-ari_on2c 2025-06-11T15:12:44,565 Created temporary directory: /tmp/pip-ephem-wheel-cache-q1ocbeda 2025-06-11T15:12:44,618 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-11T15:12:44,620 2 location(s) to search for versions of pub-worm: 2025-06-11T15:12:44,620 * https://pypi.org/simple/pub-worm/ 2025-06-11T15:12:44,620 * https://www.piwheels.org/simple/pub-worm/ 2025-06-11T15:12:44,621 Fetching project page and analyzing links: https://pypi.org/simple/pub-worm/ 2025-06-11T15:12:44,622 Getting page https://pypi.org/simple/pub-worm/ 2025-06-11T15:12:44,624 Found index url https://pypi.org/simple/ 2025-06-11T15:12:44,779 Fetched page https://pypi.org/simple/pub-worm/ as application/vnd.pypi.simple.v1+json 2025-06-11T15:12:44,783 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 2025-06-11T15:12:44,784 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 2025-06-11T15:12:44,785 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 2025-06-11T15:12:44,786 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 2025-06-11T15:12:44,786 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 2025-06-11T15:12:44,787 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 2025-06-11T15:12:44,788 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 2025-06-11T15:12:44,789 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 2025-06-11T15:12:44,790 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 2025-06-11T15:12:44,790 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 2025-06-11T15:12:44,791 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 2025-06-11T15:12:44,792 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 2025-06-11T15:12:44,793 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 2025-06-11T15:12:44,793 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 2025-06-11T15:12:44,794 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 2025-06-11T15:12:44,795 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 2025-06-11T15:12:44,796 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 2025-06-11T15:12:44,797 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 2025-06-11T15:12:44,797 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 2025-06-11T15:12:44,798 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 2025-06-11T15:12:44,799 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 2025-06-11T15:12:44,799 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 2025-06-11T15:12:44,800 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 2025-06-11T15:12:44,801 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 2025-06-11T15:12:44,801 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 2025-06-11T15:12:44,802 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 2025-06-11T15:12:44,803 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 2025-06-11T15:12:44,804 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 2025-06-11T15:12:44,804 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 2025-06-11T15:12:44,805 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 2025-06-11T15:12:44,806 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 2025-06-11T15:12:44,807 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 2025-06-11T15:12:44,807 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 2025-06-11T15:12:44,809 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 2025-06-11T15:12:44,809 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 2025-06-11T15:12:44,810 Fetching project page and analyzing links: https://www.piwheels.org/simple/pub-worm/ 2025-06-11T15:12:44,811 Getting page https://www.piwheels.org/simple/pub-worm/ 2025-06-11T15:12:44,812 Found index url https://www.piwheels.org/simple/ 2025-06-11T15:12:44,976 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/ 2025-06-11T15:12:45,636 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/ 2025-06-11T15:12:46,796 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/ 2025-06-11T15:12:48,953 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/ 2025-06-11T15:12:53,112 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/ 2025-06-11T15:12:53,283 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 2025-06-11T15:12:53,285 Skipping link: not a file: https://www.piwheels.org/simple/pub-worm/ 2025-06-11T15:12:53,286 Skipping link: not a file: https://pypi.org/simple/pub-worm/ 2025-06-11T15:12:53,307 Given no hashes to check 1 links for project 'pub-worm': discarding no candidates 2025-06-11T15:12:53,309 Collecting pub-worm==0.3.14 2025-06-11T15:12:53,312 Created temporary directory: /tmp/pip-unpack-aok4cl_x 2025-06-11T15:12:53,545 Downloading pub_worm-0.3.14.tar.gz (397 kB) 2025-06-11T15:12:53,792 Added pub-worm==0.3.14 from https://files.pythonhosted.org/packages/7f/88/9b6c038faacd7806ec013840d180c8428a718c9fd72ef87e600dfa8cff5c/pub_worm-0.3.14.tar.gz to build tracker '/tmp/pip-build-tracker-2njpu1a9' 2025-06-11T15:12:53,794 Running setup.py (path:/tmp/pip-wheel-ari_on2c/pub-worm_63036a664c864a23809498c2edc41535/setup.py) egg_info for package pub-worm 2025-06-11T15:12:53,795 Created temporary directory: /tmp/pip-pip-egg-info-ly9arx9j 2025-06-11T15:12:53,796 Preparing metadata (setup.py): started 2025-06-11T15:12:53,797 Running command python setup.py egg_info 2025-06-11T15:12:54,730 running egg_info 2025-06-11T15:12:54,758 creating /tmp/pip-pip-egg-info-ly9arx9j/pub_worm.egg-info 2025-06-11T15:12:54,759 writing /tmp/pip-pip-egg-info-ly9arx9j/pub_worm.egg-info/PKG-INFO 2025-06-11T15:12:54,763 writing dependency_links to /tmp/pip-pip-egg-info-ly9arx9j/pub_worm.egg-info/dependency_links.txt 2025-06-11T15:12:54,765 writing requirements to /tmp/pip-pip-egg-info-ly9arx9j/pub_worm.egg-info/requires.txt 2025-06-11T15:12:54,767 writing top-level names to /tmp/pip-pip-egg-info-ly9arx9j/pub_worm.egg-info/top_level.txt 2025-06-11T15:12:54,768 writing manifest file '/tmp/pip-pip-egg-info-ly9arx9j/pub_worm.egg-info/SOURCES.txt' 2025-06-11T15:12:54,870 reading manifest file '/tmp/pip-pip-egg-info-ly9arx9j/pub_worm.egg-info/SOURCES.txt' 2025-06-11T15:12:54,871 reading manifest template 'MANIFEST.in' 2025-06-11T15:12:54,892 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json' 2025-06-11T15:12:54,893 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json' 2025-06-11T15:12:54,893 warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json' 2025-06-11T15:12:54,910 writing manifest file '/tmp/pip-pip-egg-info-ly9arx9j/pub_worm.egg-info/SOURCES.txt' 2025-06-11T15:12:55,022 Preparing metadata (setup.py): finished with status 'done' 2025-06-11T15:12:55,026 Source in /tmp/pip-wheel-ari_on2c/pub-worm_63036a664c864a23809498c2edc41535 has version 0.3.14, which satisfies requirement pub-worm==0.3.14 from https://files.pythonhosted.org/packages/7f/88/9b6c038faacd7806ec013840d180c8428a718c9fd72ef87e600dfa8cff5c/pub_worm-0.3.14.tar.gz 2025-06-11T15:12:55,027 Removed pub-worm==0.3.14 from https://files.pythonhosted.org/packages/7f/88/9b6c038faacd7806ec013840d180c8428a718c9fd72ef87e600dfa8cff5c/pub_worm-0.3.14.tar.gz from build tracker '/tmp/pip-build-tracker-2njpu1a9' 2025-06-11T15:12:55,034 Created temporary directory: /tmp/pip-unpack-zkna5w8b 2025-06-11T15:12:55,035 Created temporary directory: /tmp/pip-unpack-0owp2q7d 2025-06-11T15:12:55,035 Building wheels for collected packages: pub-worm 2025-06-11T15:12:55,039 Created temporary directory: /tmp/pip-wheel-tkj0ktcb 2025-06-11T15:12:55,040 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 2025-06-11T15:12:55,042 Building wheel for pub-worm (setup.py): started 2025-06-11T15:12:55,043 Destination directory: /tmp/pip-wheel-tkj0ktcb 2025-06-11T15:12:55,043 Running command python setup.py bdist_wheel 2025-06-11T15:12:55,895 running bdist_wheel 2025-06-11T15:12:56,035 running build 2025-06-11T15:12:56,036 running build_py 2025-06-11T15:12:56,067 creating build/lib/tests 2025-06-11T15:12:56,069 copying tests/__init__.py -> build/lib/tests 2025-06-11T15:12:56,072 creating build/lib/pub_worm 2025-06-11T15:12:56,073 copying pub_worm/__init__.py -> build/lib/pub_worm 2025-06-11T15:12:56,075 creating build/lib/tests/impact_factor 2025-06-11T15:12:56,076 copying tests/impact_factor/__init__.py -> build/lib/tests/impact_factor 2025-06-11T15:12:56,078 copying tests/impact_factor/test_get_impact_factor.py -> build/lib/tests/impact_factor 2025-06-11T15:12:56,081 creating build/lib/tests/orcid 2025-06-11T15:12:56,082 copying tests/orcid/__init__.py -> build/lib/tests/orcid 2025-06-11T15:12:56,084 copying tests/orcid/test_orcid_api.py -> build/lib/tests/orcid 2025-06-11T15:12:56,086 creating build/lib/tests/ncbi 2025-06-11T15:12:56,087 copying tests/ncbi/__init__.py -> build/lib/tests/ncbi 2025-06-11T15:12:56,089 copying tests/ncbi/test_entreze_api.py -> build/lib/tests/ncbi 2025-06-11T15:12:56,092 creating build/lib/tests/wormbase 2025-06-11T15:12:56,093 copying tests/wormbase/__init__.py -> build/lib/tests/wormbase 2025-06-11T15:12:56,095 copying tests/wormbase/test_wormbase_api.py -> build/lib/tests/wormbase 2025-06-11T15:12:56,097 creating build/lib/pub_worm/impact_factor 2025-06-11T15:12:56,098 copying pub_worm/impact_factor/impact_factor_lookup.py -> build/lib/pub_worm/impact_factor 2025-06-11T15:12:56,100 copying pub_worm/impact_factor/__init__.py -> build/lib/pub_worm/impact_factor 2025-06-11T15:12:56,103 creating build/lib/pub_worm/ensembl 2025-06-11T15:12:56,104 copying pub_worm/ensembl/__init__.py -> build/lib/pub_worm/ensembl 2025-06-11T15:12:56,105 copying pub_worm/ensembl/ensembl_api.py -> build/lib/pub_worm/ensembl 2025-06-11T15:12:56,108 creating build/lib/pub_worm/biorxiv 2025-06-11T15:12:56,109 copying pub_worm/biorxiv/__init__.py -> build/lib/pub_worm/biorxiv 2025-06-11T15:12:56,110 copying pub_worm/biorxiv/biorxiv_api.py -> build/lib/pub_worm/biorxiv 2025-06-11T15:12:56,113 creating build/lib/pub_worm/orcid 2025-06-11T15:12:56,114 copying pub_worm/orcid/__init__.py -> build/lib/pub_worm/orcid 2025-06-11T15:12:56,115 copying pub_worm/orcid/orcid_api.py -> build/lib/pub_worm/orcid 2025-06-11T15:12:56,118 creating build/lib/pub_worm/ncbi 2025-06-11T15:12:56,119 copying pub_worm/ncbi/__init__.py -> build/lib/pub_worm/ncbi 2025-06-11T15:12:56,121 copying pub_worm/ncbi/entreze_api.py -> build/lib/pub_worm/ncbi 2025-06-11T15:12:56,125 creating build/lib/pub_worm/wormbase 2025-06-11T15:12:56,126 copying pub_worm/wormbase/wormbase_api.py -> build/lib/pub_worm/wormbase 2025-06-11T15:12:56,128 copying pub_worm/wormbase/__init__.py -> build/lib/pub_worm/wormbase 2025-06-11T15:12:56,130 copying pub_worm/wormbase/to_csv_helpers.py -> build/lib/pub_worm/wormbase 2025-06-11T15:12:56,132 copying pub_worm/wormbase/wormbase_util.py -> build/lib/pub_worm/wormbase 2025-06-11T15:12:56,135 running egg_info 2025-06-11T15:12:56,163 writing pub_worm.egg-info/PKG-INFO 2025-06-11T15:12:56,166 writing dependency_links to pub_worm.egg-info/dependency_links.txt 2025-06-11T15:12:56,169 writing requirements to pub_worm.egg-info/requires.txt 2025-06-11T15:12:56,170 writing top-level names to pub_worm.egg-info/top_level.txt 2025-06-11T15:12:56,210 reading manifest file 'pub_worm.egg-info/SOURCES.txt' 2025-06-11T15:12:56,242 reading manifest template 'MANIFEST.in' 2025-06-11T15:12:56,244 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json' 2025-06-11T15:12:56,245 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json' 2025-06-11T15:12:56,245 warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json' 2025-06-11T15:12:56,249 writing manifest file 'pub_worm.egg-info/SOURCES.txt' 2025-06-11T15:12:56,251 /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. 2025-06-11T15:12:56,252 !! 2025-06-11T15:12:56,253 ******************************************************************************** 2025-06-11T15:12:56,254 ############################ 2025-06-11T15:12:56,255 # Package would be ignored # 2025-06-11T15:12:56,255 ############################ 2025-06-11T15:12:56,256 Python recognizes 'pub_worm.impact_factor.data' as an importable package[^1], 2025-06-11T15:12:56,256 but it is absent from setuptools' `packages` configuration. 2025-06-11T15:12:56,257 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T15:12:56,258 package, please make sure that 'pub_worm.impact_factor.data' is explicitly added 2025-06-11T15:12:56,259 to the `packages` configuration field. 2025-06-11T15:12:56,260 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T15:12:56,260 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T15:12:56,261 instead of `find_packages(...)`/`find:`). 2025-06-11T15:12:56,262 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T15:12:56,264 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T15:12:56,265 If you don't want 'pub_worm.impact_factor.data' to be distributed and are 2025-06-11T15:12:56,265 already explicitly excluding 'pub_worm.impact_factor.data' via 2025-06-11T15:12:56,266 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T15:12:56,266 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T15:12:56,267 combination with a more fine grained `package-data` configuration. 2025-06-11T15:12:56,268 You can read more about "package data files" on setuptools documentation page: 2025-06-11T15:12:56,268 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T15:12:56,270 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T15:12:56,270 even if it does not contain any `.py` files. 2025-06-11T15:12:56,271 On the other hand, currently there is no concept of package data 2025-06-11T15:12:56,271 directory, all directories are treated like packages. 2025-06-11T15:12:56,272 ******************************************************************************** 2025-06-11T15:12:56,273 !! 2025-06-11T15:12:56,273 check.warn(importable) 2025-06-11T15:12:56,274 /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. 2025-06-11T15:12:56,274 !! 2025-06-11T15:12:56,275 ******************************************************************************** 2025-06-11T15:12:56,276 ############################ 2025-06-11T15:12:56,277 # Package would be ignored # 2025-06-11T15:12:56,277 ############################ 2025-06-11T15:12:56,278 Python recognizes 'pub_worm.wormbase.data' as an importable package[^1], 2025-06-11T15:12:56,278 but it is absent from setuptools' `packages` configuration. 2025-06-11T15:12:56,280 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T15:12:56,280 package, please make sure that 'pub_worm.wormbase.data' is explicitly added 2025-06-11T15:12:56,281 to the `packages` configuration field. 2025-06-11T15:12:56,282 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T15:12:56,283 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T15:12:56,284 instead of `find_packages(...)`/`find:`). 2025-06-11T15:12:56,285 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T15:12:56,286 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T15:12:56,287 If you don't want 'pub_worm.wormbase.data' to be distributed and are 2025-06-11T15:12:56,288 already explicitly excluding 'pub_worm.wormbase.data' via 2025-06-11T15:12:56,289 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T15:12:56,290 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T15:12:56,290 combination with a more fine grained `package-data` configuration. 2025-06-11T15:12:56,292 You can read more about "package data files" on setuptools documentation page: 2025-06-11T15:12:56,293 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T15:12:56,295 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T15:12:56,295 even if it does not contain any `.py` files. 2025-06-11T15:12:56,296 On the other hand, currently there is no concept of package data 2025-06-11T15:12:56,297 directory, all directories are treated like packages. 2025-06-11T15:12:56,297 ******************************************************************************** 2025-06-11T15:12:56,311 !! 2025-06-11T15:12:56,314 check.warn(importable) 2025-06-11T15:12:56,315 creating build/lib/pub_worm/impact_factor/data 2025-06-11T15:12:56,315 copying pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/lib/pub_worm/impact_factor/data 2025-06-11T15:12:56,316 creating build/lib/pub_worm/wormbase/data 2025-06-11T15:12:56,316 copying pub_worm/wormbase/data/wormbase_field_gene.json -> build/lib/pub_worm/wormbase/data 2025-06-11T15:12:56,319 copying pub_worm/wormbase/data/wormbase_field_paper.json -> build/lib/pub_worm/wormbase/data 2025-06-11T15:12:56,321 copying pub_worm/wormbase/data/wormbase_widget_gene.json -> build/lib/pub_worm/wormbase/data 2025-06-11T15:12:56,354 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-11T15:12:56,354 !! 2025-06-11T15:12:56,355 ******************************************************************************** 2025-06-11T15:12:56,356 Please avoid running ``setup.py`` directly. 2025-06-11T15:12:56,356 Instead, use pypa/build, pypa/installer or other 2025-06-11T15:12:56,357 standards-based tools. 2025-06-11T15:12:56,358 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-11T15:12:56,358 or your builds will no longer be supported. 2025-06-11T15:12:56,359 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-11T15:12:56,360 ******************************************************************************** 2025-06-11T15:12:56,361 !! 2025-06-11T15:12:56,362 self.initialize_options() 2025-06-11T15:12:56,382 installing to build/bdist.linux-armv7l/wheel 2025-06-11T15:12:56,382 running install 2025-06-11T15:12:56,406 running install_lib 2025-06-11T15:12:56,434 creating build/bdist.linux-armv7l/wheel 2025-06-11T15:12:56,436 creating build/bdist.linux-armv7l/wheel/tests 2025-06-11T15:12:56,438 creating build/bdist.linux-armv7l/wheel/tests/impact_factor 2025-06-11T15:12:56,439 copying build/lib/tests/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor 2025-06-11T15:12:56,441 copying build/lib/tests/impact_factor/test_get_impact_factor.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor 2025-06-11T15:12:56,443 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2025-06-11T15:12:56,445 creating build/bdist.linux-armv7l/wheel/tests/orcid 2025-06-11T15:12:56,446 copying build/lib/tests/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/orcid 2025-06-11T15:12:56,448 copying build/lib/tests/orcid/test_orcid_api.py -> build/bdist.linux-armv7l/wheel/./tests/orcid 2025-06-11T15:12:56,450 creating build/bdist.linux-armv7l/wheel/tests/ncbi 2025-06-11T15:12:56,451 copying build/lib/tests/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi 2025-06-11T15:12:56,453 copying build/lib/tests/ncbi/test_entreze_api.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi 2025-06-11T15:12:56,455 creating build/bdist.linux-armv7l/wheel/tests/wormbase 2025-06-11T15:12:56,456 copying build/lib/tests/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase 2025-06-11T15:12:56,458 copying build/lib/tests/wormbase/test_wormbase_api.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase 2025-06-11T15:12:56,460 creating build/bdist.linux-armv7l/wheel/pub_worm 2025-06-11T15:12:56,462 creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor 2025-06-11T15:12:56,463 copying build/lib/pub_worm/impact_factor/impact_factor_lookup.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor 2025-06-11T15:12:56,465 copying build/lib/pub_worm/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor 2025-06-11T15:12:56,467 creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor/data 2025-06-11T15:12:56,468 copying build/lib/pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor/data 2025-06-11T15:12:56,494 copying build/lib/pub_worm/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm 2025-06-11T15:12:56,496 creating build/bdist.linux-armv7l/wheel/pub_worm/ensembl 2025-06-11T15:12:56,497 copying build/lib/pub_worm/ensembl/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl 2025-06-11T15:12:56,498 copying build/lib/pub_worm/ensembl/ensembl_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl 2025-06-11T15:12:56,501 creating build/bdist.linux-armv7l/wheel/pub_worm/biorxiv 2025-06-11T15:12:56,502 copying build/lib/pub_worm/biorxiv/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv 2025-06-11T15:12:56,503 copying build/lib/pub_worm/biorxiv/biorxiv_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv 2025-06-11T15:12:56,506 creating build/bdist.linux-armv7l/wheel/pub_worm/orcid 2025-06-11T15:12:56,506 copying build/lib/pub_worm/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid 2025-06-11T15:12:56,508 copying build/lib/pub_worm/orcid/orcid_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid 2025-06-11T15:12:56,511 creating build/bdist.linux-armv7l/wheel/pub_worm/ncbi 2025-06-11T15:12:56,512 copying build/lib/pub_worm/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi 2025-06-11T15:12:56,514 copying build/lib/pub_worm/ncbi/entreze_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi 2025-06-11T15:12:56,517 creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase 2025-06-11T15:12:56,518 copying build/lib/pub_worm/wormbase/wormbase_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-11T15:12:56,520 copying build/lib/pub_worm/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-11T15:12:56,522 copying build/lib/pub_worm/wormbase/to_csv_helpers.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-11T15:12:56,524 creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase/data 2025-06-11T15:12:56,525 copying build/lib/pub_worm/wormbase/data/wormbase_field_paper.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data 2025-06-11T15:12:56,527 copying build/lib/pub_worm/wormbase/data/wormbase_widget_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data 2025-06-11T15:12:56,529 copying build/lib/pub_worm/wormbase/data/wormbase_field_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data 2025-06-11T15:12:56,531 copying build/lib/pub_worm/wormbase/wormbase_util.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-11T15:12:56,533 running install_egg_info 2025-06-11T15:12:56,568 Copying pub_worm.egg-info to build/bdist.linux-armv7l/wheel/./pub_worm-0.3.14-py3.11.egg-info 2025-06-11T15:12:56,580 running install_scripts 2025-06-11T15:12:56,589 creating build/bdist.linux-armv7l/wheel/pub_worm-0.3.14.dist-info/WHEEL 2025-06-11T15:12:56,592 creating '/tmp/pip-wheel-tkj0ktcb/pub_worm-0.3.14-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-11T15:12:56,594 adding 'pub_worm/__init__.py' 2025-06-11T15:12:56,596 adding 'pub_worm/biorxiv/__init__.py' 2025-06-11T15:12:56,598 adding 'pub_worm/biorxiv/biorxiv_api.py' 2025-06-11T15:12:56,599 adding 'pub_worm/ensembl/__init__.py' 2025-06-11T15:12:56,601 adding 'pub_worm/ensembl/ensembl_api.py' 2025-06-11T15:12:56,603 adding 'pub_worm/impact_factor/__init__.py' 2025-06-11T15:12:56,604 adding 'pub_worm/impact_factor/impact_factor_lookup.py' 2025-06-11T15:12:56,773 adding 'pub_worm/impact_factor/data/2022_JCR_IF.csv' 2025-06-11T15:12:56,783 adding 'pub_worm/ncbi/__init__.py' 2025-06-11T15:12:56,786 adding 'pub_worm/ncbi/entreze_api.py' 2025-06-11T15:12:56,788 adding 'pub_worm/orcid/__init__.py' 2025-06-11T15:12:56,789 adding 'pub_worm/orcid/orcid_api.py' 2025-06-11T15:12:56,791 adding 'pub_worm/wormbase/__init__.py' 2025-06-11T15:12:56,792 adding 'pub_worm/wormbase/to_csv_helpers.py' 2025-06-11T15:12:56,794 adding 'pub_worm/wormbase/wormbase_api.py' 2025-06-11T15:12:56,796 adding 'pub_worm/wormbase/wormbase_util.py' 2025-06-11T15:12:56,798 adding 'pub_worm/wormbase/data/wormbase_field_gene.json' 2025-06-11T15:12:56,799 adding 'pub_worm/wormbase/data/wormbase_field_paper.json' 2025-06-11T15:12:56,800 adding 'pub_worm/wormbase/data/wormbase_widget_gene.json' 2025-06-11T15:12:56,802 adding 'tests/__init__.py' 2025-06-11T15:12:56,804 adding 'tests/impact_factor/__init__.py' 2025-06-11T15:12:56,805 adding 'tests/impact_factor/test_get_impact_factor.py' 2025-06-11T15:12:56,806 adding 'tests/ncbi/__init__.py' 2025-06-11T15:12:56,808 adding 'tests/ncbi/test_entreze_api.py' 2025-06-11T15:12:56,809 adding 'tests/orcid/__init__.py' 2025-06-11T15:12:56,810 adding 'tests/orcid/test_orcid_api.py' 2025-06-11T15:12:56,812 adding 'tests/wormbase/__init__.py' 2025-06-11T15:12:56,813 adding 'tests/wormbase/test_wormbase_api.py' 2025-06-11T15:12:56,815 adding 'pub_worm-0.3.14.dist-info/METADATA' 2025-06-11T15:12:56,815 adding 'pub_worm-0.3.14.dist-info/WHEEL' 2025-06-11T15:12:56,816 adding 'pub_worm-0.3.14.dist-info/top_level.txt' 2025-06-11T15:12:56,817 adding 'pub_worm-0.3.14.dist-info/RECORD' 2025-06-11T15:12:56,826 removing build/bdist.linux-armv7l/wheel 2025-06-11T15:12:56,960 Building wheel for pub-worm (setup.py): finished with status 'done' 2025-06-11T15:12:56,966 Created wheel for pub-worm: filename=pub_worm-0.3.14-py3-none-any.whl size=403780 sha256=32fbbc0d8eb33a4b2dc90328eb09204433f41db0eb98e6d73aa73dec74cd89c8 2025-06-11T15:12:56,967 Stored in directory: /tmp/pip-ephem-wheel-cache-q1ocbeda/wheels/52/89/c3/cc8d3dcb073ee0416cdd0d43e22e9f0853bae62f5305b9bf21 2025-06-11T15:12:56,979 Successfully built pub-worm 2025-06-11T15:12:56,998 Removed build tracker: '/tmp/pip-build-tracker-2njpu1a9'