2025-06-01T02:38:41,035 Created temporary directory: /tmp/pip-build-tracker-b4_lanf5
2025-06-01T02:38:41,038 Initialized build tracking at /tmp/pip-build-tracker-b4_lanf5
2025-06-01T02:38:41,039 Created build tracker: /tmp/pip-build-tracker-b4_lanf5
2025-06-01T02:38:41,041 Entered build tracker: /tmp/pip-build-tracker-b4_lanf5
2025-06-01T02:38:41,043 Created temporary directory: /tmp/pip-wheel-5uhs1pjw
2025-06-01T02:38:41,059 Created temporary directory: /tmp/pip-ephem-wheel-cache-ga47end2
2025-06-01T02:38:41,243 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-01T02:38:41,259 2 location(s) to search for versions of pub-worm:
2025-06-01T02:38:41,259 * https://pypi.org/simple/pub-worm/
2025-06-01T02:38:41,259 * https://www.piwheels.org/simple/pub-worm/
2025-06-01T02:38:41,260 Fetching project page and analyzing links: https://pypi.org/simple/pub-worm/
2025-06-01T02:38:41,277 Getting page https://pypi.org/simple/pub-worm/
2025-06-01T02:38:41,281 Found index url https://pypi.org/simple/
2025-06-01T02:38:41,753 Fetched page https://pypi.org/simple/pub-worm/ as application/vnd.pypi.simple.v1+json
2025-06-01T02:38:41,760   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
2025-06-01T02:38:41,769   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
2025-06-01T02:38:41,770   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
2025-06-01T02:38:41,772   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
2025-06-01T02:38:41,774   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
2025-06-01T02:38:41,775   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
2025-06-01T02:38:41,776   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
2025-06-01T02:38:41,778   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
2025-06-01T02:38:41,780   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
2025-06-01T02:38:41,783   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
2025-06-01T02:38:41,784   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
2025-06-01T02:38:41,785   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
2025-06-01T02:38:41,789   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
2025-06-01T02:38:41,792   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
2025-06-01T02:38:41,807   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
2025-06-01T02:38:41,809   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
2025-06-01T02:38:41,810   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
2025-06-01T02:38:41,811   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
2025-06-01T02:38:41,812   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
2025-06-01T02:38:41,813   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
2025-06-01T02:38:41,814   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
2025-06-01T02:38:41,815   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
2025-06-01T02:38:41,817   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
2025-06-01T02:38:41,818   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
2025-06-01T02:38:41,820   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
2025-06-01T02:38:41,821   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
2025-06-01T02:38:41,822   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
2025-06-01T02:38:41,824   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
2025-06-01T02:38:41,826   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
2025-06-01T02:38:41,827   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
2025-06-01T02:38:41,829   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
2025-06-01T02:38:41,833   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
2025-06-01T02:38:41,836   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
2025-06-01T02:38:41,837   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
2025-06-01T02:38:41,839   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
2025-06-01T02:38:41,840 Fetching project page and analyzing links: https://www.piwheels.org/simple/pub-worm/
2025-06-01T02:38:41,841 Getting page https://www.piwheels.org/simple/pub-worm/
2025-06-01T02:38:41,844 Found index url https://www.piwheels.org/simple/
2025-06-01T02:38:42,124 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/
2025-06-01T02:38:42,877 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/
2025-06-01T02:38:44,159 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/
2025-06-01T02:38:46,640 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/
2025-06-01T02:38:50,980 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/
2025-06-01T02:38:51,348 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
2025-06-01T02:38:51,351 Skipping link: not a file: https://www.piwheels.org/simple/pub-worm/
2025-06-01T02:38:51,352 Skipping link: not a file: https://pypi.org/simple/pub-worm/
2025-06-01T02:38:51,405 Given no hashes to check 1 links for project 'pub-worm': discarding no candidates
2025-06-01T02:38:51,420 Collecting pub-worm==0.3.8
2025-06-01T02:38:51,426   Created temporary directory: /tmp/pip-unpack-ew8ndk5_
2025-06-01T02:38:51,863   Downloading pub_worm-0.3.8.tar.gz (396 kB)
2025-06-01T02:38:52,411   Added pub-worm==0.3.8 from https://files.pythonhosted.org/packages/1a/78/e345c49eee5b968f3766c1bd34690a53fdad25695df6d793ebb3879bb715/pub_worm-0.3.8.tar.gz to build tracker '/tmp/pip-build-tracker-b4_lanf5'
2025-06-01T02:38:52,414   Running setup.py (path:/tmp/pip-wheel-5uhs1pjw/pub-worm_fd06957630224e5ba1999c4182ed0ac1/setup.py) egg_info for package pub-worm
2025-06-01T02:38:52,416   Created temporary directory: /tmp/pip-pip-egg-info-vdvajyb7
2025-06-01T02:38:52,417   Preparing metadata (setup.py): started
2025-06-01T02:38:52,420   Running command python setup.py egg_info
2025-06-01T02:38:54,951   running egg_info
2025-06-01T02:38:55,072   creating /tmp/pip-pip-egg-info-vdvajyb7/pub_worm.egg-info
2025-06-01T02:38:55,075   writing /tmp/pip-pip-egg-info-vdvajyb7/pub_worm.egg-info/PKG-INFO
2025-06-01T02:38:55,084   writing dependency_links to /tmp/pip-pip-egg-info-vdvajyb7/pub_worm.egg-info/dependency_links.txt
2025-06-01T02:38:55,089   writing requirements to /tmp/pip-pip-egg-info-vdvajyb7/pub_worm.egg-info/requires.txt
2025-06-01T02:38:55,091   writing top-level names to /tmp/pip-pip-egg-info-vdvajyb7/pub_worm.egg-info/top_level.txt
2025-06-01T02:38:55,095   writing manifest file '/tmp/pip-pip-egg-info-vdvajyb7/pub_worm.egg-info/SOURCES.txt'
2025-06-01T02:38:55,545   reading manifest file '/tmp/pip-pip-egg-info-vdvajyb7/pub_worm.egg-info/SOURCES.txt'
2025-06-01T02:38:55,549   reading manifest template 'MANIFEST.in'
2025-06-01T02:38:55,557   warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json'
2025-06-01T02:38:55,558   warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json'
2025-06-01T02:38:55,559   warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json'
2025-06-01T02:38:55,565   writing manifest file '/tmp/pip-pip-egg-info-vdvajyb7/pub_worm.egg-info/SOURCES.txt'
2025-06-01T02:38:55,820   Preparing metadata (setup.py): finished with status 'done'
2025-06-01T02:38:55,827   Source in /tmp/pip-wheel-5uhs1pjw/pub-worm_fd06957630224e5ba1999c4182ed0ac1 has version 0.3.8, which satisfies requirement pub-worm==0.3.8 from https://files.pythonhosted.org/packages/1a/78/e345c49eee5b968f3766c1bd34690a53fdad25695df6d793ebb3879bb715/pub_worm-0.3.8.tar.gz
2025-06-01T02:38:55,829   Removed pub-worm==0.3.8 from https://files.pythonhosted.org/packages/1a/78/e345c49eee5b968f3766c1bd34690a53fdad25695df6d793ebb3879bb715/pub_worm-0.3.8.tar.gz from build tracker '/tmp/pip-build-tracker-b4_lanf5'
2025-06-01T02:38:55,858 Created temporary directory: /tmp/pip-unpack-hgzuk_9f
2025-06-01T02:38:55,861 Created temporary directory: /tmp/pip-unpack-lluvazqn
2025-06-01T02:38:55,862 Building wheels for collected packages: pub-worm
2025-06-01T02:38:55,872   Created temporary directory: /tmp/pip-wheel-feweymj_
2025-06-01T02:38:55,873   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
2025-06-01T02:38:55,876   Building wheel for pub-worm (setup.py): started
2025-06-01T02:38:55,887   Destination directory: /tmp/pip-wheel-feweymj_
2025-06-01T02:38:55,889   Running command python setup.py bdist_wheel
2025-06-01T02:38:57,944   running bdist_wheel
2025-06-01T02:38:58,444   running build
2025-06-01T02:38:58,446   running build_py
2025-06-01T02:38:58,619   creating build/lib/pub_worm
2025-06-01T02:38:58,624   copying pub_worm/__init__.py -> build/lib/pub_worm
2025-06-01T02:38:58,630   creating build/lib/tests
2025-06-01T02:38:58,633   copying tests/__init__.py -> build/lib/tests
2025-06-01T02:38:58,640   creating build/lib/pub_worm/impact_factor
2025-06-01T02:38:58,643   copying pub_worm/impact_factor/__init__.py -> build/lib/pub_worm/impact_factor
2025-06-01T02:38:58,649   copying pub_worm/impact_factor/impact_factor_lookup.py -> build/lib/pub_worm/impact_factor
2025-06-01T02:38:58,655   creating build/lib/pub_worm/ensembl
2025-06-01T02:38:58,659   copying pub_worm/ensembl/__init__.py -> build/lib/pub_worm/ensembl
2025-06-01T02:38:58,664   copying pub_worm/ensembl/ensembl_api.py -> build/lib/pub_worm/ensembl
2025-06-01T02:38:58,670   creating build/lib/pub_worm/biorxiv
2025-06-01T02:38:58,674   copying pub_worm/biorxiv/__init__.py -> build/lib/pub_worm/biorxiv
2025-06-01T02:38:58,679   copying pub_worm/biorxiv/biorxiv_api.py -> build/lib/pub_worm/biorxiv
2025-06-01T02:38:58,684   creating build/lib/pub_worm/ncbi
2025-06-01T02:38:58,686   copying pub_worm/ncbi/entreze_api.py -> build/lib/pub_worm/ncbi
2025-06-01T02:38:58,693   copying pub_worm/ncbi/__init__.py -> build/lib/pub_worm/ncbi
2025-06-01T02:38:58,699   creating build/lib/pub_worm/orcid
2025-06-01T02:38:58,702   copying pub_worm/orcid/orcid_api.py -> build/lib/pub_worm/orcid
2025-06-01T02:38:58,707   copying pub_worm/orcid/__init__.py -> build/lib/pub_worm/orcid
2025-06-01T02:38:58,712   creating build/lib/pub_worm/wormbase
2025-06-01T02:38:58,715   copying pub_worm/wormbase/wormbase_util.py -> build/lib/pub_worm/wormbase
2025-06-01T02:38:58,720   copying pub_worm/wormbase/__init__.py -> build/lib/pub_worm/wormbase
2025-06-01T02:38:58,726   copying pub_worm/wormbase/to_csv_helpers.py -> build/lib/pub_worm/wormbase
2025-06-01T02:38:58,731   copying pub_worm/wormbase/wormbase_api.py -> build/lib/pub_worm/wormbase
2025-06-01T02:38:58,738   creating build/lib/tests/impact_factor
2025-06-01T02:38:58,742   copying tests/impact_factor/__init__.py -> build/lib/tests/impact_factor
2025-06-01T02:38:58,747   copying tests/impact_factor/test_get_impact_factor.py -> build/lib/tests/impact_factor
2025-06-01T02:38:58,753   creating build/lib/tests/ncbi
2025-06-01T02:38:58,755   copying tests/ncbi/test_entreze_api.py -> build/lib/tests/ncbi
2025-06-01T02:38:58,760   copying tests/ncbi/__init__.py -> build/lib/tests/ncbi
2025-06-01T02:38:58,765   creating build/lib/tests/orcid
2025-06-01T02:38:58,767   copying tests/orcid/__init__.py -> build/lib/tests/orcid
2025-06-01T02:38:58,772   copying tests/orcid/test_orcid_api.py -> build/lib/tests/orcid
2025-06-01T02:38:58,778   creating build/lib/tests/wormbase
2025-06-01T02:38:58,780   copying tests/wormbase/__init__.py -> build/lib/tests/wormbase
2025-06-01T02:38:58,784   copying tests/wormbase/test_wormbase_api.py -> build/lib/tests/wormbase
2025-06-01T02:38:58,789   running egg_info
2025-06-01T02:38:58,892   writing pub_worm.egg-info/PKG-INFO
2025-06-01T02:38:58,900   writing dependency_links to pub_worm.egg-info/dependency_links.txt
2025-06-01T02:38:58,905   writing requirements to pub_worm.egg-info/requires.txt
2025-06-01T02:38:58,920   writing top-level names to pub_worm.egg-info/top_level.txt
2025-06-01T02:38:59,144   reading manifest file 'pub_worm.egg-info/SOURCES.txt'
2025-06-01T02:38:59,168   reading manifest template 'MANIFEST.in'
2025-06-01T02:38:59,171   warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json'
2025-06-01T02:38:59,172   warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json'
2025-06-01T02:38:59,173   warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json'
2025-06-01T02:38:59,178   writing manifest file 'pub_worm.egg-info/SOURCES.txt'
2025-06-01T02:38:59,200   /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.
2025-06-01T02:38:59,201   !!

2025-06-01T02:38:59,203           ********************************************************************************
2025-06-01T02:38:59,204           ############################
2025-06-01T02:38:59,206           # Package would be ignored #
2025-06-01T02:38:59,207           ############################
2025-06-01T02:38:59,208           Python recognizes 'pub_worm.impact_factor.data' as an importable package[^1],
2025-06-01T02:38:59,209           but it is absent from setuptools' `packages` configuration.

2025-06-01T02:38:59,212           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-01T02:38:59,213           package, please make sure that 'pub_worm.impact_factor.data' is explicitly added
2025-06-01T02:38:59,214           to the `packages` configuration field.

2025-06-01T02:38:59,216           Alternatively, you can also rely on setuptools' discovery methods
2025-06-01T02:38:59,217           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-01T02:38:59,218           instead of `find_packages(...)`/`find:`).

2025-06-01T02:38:59,220           You can read more about "package discovery" on setuptools documentation page:

2025-06-01T02:38:59,222           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-01T02:38:59,224           If you don't want 'pub_worm.impact_factor.data' to be distributed and are
2025-06-01T02:38:59,225           already explicitly excluding 'pub_worm.impact_factor.data' via
2025-06-01T02:38:59,226           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-01T02:38:59,226           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-01T02:38:59,227           combination with a more fine grained `package-data` configuration.

2025-06-01T02:38:59,244           You can read more about "package data files" on setuptools documentation page:

2025-06-01T02:38:59,247           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-01T02:38:59,250           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-01T02:38:59,251                 even if it does not contain any `.py` files.
2025-06-01T02:38:59,252                 On the other hand, currently there is no concept of package data
2025-06-01T02:38:59,252                 directory, all directories are treated like packages.
2025-06-01T02:38:59,253           ********************************************************************************

2025-06-01T02:38:59,255   !!
2025-06-01T02:38:59,255     check.warn(importable)
2025-06-01T02:38:59,256   /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.
2025-06-01T02:38:59,257   !!

2025-06-01T02:38:59,259           ********************************************************************************
2025-06-01T02:38:59,260           ############################
2025-06-01T02:38:59,261           # Package would be ignored #
2025-06-01T02:38:59,262           ############################
2025-06-01T02:38:59,263           Python recognizes 'pub_worm.wormbase.data' as an importable package[^1],
2025-06-01T02:38:59,264           but it is absent from setuptools' `packages` configuration.

2025-06-01T02:38:59,266           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-01T02:38:59,267           package, please make sure that 'pub_worm.wormbase.data' is explicitly added
2025-06-01T02:38:59,268           to the `packages` configuration field.

2025-06-01T02:38:59,270           Alternatively, you can also rely on setuptools' discovery methods
2025-06-01T02:38:59,272           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-01T02:38:59,273           instead of `find_packages(...)`/`find:`).

2025-06-01T02:38:59,275           You can read more about "package discovery" on setuptools documentation page:

2025-06-01T02:38:59,277           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-01T02:38:59,279           If you don't want 'pub_worm.wormbase.data' to be distributed and are
2025-06-01T02:38:59,280           already explicitly excluding 'pub_worm.wormbase.data' via
2025-06-01T02:38:59,282           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-01T02:38:59,283           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-01T02:38:59,284           combination with a more fine grained `package-data` configuration.

2025-06-01T02:38:59,293           You can read more about "package data files" on setuptools documentation page:

2025-06-01T02:38:59,294           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-01T02:38:59,298           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-01T02:38:59,299                 even if it does not contain any `.py` files.
2025-06-01T02:38:59,300                 On the other hand, currently there is no concept of package data
2025-06-01T02:38:59,301                 directory, all directories are treated like packages.
2025-06-01T02:38:59,303           ********************************************************************************

2025-06-01T02:38:59,305   !!
2025-06-01T02:38:59,306     check.warn(importable)
2025-06-01T02:38:59,307   creating build/lib/pub_worm/impact_factor/data
2025-06-01T02:38:59,308   copying pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/lib/pub_worm/impact_factor/data
2025-06-01T02:38:59,309   creating build/lib/pub_worm/wormbase/data
2025-06-01T02:38:59,310   copying pub_worm/wormbase/data/wormbase_field_gene.json -> build/lib/pub_worm/wormbase/data
2025-06-01T02:38:59,311   copying pub_worm/wormbase/data/wormbase_field_paper.json -> build/lib/pub_worm/wormbase/data
2025-06-01T02:38:59,312   copying pub_worm/wormbase/data/wormbase_widget_gene.json -> build/lib/pub_worm/wormbase/data
2025-06-01T02:38:59,349   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-01T02:38:59,350   !!

2025-06-01T02:38:59,352           ********************************************************************************
2025-06-01T02:38:59,353           Please avoid running ``setup.py`` directly.
2025-06-01T02:38:59,354           Instead, use pypa/build, pypa/installer or other
2025-06-01T02:38:59,355           standards-based tools.

2025-06-01T02:38:59,357           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-01T02:38:59,357           or your builds will no longer be supported.

2025-06-01T02:38:59,360           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-01T02:38:59,361           ********************************************************************************

2025-06-01T02:38:59,363   !!
2025-06-01T02:38:59,364     self.initialize_options()
2025-06-01T02:38:59,426   installing to build/bdist.linux-armv7l/wheel
2025-06-01T02:38:59,428   running install
2025-06-01T02:38:59,458   running install_lib
2025-06-01T02:38:59,543   creating build/bdist.linux-armv7l/wheel
2025-06-01T02:38:59,547   creating build/bdist.linux-armv7l/wheel/pub_worm
2025-06-01T02:38:59,551   creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor
2025-06-01T02:38:59,555   creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor/data
2025-06-01T02:38:59,558   copying build/lib/pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor/data
2025-06-01T02:38:59,603   copying build/lib/pub_worm/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor
2025-06-01T02:38:59,608   copying build/lib/pub_worm/impact_factor/impact_factor_lookup.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor
2025-06-01T02:38:59,613   creating build/bdist.linux-armv7l/wheel/pub_worm/ensembl
2025-06-01T02:38:59,615   copying build/lib/pub_worm/ensembl/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl
2025-06-01T02:38:59,619   copying build/lib/pub_worm/ensembl/ensembl_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl
2025-06-01T02:38:59,623   creating build/bdist.linux-armv7l/wheel/pub_worm/biorxiv
2025-06-01T02:38:59,625   copying build/lib/pub_worm/biorxiv/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv
2025-06-01T02:38:59,628   copying build/lib/pub_worm/biorxiv/biorxiv_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv
2025-06-01T02:38:59,633   creating build/bdist.linux-armv7l/wheel/pub_worm/ncbi
2025-06-01T02:38:59,635   copying build/lib/pub_worm/ncbi/entreze_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi
2025-06-01T02:38:59,641   copying build/lib/pub_worm/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi
2025-06-01T02:38:59,645   copying build/lib/pub_worm/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm
2025-06-01T02:38:59,650   creating build/bdist.linux-armv7l/wheel/pub_worm/orcid
2025-06-01T02:38:59,652   copying build/lib/pub_worm/orcid/orcid_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid
2025-06-01T02:38:59,657   copying build/lib/pub_worm/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid
2025-06-01T02:38:59,662   creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase
2025-06-01T02:38:59,666   creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase/data
2025-06-01T02:38:59,669   copying build/lib/pub_worm/wormbase/data/wormbase_field_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data
2025-06-01T02:38:59,674   copying build/lib/pub_worm/wormbase/data/wormbase_widget_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data
2025-06-01T02:38:59,678   copying build/lib/pub_worm/wormbase/data/wormbase_field_paper.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data
2025-06-01T02:38:59,681   copying build/lib/pub_worm/wormbase/wormbase_util.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase
2025-06-01T02:38:59,685   copying build/lib/pub_worm/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase
2025-06-01T02:38:59,688   copying build/lib/pub_worm/wormbase/to_csv_helpers.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase
2025-06-01T02:38:59,692   copying build/lib/pub_worm/wormbase/wormbase_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase
2025-06-01T02:38:59,697   creating build/bdist.linux-armv7l/wheel/tests
2025-06-01T02:38:59,700   creating build/bdist.linux-armv7l/wheel/tests/impact_factor
2025-06-01T02:38:59,702   copying build/lib/tests/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor
2025-06-01T02:38:59,706   copying build/lib/tests/impact_factor/test_get_impact_factor.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor
2025-06-01T02:38:59,711   creating build/bdist.linux-armv7l/wheel/tests/ncbi
2025-06-01T02:38:59,713   copying build/lib/tests/ncbi/test_entreze_api.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi
2025-06-01T02:38:59,718   copying build/lib/tests/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi
2025-06-01T02:38:59,721   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests
2025-06-01T02:38:59,725   creating build/bdist.linux-armv7l/wheel/tests/orcid
2025-06-01T02:38:59,727   copying build/lib/tests/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/orcid
2025-06-01T02:38:59,730   copying build/lib/tests/orcid/test_orcid_api.py -> build/bdist.linux-armv7l/wheel/./tests/orcid
2025-06-01T02:38:59,735   creating build/bdist.linux-armv7l/wheel/tests/wormbase
2025-06-01T02:38:59,737   copying build/lib/tests/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase
2025-06-01T02:38:59,741   copying build/lib/tests/wormbase/test_wormbase_api.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase
2025-06-01T02:38:59,745   running install_egg_info
2025-06-01T02:38:59,842   Copying pub_worm.egg-info to build/bdist.linux-armv7l/wheel/./pub_worm-0.3.8-py3.11.egg-info
2025-06-01T02:38:59,897   running install_scripts
2025-06-01T02:38:59,928   creating build/bdist.linux-armv7l/wheel/pub_worm-0.3.8.dist-info/WHEEL
2025-06-01T02:38:59,934   creating '/tmp/pip-wheel-feweymj_/pub_worm-0.3.8-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-01T02:38:59,941   adding 'pub_worm/__init__.py'
2025-06-01T02:38:59,946   adding 'pub_worm/biorxiv/__init__.py'
2025-06-01T02:38:59,950   adding 'pub_worm/biorxiv/biorxiv_api.py'
2025-06-01T02:38:59,954   adding 'pub_worm/ensembl/__init__.py'
2025-06-01T02:38:59,959   adding 'pub_worm/ensembl/ensembl_api.py'
2025-06-01T02:38:59,964   adding 'pub_worm/impact_factor/__init__.py'
2025-06-01T02:38:59,968   adding 'pub_worm/impact_factor/impact_factor_lookup.py'
2025-06-01T02:39:00,213   adding 'pub_worm/impact_factor/data/2022_JCR_IF.csv'
2025-06-01T02:39:00,227   adding 'pub_worm/ncbi/__init__.py'
2025-06-01T02:39:00,232   adding 'pub_worm/ncbi/entreze_api.py'
2025-06-01T02:39:00,237   adding 'pub_worm/orcid/__init__.py'
2025-06-01T02:39:00,239   adding 'pub_worm/orcid/orcid_api.py'
2025-06-01T02:39:00,244   adding 'pub_worm/wormbase/__init__.py'
2025-06-01T02:39:00,246   adding 'pub_worm/wormbase/to_csv_helpers.py'
2025-06-01T02:39:00,250   adding 'pub_worm/wormbase/wormbase_api.py'
2025-06-01T02:39:00,255   adding 'pub_worm/wormbase/wormbase_util.py'
2025-06-01T02:39:00,260   adding 'pub_worm/wormbase/data/wormbase_field_gene.json'
2025-06-01T02:39:00,263   adding 'pub_worm/wormbase/data/wormbase_field_paper.json'
2025-06-01T02:39:00,265   adding 'pub_worm/wormbase/data/wormbase_widget_gene.json'
2025-06-01T02:39:00,279   adding 'tests/__init__.py'
2025-06-01T02:39:00,283   adding 'tests/impact_factor/__init__.py'
2025-06-01T02:39:00,285   adding 'tests/impact_factor/test_get_impact_factor.py'
2025-06-01T02:39:00,289   adding 'tests/ncbi/__init__.py'
2025-06-01T02:39:00,295   adding 'tests/ncbi/test_entreze_api.py'
2025-06-01T02:39:00,308   adding 'tests/orcid/__init__.py'
2025-06-01T02:39:00,312   adding 'tests/orcid/test_orcid_api.py'
2025-06-01T02:39:00,315   adding 'tests/wormbase/__init__.py'
2025-06-01T02:39:00,318   adding 'tests/wormbase/test_wormbase_api.py'
2025-06-01T02:39:00,328   adding 'pub_worm-0.3.8.dist-info/METADATA'
2025-06-01T02:39:00,331   adding 'pub_worm-0.3.8.dist-info/WHEEL'
2025-06-01T02:39:00,333   adding 'pub_worm-0.3.8.dist-info/top_level.txt'
2025-06-01T02:39:00,336   adding 'pub_worm-0.3.8.dist-info/RECORD'
2025-06-01T02:39:00,345   removing build/bdist.linux-armv7l/wheel
2025-06-01T02:39:00,673   Building wheel for pub-worm (setup.py): finished with status 'done'
2025-06-01T02:39:00,692   Created wheel for pub-worm: filename=pub_worm-0.3.8-py3-none-any.whl size=402730 sha256=b97b2db5010e83426236299252c1946bc54d84f7a1a1f97c4e333d8a21c04db2
2025-06-01T02:39:00,697   Stored in directory: /tmp/pip-ephem-wheel-cache-ga47end2/wheels/92/31/f5/4cd4eb54d0afb48b0401fefdd8056ff1bcc00381dac8428d12
2025-06-01T02:39:00,758 Successfully built pub-worm
2025-06-01T02:39:00,776 Removed build tracker: '/tmp/pip-build-tracker-b4_lanf5'