2025-06-10T22:41:15,115 Created temporary directory: /tmp/pip-build-tracker-_p8rs8yw
2025-06-10T22:41:15,116 Initialized build tracking at /tmp/pip-build-tracker-_p8rs8yw
2025-06-10T22:41:15,117 Created build tracker: /tmp/pip-build-tracker-_p8rs8yw
2025-06-10T22:41:15,117 Entered build tracker: /tmp/pip-build-tracker-_p8rs8yw
2025-06-10T22:41:15,118 Created temporary directory: /tmp/pip-wheel-o6wnnen_
2025-06-10T22:41:15,123 Created temporary directory: /tmp/pip-ephem-wheel-cache-m5s171td
2025-06-10T22:41:15,175 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-10T22:41:15,177 2 location(s) to search for versions of pub-worm:
2025-06-10T22:41:15,177 * https://pypi.org/simple/pub-worm/
2025-06-10T22:41:15,177 * https://www.piwheels.org/simple/pub-worm/
2025-06-10T22:41:15,178 Fetching project page and analyzing links: https://pypi.org/simple/pub-worm/
2025-06-10T22:41:15,179 Getting page https://pypi.org/simple/pub-worm/
2025-06-10T22:41:15,182 Found index url https://pypi.org/simple/
2025-06-10T22:41:15,335 Fetched page https://pypi.org/simple/pub-worm/ as application/vnd.pypi.simple.v1+json
2025-06-10T22:41:15,340   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
2025-06-10T22:41:15,341   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
2025-06-10T22:41:15,342   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
2025-06-10T22:41:15,342   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
2025-06-10T22:41:15,343   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
2025-06-10T22:41:15,344   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
2025-06-10T22:41:15,345   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
2025-06-10T22:41:15,346   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
2025-06-10T22:41:15,347   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
2025-06-10T22:41:15,347   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
2025-06-10T22:41:15,348   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
2025-06-10T22:41:15,349   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
2025-06-10T22:41:15,350   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
2025-06-10T22:41:15,351   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
2025-06-10T22:41:15,352   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
2025-06-10T22:41:15,353   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
2025-06-10T22:41:15,353   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
2025-06-10T22:41:15,354   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
2025-06-10T22:41:15,355   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
2025-06-10T22:41:15,355   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
2025-06-10T22:41:15,356   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
2025-06-10T22:41:15,357   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
2025-06-10T22:41:15,357   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
2025-06-10T22:41:15,358   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
2025-06-10T22:41:15,359   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
2025-06-10T22:41:15,360   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
2025-06-10T22:41:15,360   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
2025-06-10T22:41:15,361   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
2025-06-10T22:41:15,362   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
2025-06-10T22:41:15,363   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
2025-06-10T22:41:15,364   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
2025-06-10T22:41:15,364   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
2025-06-10T22:41:15,365   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
2025-06-10T22:41:15,366   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
2025-06-10T22:41:15,367   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
2025-06-10T22:41:15,368 Fetching project page and analyzing links: https://www.piwheels.org/simple/pub-worm/
2025-06-10T22:41:15,369 Getting page https://www.piwheels.org/simple/pub-worm/
2025-06-10T22:41:15,370 Found index url https://www.piwheels.org/simple/
2025-06-10T22:41:15,537 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/
2025-06-10T22:41:16,198 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/
2025-06-10T22:41:17,365 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/
2025-06-10T22:41:19,534 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/
2025-06-10T22:41:23,703 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/
2025-06-10T22:41:23,867 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
2025-06-10T22:41:23,869 Skipping link: not a file: https://www.piwheels.org/simple/pub-worm/
2025-06-10T22:41:23,870 Skipping link: not a file: https://pypi.org/simple/pub-worm/
2025-06-10T22:41:23,892 Given no hashes to check 1 links for project 'pub-worm': discarding no candidates
2025-06-10T22:41:23,894 Collecting pub-worm==0.3.12
2025-06-10T22:41:23,897   Created temporary directory: /tmp/pip-unpack-r9auaove
2025-06-10T22:41:24,534   Downloading pub_worm-0.3.12.tar.gz (397 kB)
2025-06-10T22:41:24,765   Added pub-worm==0.3.12 from https://files.pythonhosted.org/packages/ab/bb/4a6eb4bf7849059ff077a76690d91a44d4aa67fbfc2dca814c640da0a30f/pub_worm-0.3.12.tar.gz to build tracker '/tmp/pip-build-tracker-_p8rs8yw'
2025-06-10T22:41:24,768   Running setup.py (path:/tmp/pip-wheel-o6wnnen_/pub-worm_8396fc1c96f8418ca509526257f3f0f5/setup.py) egg_info for package pub-worm
2025-06-10T22:41:24,769   Created temporary directory: /tmp/pip-pip-egg-info-f_bc4u5p
2025-06-10T22:41:24,770   Preparing metadata (setup.py): started
2025-06-10T22:41:24,771   Running command python setup.py egg_info
2025-06-10T22:41:25,693   running egg_info
2025-06-10T22:41:25,721   creating /tmp/pip-pip-egg-info-f_bc4u5p/pub_worm.egg-info
2025-06-10T22:41:25,722   writing /tmp/pip-pip-egg-info-f_bc4u5p/pub_worm.egg-info/PKG-INFO
2025-06-10T22:41:25,727   writing dependency_links to /tmp/pip-pip-egg-info-f_bc4u5p/pub_worm.egg-info/dependency_links.txt
2025-06-10T22:41:25,729   writing requirements to /tmp/pip-pip-egg-info-f_bc4u5p/pub_worm.egg-info/requires.txt
2025-06-10T22:41:25,730   writing top-level names to /tmp/pip-pip-egg-info-f_bc4u5p/pub_worm.egg-info/top_level.txt
2025-06-10T22:41:25,731   writing manifest file '/tmp/pip-pip-egg-info-f_bc4u5p/pub_worm.egg-info/SOURCES.txt'
2025-06-10T22:41:25,832   reading manifest file '/tmp/pip-pip-egg-info-f_bc4u5p/pub_worm.egg-info/SOURCES.txt'
2025-06-10T22:41:25,834   reading manifest template 'MANIFEST.in'
2025-06-10T22:41:25,836   warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json'
2025-06-10T22:41:25,836   warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json'
2025-06-10T22:41:25,837   warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json'
2025-06-10T22:41:25,840   writing manifest file '/tmp/pip-pip-egg-info-f_bc4u5p/pub_worm.egg-info/SOURCES.txt'
2025-06-10T22:41:25,951   Preparing metadata (setup.py): finished with status 'done'
2025-06-10T22:41:25,955   Source in /tmp/pip-wheel-o6wnnen_/pub-worm_8396fc1c96f8418ca509526257f3f0f5 has version 0.3.12, which satisfies requirement pub-worm==0.3.12 from https://files.pythonhosted.org/packages/ab/bb/4a6eb4bf7849059ff077a76690d91a44d4aa67fbfc2dca814c640da0a30f/pub_worm-0.3.12.tar.gz
2025-06-10T22:41:25,956   Removed pub-worm==0.3.12 from https://files.pythonhosted.org/packages/ab/bb/4a6eb4bf7849059ff077a76690d91a44d4aa67fbfc2dca814c640da0a30f/pub_worm-0.3.12.tar.gz from build tracker '/tmp/pip-build-tracker-_p8rs8yw'
2025-06-10T22:41:25,963 Created temporary directory: /tmp/pip-unpack-wknud45z
2025-06-10T22:41:25,964 Created temporary directory: /tmp/pip-unpack-ae1dgq_9
2025-06-10T22:41:25,964 Building wheels for collected packages: pub-worm
2025-06-10T22:41:25,969   Created temporary directory: /tmp/pip-wheel-0sfk3l_c
2025-06-10T22:41:25,970   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
2025-06-10T22:41:25,971   Building wheel for pub-worm (setup.py): started
2025-06-10T22:41:25,972   Destination directory: /tmp/pip-wheel-0sfk3l_c
2025-06-10T22:41:25,973   Running command python setup.py bdist_wheel
2025-06-10T22:41:26,828   running bdist_wheel
2025-06-10T22:41:26,965   running build
2025-06-10T22:41:26,966   running build_py
2025-06-10T22:41:26,997   creating build/lib/tests
2025-06-10T22:41:26,999   copying tests/__init__.py -> build/lib/tests
2025-06-10T22:41:27,002   creating build/lib/pub_worm
2025-06-10T22:41:27,003   copying pub_worm/__init__.py -> build/lib/pub_worm
2025-06-10T22:41:27,005   creating build/lib/tests/impact_factor
2025-06-10T22:41:27,006   copying tests/impact_factor/test_get_impact_factor.py -> build/lib/tests/impact_factor
2025-06-10T22:41:27,008   copying tests/impact_factor/__init__.py -> build/lib/tests/impact_factor
2025-06-10T22:41:27,011   creating build/lib/tests/ncbi
2025-06-10T22:41:27,012   copying tests/ncbi/__init__.py -> build/lib/tests/ncbi
2025-06-10T22:41:27,014   copying tests/ncbi/test_entreze_api.py -> build/lib/tests/ncbi
2025-06-10T22:41:27,017   creating build/lib/tests/orcid
2025-06-10T22:41:27,018   copying tests/orcid/__init__.py -> build/lib/tests/orcid
2025-06-10T22:41:27,020   copying tests/orcid/test_orcid_api.py -> build/lib/tests/orcid
2025-06-10T22:41:27,022   creating build/lib/tests/wormbase
2025-06-10T22:41:27,023   copying tests/wormbase/__init__.py -> build/lib/tests/wormbase
2025-06-10T22:41:27,025   copying tests/wormbase/test_wormbase_api.py -> build/lib/tests/wormbase
2025-06-10T22:41:27,028   creating build/lib/pub_worm/impact_factor
2025-06-10T22:41:27,029   copying pub_worm/impact_factor/__init__.py -> build/lib/pub_worm/impact_factor
2025-06-10T22:41:27,030   copying pub_worm/impact_factor/impact_factor_lookup.py -> build/lib/pub_worm/impact_factor
2025-06-10T22:41:27,033   creating build/lib/pub_worm/biorxiv
2025-06-10T22:41:27,034   copying pub_worm/biorxiv/biorxiv_api.py -> build/lib/pub_worm/biorxiv
2025-06-10T22:41:27,036   copying pub_worm/biorxiv/__init__.py -> build/lib/pub_worm/biorxiv
2025-06-10T22:41:27,037   creating build/lib/pub_worm/ncbi
2025-06-10T22:41:27,038   copying pub_worm/ncbi/entreze_api.py -> build/lib/pub_worm/ncbi
2025-06-10T22:41:27,041   copying pub_worm/ncbi/__init__.py -> build/lib/pub_worm/ncbi
2025-06-10T22:41:27,043   creating build/lib/pub_worm/orcid
2025-06-10T22:41:27,044   copying pub_worm/orcid/__init__.py -> build/lib/pub_worm/orcid
2025-06-10T22:41:27,046   copying pub_worm/orcid/orcid_api.py -> build/lib/pub_worm/orcid
2025-06-10T22:41:27,048   creating build/lib/pub_worm/ensembl
2025-06-10T22:41:27,049   copying pub_worm/ensembl/__init__.py -> build/lib/pub_worm/ensembl
2025-06-10T22:41:27,051   copying pub_worm/ensembl/ensembl_api.py -> build/lib/pub_worm/ensembl
2025-06-10T22:41:27,053   creating build/lib/pub_worm/wormbase
2025-06-10T22:41:27,054   copying pub_worm/wormbase/wormbase_util.py -> build/lib/pub_worm/wormbase
2025-06-10T22:41:27,056   copying pub_worm/wormbase/to_csv_helpers.py -> build/lib/pub_worm/wormbase
2025-06-10T22:41:27,058   copying pub_worm/wormbase/__init__.py -> build/lib/pub_worm/wormbase
2025-06-10T22:41:27,060   copying pub_worm/wormbase/wormbase_api.py -> build/lib/pub_worm/wormbase
2025-06-10T22:41:27,062   running egg_info
2025-06-10T22:41:27,091   writing pub_worm.egg-info/PKG-INFO
2025-06-10T22:41:27,094   writing dependency_links to pub_worm.egg-info/dependency_links.txt
2025-06-10T22:41:27,096   writing requirements to pub_worm.egg-info/requires.txt
2025-06-10T22:41:27,097   writing top-level names to pub_worm.egg-info/top_level.txt
2025-06-10T22:41:27,137   reading manifest file 'pub_worm.egg-info/SOURCES.txt'
2025-06-10T22:41:27,141   reading manifest template 'MANIFEST.in'
2025-06-10T22:41:27,143   warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json'
2025-06-10T22:41:27,143   warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json'
2025-06-10T22:41:27,144   warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json'
2025-06-10T22:41:27,147   writing manifest file 'pub_worm.egg-info/SOURCES.txt'
2025-06-10T22:41:27,149   /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.
2025-06-10T22:41:27,150   !!

2025-06-10T22:41:27,151           ********************************************************************************
2025-06-10T22:41:27,152           ############################
2025-06-10T22:41:27,152           # Package would be ignored #
2025-06-10T22:41:27,153           ############################
2025-06-10T22:41:27,154           Python recognizes 'pub_worm.impact_factor.data' as an importable package[^1],
2025-06-10T22:41:27,154           but it is absent from setuptools' `packages` configuration.

2025-06-10T22:41:27,155           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-10T22:41:27,156           package, please make sure that 'pub_worm.impact_factor.data' is explicitly added
2025-06-10T22:41:27,157           to the `packages` configuration field.

2025-06-10T22:41:27,158           Alternatively, you can also rely on setuptools' discovery methods
2025-06-10T22:41:27,159           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-10T22:41:27,159           instead of `find_packages(...)`/`find:`).

2025-06-10T22:41:27,160           You can read more about "package discovery" on setuptools documentation page:

2025-06-10T22:41:27,162           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-10T22:41:27,163           If you don't want 'pub_worm.impact_factor.data' to be distributed and are
2025-06-10T22:41:27,163           already explicitly excluding 'pub_worm.impact_factor.data' via
2025-06-10T22:41:27,164           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-10T22:41:27,164           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-10T22:41:27,165           combination with a more fine grained `package-data` configuration.

2025-06-10T22:41:27,166           You can read more about "package data files" on setuptools documentation page:

2025-06-10T22:41:27,167           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-10T22:41:27,184           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-10T22:41:27,185                 even if it does not contain any `.py` files.
2025-06-10T22:41:27,185                 On the other hand, currently there is no concept of package data
2025-06-10T22:41:27,186                 directory, all directories are treated like packages.
2025-06-10T22:41:27,186           ********************************************************************************

2025-06-10T22:41:27,187   !!
2025-06-10T22:41:27,188     check.warn(importable)
2025-06-10T22:41:27,188   /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.
2025-06-10T22:41:27,189   !!

2025-06-10T22:41:27,190           ********************************************************************************
2025-06-10T22:41:27,190           ############################
2025-06-10T22:41:27,191           # Package would be ignored #
2025-06-10T22:41:27,191           ############################
2025-06-10T22:41:27,192           Python recognizes 'pub_worm.wormbase.data' as an importable package[^1],
2025-06-10T22:41:27,193           but it is absent from setuptools' `packages` configuration.

2025-06-10T22:41:27,194           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-10T22:41:27,194           package, please make sure that 'pub_worm.wormbase.data' is explicitly added
2025-06-10T22:41:27,195           to the `packages` configuration field.

2025-06-10T22:41:27,196           Alternatively, you can also rely on setuptools' discovery methods
2025-06-10T22:41:27,197           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-10T22:41:27,197           instead of `find_packages(...)`/`find:`).

2025-06-10T22:41:27,198           You can read more about "package discovery" on setuptools documentation page:

2025-06-10T22:41:27,200           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-10T22:41:27,201           If you don't want 'pub_worm.wormbase.data' to be distributed and are
2025-06-10T22:41:27,201           already explicitly excluding 'pub_worm.wormbase.data' via
2025-06-10T22:41:27,202           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-10T22:41:27,202           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-10T22:41:27,203           combination with a more fine grained `package-data` configuration.

2025-06-10T22:41:27,204           You can read more about "package data files" on setuptools documentation page:

2025-06-10T22:41:27,206           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-10T22:41:27,207           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-10T22:41:27,208                 even if it does not contain any `.py` files.
2025-06-10T22:41:27,209                 On the other hand, currently there is no concept of package data
2025-06-10T22:41:27,209                 directory, all directories are treated like packages.
2025-06-10T22:41:27,210           ********************************************************************************

2025-06-10T22:41:27,211   !!
2025-06-10T22:41:27,212     check.warn(importable)
2025-06-10T22:41:27,212   creating build/lib/pub_worm/impact_factor/data
2025-06-10T22:41:27,213   copying pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/lib/pub_worm/impact_factor/data
2025-06-10T22:41:27,213   creating build/lib/pub_worm/wormbase/data
2025-06-10T22:41:27,214   copying pub_worm/wormbase/data/wormbase_field_gene.json -> build/lib/pub_worm/wormbase/data
2025-06-10T22:41:27,214   copying pub_worm/wormbase/data/wormbase_field_paper.json -> build/lib/pub_worm/wormbase/data
2025-06-10T22:41:27,215   copying pub_worm/wormbase/data/wormbase_widget_gene.json -> build/lib/pub_worm/wormbase/data
2025-06-10T22:41:27,232   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-10T22:41:27,232   !!

2025-06-10T22:41:27,233           ********************************************************************************
2025-06-10T22:41:27,234           Please avoid running ``setup.py`` directly.
2025-06-10T22:41:27,234           Instead, use pypa/build, pypa/installer or other
2025-06-10T22:41:27,235           standards-based tools.

2025-06-10T22:41:27,236           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-10T22:41:27,237           or your builds will no longer be supported.

2025-06-10T22:41:27,238           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-10T22:41:27,238           ********************************************************************************

2025-06-10T22:41:27,239   !!
2025-06-10T22:41:27,240     self.initialize_options()
2025-06-10T22:41:27,260   installing to build/bdist.linux-armv7l/wheel
2025-06-10T22:41:27,261   running install
2025-06-10T22:41:27,284   running install_lib
2025-06-10T22:41:27,312   creating build/bdist.linux-armv7l/wheel
2025-06-10T22:41:27,314   creating build/bdist.linux-armv7l/wheel/tests
2025-06-10T22:41:27,316   creating build/bdist.linux-armv7l/wheel/tests/impact_factor
2025-06-10T22:41:27,317   copying build/lib/tests/impact_factor/test_get_impact_factor.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor
2025-06-10T22:41:27,319   copying build/lib/tests/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor
2025-06-10T22:41:27,321   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests
2025-06-10T22:41:27,323   creating build/bdist.linux-armv7l/wheel/tests/ncbi
2025-06-10T22:41:27,324   copying build/lib/tests/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi
2025-06-10T22:41:27,326   copying build/lib/tests/ncbi/test_entreze_api.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi
2025-06-10T22:41:27,329   creating build/bdist.linux-armv7l/wheel/tests/orcid
2025-06-10T22:41:27,330   copying build/lib/tests/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/orcid
2025-06-10T22:41:27,331   copying build/lib/tests/orcid/test_orcid_api.py -> build/bdist.linux-armv7l/wheel/./tests/orcid
2025-06-10T22:41:27,334   creating build/bdist.linux-armv7l/wheel/tests/wormbase
2025-06-10T22:41:27,335   copying build/lib/tests/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase
2025-06-10T22:41:27,337   copying build/lib/tests/wormbase/test_wormbase_api.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase
2025-06-10T22:41:27,339   creating build/bdist.linux-armv7l/wheel/pub_worm
2025-06-10T22:41:27,341   creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor
2025-06-10T22:41:27,342   copying build/lib/pub_worm/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor
2025-06-10T22:41:27,344   creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor/data
2025-06-10T22:41:27,345   copying build/lib/pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor/data
2025-06-10T22:41:27,372   copying build/lib/pub_worm/impact_factor/impact_factor_lookup.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor
2025-06-10T22:41:27,374   copying build/lib/pub_worm/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm
2025-06-10T22:41:27,376   creating build/bdist.linux-armv7l/wheel/pub_worm/biorxiv
2025-06-10T22:41:27,377   copying build/lib/pub_worm/biorxiv/biorxiv_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv
2025-06-10T22:41:27,379   copying build/lib/pub_worm/biorxiv/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv
2025-06-10T22:41:27,381   creating build/bdist.linux-armv7l/wheel/pub_worm/ncbi
2025-06-10T22:41:27,382   copying build/lib/pub_worm/ncbi/entreze_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi
2025-06-10T22:41:27,385   copying build/lib/pub_worm/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi
2025-06-10T22:41:27,387   creating build/bdist.linux-armv7l/wheel/pub_worm/orcid
2025-06-10T22:41:27,388   copying build/lib/pub_worm/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid
2025-06-10T22:41:27,390   copying build/lib/pub_worm/orcid/orcid_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid
2025-06-10T22:41:27,392   creating build/bdist.linux-armv7l/wheel/pub_worm/ensembl
2025-06-10T22:41:27,393   copying build/lib/pub_worm/ensembl/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl
2025-06-10T22:41:27,395   copying build/lib/pub_worm/ensembl/ensembl_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl
2025-06-10T22:41:27,397   creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase
2025-06-10T22:41:27,398   copying build/lib/pub_worm/wormbase/wormbase_util.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase
2025-06-10T22:41:27,401   copying build/lib/pub_worm/wormbase/to_csv_helpers.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase
2025-06-10T22:41:27,403   copying build/lib/pub_worm/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase
2025-06-10T22:41:27,404   copying build/lib/pub_worm/wormbase/wormbase_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase
2025-06-10T22:41:27,407   creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase/data
2025-06-10T22:41:27,408   copying build/lib/pub_worm/wormbase/data/wormbase_widget_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data
2025-06-10T22:41:27,410   copying build/lib/pub_worm/wormbase/data/wormbase_field_paper.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data
2025-06-10T22:41:27,412   copying build/lib/pub_worm/wormbase/data/wormbase_field_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data
2025-06-10T22:41:27,414   running install_egg_info
2025-06-10T22:41:27,450   Copying pub_worm.egg-info to build/bdist.linux-armv7l/wheel/./pub_worm-0.3.12-py3.11.egg-info
2025-06-10T22:41:27,462   running install_scripts
2025-06-10T22:41:27,471   creating build/bdist.linux-armv7l/wheel/pub_worm-0.3.12.dist-info/WHEEL
2025-06-10T22:41:27,474   creating '/tmp/pip-wheel-0sfk3l_c/pub_worm-0.3.12-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-10T22:41:27,476   adding 'pub_worm/__init__.py'
2025-06-10T22:41:27,478   adding 'pub_worm/biorxiv/__init__.py'
2025-06-10T22:41:27,480   adding 'pub_worm/biorxiv/biorxiv_api.py'
2025-06-10T22:41:27,481   adding 'pub_worm/ensembl/__init__.py'
2025-06-10T22:41:27,483   adding 'pub_worm/ensembl/ensembl_api.py'
2025-06-10T22:41:27,485   adding 'pub_worm/impact_factor/__init__.py'
2025-06-10T22:41:27,486   adding 'pub_worm/impact_factor/impact_factor_lookup.py'
2025-06-10T22:41:27,655   adding 'pub_worm/impact_factor/data/2022_JCR_IF.csv'
2025-06-10T22:41:27,666   adding 'pub_worm/ncbi/__init__.py'
2025-06-10T22:41:27,668   adding 'pub_worm/ncbi/entreze_api.py'
2025-06-10T22:41:27,670   adding 'pub_worm/orcid/__init__.py'
2025-06-10T22:41:27,671   adding 'pub_worm/orcid/orcid_api.py'
2025-06-10T22:41:27,673   adding 'pub_worm/wormbase/__init__.py'
2025-06-10T22:41:27,675   adding 'pub_worm/wormbase/to_csv_helpers.py'
2025-06-10T22:41:27,677   adding 'pub_worm/wormbase/wormbase_api.py'
2025-06-10T22:41:27,678   adding 'pub_worm/wormbase/wormbase_util.py'
2025-06-10T22:41:27,680   adding 'pub_worm/wormbase/data/wormbase_field_gene.json'
2025-06-10T22:41:27,681   adding 'pub_worm/wormbase/data/wormbase_field_paper.json'
2025-06-10T22:41:27,683   adding 'pub_worm/wormbase/data/wormbase_widget_gene.json'
2025-06-10T22:41:27,685   adding 'tests/__init__.py'
2025-06-10T22:41:27,686   adding 'tests/impact_factor/__init__.py'
2025-06-10T22:41:27,688   adding 'tests/impact_factor/test_get_impact_factor.py'
2025-06-10T22:41:27,689   adding 'tests/ncbi/__init__.py'
2025-06-10T22:41:27,691   adding 'tests/ncbi/test_entreze_api.py'
2025-06-10T22:41:27,692   adding 'tests/orcid/__init__.py'
2025-06-10T22:41:27,693   adding 'tests/orcid/test_orcid_api.py'
2025-06-10T22:41:27,695   adding 'tests/wormbase/__init__.py'
2025-06-10T22:41:27,696   adding 'tests/wormbase/test_wormbase_api.py'
2025-06-10T22:41:27,698   adding 'pub_worm-0.3.12.dist-info/METADATA'
2025-06-10T22:41:27,699   adding 'pub_worm-0.3.12.dist-info/WHEEL'
2025-06-10T22:41:27,700   adding 'pub_worm-0.3.12.dist-info/top_level.txt'
2025-06-10T22:41:27,701   adding 'pub_worm-0.3.12.dist-info/RECORD'
2025-06-10T22:41:27,708   removing build/bdist.linux-armv7l/wheel
2025-06-10T22:41:27,835   Building wheel for pub-worm (setup.py): finished with status 'done'
2025-06-10T22:41:27,846   Created wheel for pub-worm: filename=pub_worm-0.3.12-py3-none-any.whl size=403561 sha256=3dd09e8fd4a48ae16c7179b9aeb3bc867904df34d1f954376ed210c866a22034
2025-06-10T22:41:27,847   Stored in directory: /tmp/pip-ephem-wheel-cache-m5s171td/wheels/be/02/f2/af0077d37be6e02c7b58e368a5073b3119b559efe921334eac
2025-06-10T22:41:27,859 Successfully built pub-worm
2025-06-10T22:41:27,877 Removed build tracker: '/tmp/pip-build-tracker-_p8rs8yw'