2025-05-31T16:07:54,912 Created temporary directory: /tmp/pip-build-tracker-akxshrvn
2025-05-31T16:07:54,913 Initialized build tracking at /tmp/pip-build-tracker-akxshrvn
2025-05-31T16:07:54,913 Created build tracker: /tmp/pip-build-tracker-akxshrvn
2025-05-31T16:07:54,914 Entered build tracker: /tmp/pip-build-tracker-akxshrvn
2025-05-31T16:07:54,915 Created temporary directory: /tmp/pip-wheel-1jziwemt
2025-05-31T16:07:54,919 Created temporary directory: /tmp/pip-ephem-wheel-cache-tq8q0_67
2025-05-31T16:07:54,972 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-05-31T16:07:54,974 2 location(s) to search for versions of pub-worm:
2025-05-31T16:07:54,974 * https://pypi.org/simple/pub-worm/
2025-05-31T16:07:54,974 * https://www.piwheels.org/simple/pub-worm/
2025-05-31T16:07:54,975 Fetching project page and analyzing links: https://pypi.org/simple/pub-worm/
2025-05-31T16:07:54,976 Getting page https://pypi.org/simple/pub-worm/
2025-05-31T16:07:54,977 Found index url https://pypi.org/simple/
2025-05-31T16:07:55,128 Fetched page https://pypi.org/simple/pub-worm/ as application/vnd.pypi.simple.v1+json
2025-05-31T16:07:55,132   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
2025-05-31T16:07:55,133   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
2025-05-31T16:07:55,134   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
2025-05-31T16:07:55,134   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
2025-05-31T16:07:55,135   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
2025-05-31T16:07:55,136   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
2025-05-31T16:07:55,136   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
2025-05-31T16:07:55,137   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
2025-05-31T16:07:55,138   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
2025-05-31T16:07:55,139   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
2025-05-31T16:07:55,139   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
2025-05-31T16:07:55,140   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
2025-05-31T16:07:55,141   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
2025-05-31T16:07:55,141   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
2025-05-31T16:07:55,142   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
2025-05-31T16:07:55,143   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
2025-05-31T16:07:55,144   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
2025-05-31T16:07:55,144   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
2025-05-31T16:07:55,145   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
2025-05-31T16:07:55,146   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
2025-05-31T16:07:55,146   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
2025-05-31T16:07:55,147   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
2025-05-31T16:07:55,148   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
2025-05-31T16:07:55,148   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
2025-05-31T16:07:55,149   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
2025-05-31T16:07:55,150   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
2025-05-31T16:07:55,150   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
2025-05-31T16:07:55,151   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
2025-05-31T16:07:55,152   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
2025-05-31T16:07:55,153   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
2025-05-31T16:07:55,153   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
2025-05-31T16:07:55,154   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
2025-05-31T16:07:55,155   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
2025-05-31T16:07:55,156   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
2025-05-31T16:07:55,157   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
2025-05-31T16:07:55,158 Fetching project page and analyzing links: https://www.piwheels.org/simple/pub-worm/
2025-05-31T16:07:55,158 Getting page https://www.piwheels.org/simple/pub-worm/
2025-05-31T16:07:55,160 Found index url https://www.piwheels.org/simple/
2025-05-31T16:07:55,318 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/
2025-05-31T16:07:55,999 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/
2025-05-31T16:07:57,173 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/
2025-05-31T16:07:59,343 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/
2025-05-31T16:08:03,511 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/
2025-05-31T16:08:03,693 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
2025-05-31T16:08:03,695 Skipping link: not a file: https://www.piwheels.org/simple/pub-worm/
2025-05-31T16:08:03,696 Skipping link: not a file: https://pypi.org/simple/pub-worm/
2025-05-31T16:08:03,723 Given no hashes to check 1 links for project 'pub-worm': discarding no candidates
2025-05-31T16:08:03,725 Collecting pub-worm==0.3.9
2025-05-31T16:08:03,727   Created temporary directory: /tmp/pip-unpack-1dsg9hjo
2025-05-31T16:08:03,962   Downloading pub_worm-0.3.9.tar.gz (396 kB)
2025-05-31T16:08:04,191   Added pub-worm==0.3.9 from https://files.pythonhosted.org/packages/60/1a/b9e6351cdffb27c2ed342a6fcd2fa8f18e3a22a7ca93ca0f8dc0d535941b/pub_worm-0.3.9.tar.gz to build tracker '/tmp/pip-build-tracker-akxshrvn'
2025-05-31T16:08:04,193   Running setup.py (path:/tmp/pip-wheel-1jziwemt/pub-worm_311d590683194e29ab20ff3cbcb82004/setup.py) egg_info for package pub-worm
2025-05-31T16:08:04,195   Created temporary directory: /tmp/pip-pip-egg-info-670qw4k3
2025-05-31T16:08:04,195   Preparing metadata (setup.py): started
2025-05-31T16:08:04,197   Running command python setup.py egg_info
2025-05-31T16:08:05,097   running egg_info
2025-05-31T16:08:05,126   creating /tmp/pip-pip-egg-info-670qw4k3/pub_worm.egg-info
2025-05-31T16:08:05,127   writing /tmp/pip-pip-egg-info-670qw4k3/pub_worm.egg-info/PKG-INFO
2025-05-31T16:08:05,131   writing dependency_links to /tmp/pip-pip-egg-info-670qw4k3/pub_worm.egg-info/dependency_links.txt
2025-05-31T16:08:05,133   writing requirements to /tmp/pip-pip-egg-info-670qw4k3/pub_worm.egg-info/requires.txt
2025-05-31T16:08:05,134   writing top-level names to /tmp/pip-pip-egg-info-670qw4k3/pub_worm.egg-info/top_level.txt
2025-05-31T16:08:05,136   writing manifest file '/tmp/pip-pip-egg-info-670qw4k3/pub_worm.egg-info/SOURCES.txt'
2025-05-31T16:08:05,239   reading manifest file '/tmp/pip-pip-egg-info-670qw4k3/pub_worm.egg-info/SOURCES.txt'
2025-05-31T16:08:05,241   reading manifest template 'MANIFEST.in'
2025-05-31T16:08:05,243   warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json'
2025-05-31T16:08:05,243   warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json'
2025-05-31T16:08:05,244   warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json'
2025-05-31T16:08:05,247   writing manifest file '/tmp/pip-pip-egg-info-670qw4k3/pub_worm.egg-info/SOURCES.txt'
2025-05-31T16:08:05,353   Preparing metadata (setup.py): finished with status 'done'
2025-05-31T16:08:05,357   Source in /tmp/pip-wheel-1jziwemt/pub-worm_311d590683194e29ab20ff3cbcb82004 has version 0.3.9, which satisfies requirement pub-worm==0.3.9 from https://files.pythonhosted.org/packages/60/1a/b9e6351cdffb27c2ed342a6fcd2fa8f18e3a22a7ca93ca0f8dc0d535941b/pub_worm-0.3.9.tar.gz
2025-05-31T16:08:05,358   Removed pub-worm==0.3.9 from https://files.pythonhosted.org/packages/60/1a/b9e6351cdffb27c2ed342a6fcd2fa8f18e3a22a7ca93ca0f8dc0d535941b/pub_worm-0.3.9.tar.gz from build tracker '/tmp/pip-build-tracker-akxshrvn'
2025-05-31T16:08:05,364 Created temporary directory: /tmp/pip-unpack-mfbnpis0
2025-05-31T16:08:05,365 Created temporary directory: /tmp/pip-unpack-cuiepmax
2025-05-31T16:08:05,366 Building wheels for collected packages: pub-worm
2025-05-31T16:08:05,370   Created temporary directory: /tmp/pip-wheel-y7gf2qco
2025-05-31T16:08:05,371   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
2025-05-31T16:08:05,372   Building wheel for pub-worm (setup.py): started
2025-05-31T16:08:05,374   Destination directory: /tmp/pip-wheel-y7gf2qco
2025-05-31T16:08:05,375   Running command python setup.py bdist_wheel
2025-05-31T16:08:06,223   running bdist_wheel
2025-05-31T16:08:06,362   running build
2025-05-31T16:08:06,363   running build_py
2025-05-31T16:08:06,396   creating build/lib/pub_worm
2025-05-31T16:08:06,399   copying pub_worm/__init__.py -> build/lib/pub_worm
2025-05-31T16:08:06,402   creating build/lib/tests
2025-05-31T16:08:06,403   copying tests/__init__.py -> build/lib/tests
2025-05-31T16:08:06,405   creating build/lib/pub_worm/orcid
2025-05-31T16:08:06,406   copying pub_worm/orcid/orcid_api.py -> build/lib/pub_worm/orcid
2025-05-31T16:08:06,409   copying pub_worm/orcid/__init__.py -> build/lib/pub_worm/orcid
2025-05-31T16:08:06,411   creating build/lib/pub_worm/ensembl
2025-05-31T16:08:06,412   copying pub_worm/ensembl/__init__.py -> build/lib/pub_worm/ensembl
2025-05-31T16:08:06,414   copying pub_worm/ensembl/ensembl_api.py -> build/lib/pub_worm/ensembl
2025-05-31T16:08:06,417   creating build/lib/pub_worm/biorxiv
2025-05-31T16:08:06,418   copying pub_worm/biorxiv/__init__.py -> build/lib/pub_worm/biorxiv
2025-05-31T16:08:06,420   copying pub_worm/biorxiv/biorxiv_api.py -> build/lib/pub_worm/biorxiv
2025-05-31T16:08:06,423   creating build/lib/pub_worm/wormbase
2025-05-31T16:08:06,424   copying pub_worm/wormbase/to_csv_helpers.py -> build/lib/pub_worm/wormbase
2025-05-31T16:08:06,426   copying pub_worm/wormbase/wormbase_util.py -> build/lib/pub_worm/wormbase
2025-05-31T16:08:06,430   copying pub_worm/wormbase/__init__.py -> build/lib/pub_worm/wormbase
2025-05-31T16:08:06,434   copying pub_worm/wormbase/wormbase_api.py -> build/lib/pub_worm/wormbase
2025-05-31T16:08:06,440   creating build/lib/pub_worm/ncbi
2025-05-31T16:08:06,441   copying pub_worm/ncbi/__init__.py -> build/lib/pub_worm/ncbi
2025-05-31T16:08:06,444   copying pub_worm/ncbi/entreze_api.py -> build/lib/pub_worm/ncbi
2025-05-31T16:08:06,448   creating build/lib/pub_worm/impact_factor
2025-05-31T16:08:06,449   copying pub_worm/impact_factor/__init__.py -> build/lib/pub_worm/impact_factor
2025-05-31T16:08:06,452   copying pub_worm/impact_factor/impact_factor_lookup.py -> build/lib/pub_worm/impact_factor
2025-05-31T16:08:06,454   creating build/lib/tests/orcid
2025-05-31T16:08:06,455   copying tests/orcid/test_orcid_api.py -> build/lib/tests/orcid
2025-05-31T16:08:06,458   copying tests/orcid/__init__.py -> build/lib/tests/orcid
2025-05-31T16:08:06,460   creating build/lib/tests/wormbase
2025-05-31T16:08:06,461   copying tests/wormbase/__init__.py -> build/lib/tests/wormbase
2025-05-31T16:08:06,463   copying tests/wormbase/test_wormbase_api.py -> build/lib/tests/wormbase
2025-05-31T16:08:06,466   creating build/lib/tests/ncbi
2025-05-31T16:08:06,467   copying tests/ncbi/test_entreze_api.py -> build/lib/tests/ncbi
2025-05-31T16:08:06,470   copying tests/ncbi/__init__.py -> build/lib/tests/ncbi
2025-05-31T16:08:06,472   creating build/lib/tests/impact_factor
2025-05-31T16:08:06,473   copying tests/impact_factor/__init__.py -> build/lib/tests/impact_factor
2025-05-31T16:08:06,475   copying tests/impact_factor/test_get_impact_factor.py -> build/lib/tests/impact_factor
2025-05-31T16:08:06,477   running egg_info
2025-05-31T16:08:06,508   writing pub_worm.egg-info/PKG-INFO
2025-05-31T16:08:06,511   writing dependency_links to pub_worm.egg-info/dependency_links.txt
2025-05-31T16:08:06,513   writing requirements to pub_worm.egg-info/requires.txt
2025-05-31T16:08:06,514   writing top-level names to pub_worm.egg-info/top_level.txt
2025-05-31T16:08:06,556   reading manifest file 'pub_worm.egg-info/SOURCES.txt'
2025-05-31T16:08:06,560   reading manifest template 'MANIFEST.in'
2025-05-31T16:08:06,561   warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json'
2025-05-31T16:08:06,562   warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json'
2025-05-31T16:08:06,563   warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json'
2025-05-31T16:08:06,566   writing manifest file 'pub_worm.egg-info/SOURCES.txt'
2025-05-31T16:08:06,568   /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.
2025-05-31T16:08:06,569   !!

2025-05-31T16:08:06,570           ********************************************************************************
2025-05-31T16:08:06,571           ############################
2025-05-31T16:08:06,571           # Package would be ignored #
2025-05-31T16:08:06,572           ############################
2025-05-31T16:08:06,573           Python recognizes 'pub_worm.impact_factor.data' as an importable package[^1],
2025-05-31T16:08:06,573           but it is absent from setuptools' `packages` configuration.

2025-05-31T16:08:06,575           This leads to an ambiguous overall configuration. If you want to distribute this
2025-05-31T16:08:06,575           package, please make sure that 'pub_worm.impact_factor.data' is explicitly added
2025-05-31T16:08:06,576           to the `packages` configuration field.

2025-05-31T16:08:06,577           Alternatively, you can also rely on setuptools' discovery methods
2025-05-31T16:08:06,577           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-05-31T16:08:06,578           instead of `find_packages(...)`/`find:`).

2025-05-31T16:08:06,579           You can read more about "package discovery" on setuptools documentation page:

2025-05-31T16:08:06,581           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-05-31T16:08:06,581           If you don't want 'pub_worm.impact_factor.data' to be distributed and are
2025-05-31T16:08:06,582           already explicitly excluding 'pub_worm.impact_factor.data' via
2025-05-31T16:08:06,582           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-05-31T16:08:06,583           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-05-31T16:08:06,583           combination with a more fine grained `package-data` configuration.

2025-05-31T16:08:06,584           You can read more about "package data files" on setuptools documentation page:

2025-05-31T16:08:06,586           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-05-31T16:08:06,587           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-05-31T16:08:06,588                 even if it does not contain any `.py` files.
2025-05-31T16:08:06,588                 On the other hand, currently there is no concept of package data
2025-05-31T16:08:06,589                 directory, all directories are treated like packages.
2025-05-31T16:08:06,589           ********************************************************************************

2025-05-31T16:08:06,590   !!
2025-05-31T16:08:06,591     check.warn(importable)
2025-05-31T16:08:06,592   /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.
2025-05-31T16:08:06,592   !!

2025-05-31T16:08:06,593           ********************************************************************************
2025-05-31T16:08:06,594           ############################
2025-05-31T16:08:06,594           # Package would be ignored #
2025-05-31T16:08:06,595           ############################
2025-05-31T16:08:06,595           Python recognizes 'pub_worm.wormbase.data' as an importable package[^1],
2025-05-31T16:08:06,596           but it is absent from setuptools' `packages` configuration.

2025-05-31T16:08:06,602           This leads to an ambiguous overall configuration. If you want to distribute this
2025-05-31T16:08:06,604           package, please make sure that 'pub_worm.wormbase.data' is explicitly added
2025-05-31T16:08:06,608           to the `packages` configuration field.

2025-05-31T16:08:06,614           Alternatively, you can also rely on setuptools' discovery methods
2025-05-31T16:08:06,615           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-05-31T16:08:06,615           instead of `find_packages(...)`/`find:`).

2025-05-31T16:08:06,623           You can read more about "package discovery" on setuptools documentation page:

2025-05-31T16:08:06,626           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-05-31T16:08:06,628           If you don't want 'pub_worm.wormbase.data' to be distributed and are
2025-05-31T16:08:06,630           already explicitly excluding 'pub_worm.wormbase.data' via
2025-05-31T16:08:06,633           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-05-31T16:08:06,634           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-05-31T16:08:06,642           combination with a more fine grained `package-data` configuration.

2025-05-31T16:08:06,647           You can read more about "package data files" on setuptools documentation page:

2025-05-31T16:08:06,650           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-05-31T16:08:06,656           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-05-31T16:08:06,658                 even if it does not contain any `.py` files.
2025-05-31T16:08:06,659                 On the other hand, currently there is no concept of package data
2025-05-31T16:08:06,661                 directory, all directories are treated like packages.
2025-05-31T16:08:06,663           ********************************************************************************

2025-05-31T16:08:06,665   !!
2025-05-31T16:08:06,666     check.warn(importable)
2025-05-31T16:08:06,667   creating build/lib/pub_worm/wormbase/data
2025-05-31T16:08:06,667   copying pub_worm/wormbase/data/wormbase_field_gene.json -> build/lib/pub_worm/wormbase/data
2025-05-31T16:08:06,668   copying pub_worm/wormbase/data/wormbase_field_paper.json -> build/lib/pub_worm/wormbase/data
2025-05-31T16:08:06,670   copying pub_worm/wormbase/data/wormbase_widget_gene.json -> build/lib/pub_worm/wormbase/data
2025-05-31T16:08:06,670   creating build/lib/pub_worm/impact_factor/data
2025-05-31T16:08:06,672   copying pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/lib/pub_worm/impact_factor/data
2025-05-31T16:08:06,697   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-05-31T16:08:06,698   !!

2025-05-31T16:08:06,699           ********************************************************************************
2025-05-31T16:08:06,699           Please avoid running ``setup.py`` directly.
2025-05-31T16:08:06,700           Instead, use pypa/build, pypa/installer or other
2025-05-31T16:08:06,700           standards-based tools.

2025-05-31T16:08:06,701           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-05-31T16:08:06,701           or your builds will no longer be supported.

2025-05-31T16:08:06,702           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-05-31T16:08:06,703           ********************************************************************************

2025-05-31T16:08:06,704   !!
2025-05-31T16:08:06,704     self.initialize_options()
2025-05-31T16:08:06,726   installing to build/bdist.linux-armv7l/wheel
2025-05-31T16:08:06,727   running install
2025-05-31T16:08:06,751   running install_lib
2025-05-31T16:08:06,777   creating build/bdist.linux-armv7l/wheel
2025-05-31T16:08:06,779   creating build/bdist.linux-armv7l/wheel/pub_worm
2025-05-31T16:08:06,780   copying build/lib/pub_worm/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm
2025-05-31T16:08:06,783   creating build/bdist.linux-armv7l/wheel/pub_worm/orcid
2025-05-31T16:08:06,784   copying build/lib/pub_worm/orcid/orcid_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid
2025-05-31T16:08:06,786   copying build/lib/pub_worm/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid
2025-05-31T16:08:06,788   creating build/bdist.linux-armv7l/wheel/pub_worm/ensembl
2025-05-31T16:08:06,789   copying build/lib/pub_worm/ensembl/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl
2025-05-31T16:08:06,791   copying build/lib/pub_worm/ensembl/ensembl_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl
2025-05-31T16:08:06,794   creating build/bdist.linux-armv7l/wheel/pub_worm/biorxiv
2025-05-31T16:08:06,795   copying build/lib/pub_worm/biorxiv/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv
2025-05-31T16:08:06,796   copying build/lib/pub_worm/biorxiv/biorxiv_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv
2025-05-31T16:08:06,799   creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase
2025-05-31T16:08:06,800   copying build/lib/pub_worm/wormbase/to_csv_helpers.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase
2025-05-31T16:08:06,802   copying build/lib/pub_worm/wormbase/wormbase_util.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase
2025-05-31T16:08:06,805   copying build/lib/pub_worm/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase
2025-05-31T16:08:06,807   creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase/data
2025-05-31T16:08:06,808   copying build/lib/pub_worm/wormbase/data/wormbase_field_paper.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data
2025-05-31T16:08:06,811   copying build/lib/pub_worm/wormbase/data/wormbase_widget_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data
2025-05-31T16:08:06,813   copying build/lib/pub_worm/wormbase/data/wormbase_field_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data
2025-05-31T16:08:06,815   copying build/lib/pub_worm/wormbase/wormbase_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase
2025-05-31T16:08:06,818   creating build/bdist.linux-armv7l/wheel/pub_worm/ncbi
2025-05-31T16:08:06,819   copying build/lib/pub_worm/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi
2025-05-31T16:08:06,821   copying build/lib/pub_worm/ncbi/entreze_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi
2025-05-31T16:08:06,824   creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor
2025-05-31T16:08:06,826   copying build/lib/pub_worm/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor
2025-05-31T16:08:06,828   creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor/data
2025-05-31T16:08:06,845   copying build/lib/pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor/data
2025-05-31T16:08:06,914   copying build/lib/pub_worm/impact_factor/impact_factor_lookup.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor
2025-05-31T16:08:06,916   creating build/bdist.linux-armv7l/wheel/tests
2025-05-31T16:08:06,918   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests
2025-05-31T16:08:06,920   creating build/bdist.linux-armv7l/wheel/tests/orcid
2025-05-31T16:08:06,922   copying build/lib/tests/orcid/test_orcid_api.py -> build/bdist.linux-armv7l/wheel/./tests/orcid
2025-05-31T16:08:06,924   copying build/lib/tests/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/orcid
2025-05-31T16:08:06,926   creating build/bdist.linux-armv7l/wheel/tests/wormbase
2025-05-31T16:08:06,928   copying build/lib/tests/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase
2025-05-31T16:08:06,931   copying build/lib/tests/wormbase/test_wormbase_api.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase
2025-05-31T16:08:06,934   creating build/bdist.linux-armv7l/wheel/tests/ncbi
2025-05-31T16:08:06,935   copying build/lib/tests/ncbi/test_entreze_api.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi
2025-05-31T16:08:06,938   copying build/lib/tests/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi
2025-05-31T16:08:06,941   creating build/bdist.linux-armv7l/wheel/tests/impact_factor
2025-05-31T16:08:06,943   copying build/lib/tests/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor
2025-05-31T16:08:06,945   copying build/lib/tests/impact_factor/test_get_impact_factor.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor
2025-05-31T16:08:06,947   running install_egg_info
2025-05-31T16:08:06,985   Copying pub_worm.egg-info to build/bdist.linux-armv7l/wheel/./pub_worm-0.3.9-py3.11.egg-info
2025-05-31T16:08:06,997   running install_scripts
2025-05-31T16:08:07,008   creating build/bdist.linux-armv7l/wheel/pub_worm-0.3.9.dist-info/WHEEL
2025-05-31T16:08:07,011   creating '/tmp/pip-wheel-y7gf2qco/pub_worm-0.3.9-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-05-31T16:08:07,014   adding 'pub_worm/__init__.py'
2025-05-31T16:08:07,017   adding 'pub_worm/biorxiv/__init__.py'
2025-05-31T16:08:07,020   adding 'pub_worm/biorxiv/biorxiv_api.py'
2025-05-31T16:08:07,022   adding 'pub_worm/ensembl/__init__.py'
2025-05-31T16:08:07,024   adding 'pub_worm/ensembl/ensembl_api.py'
2025-05-31T16:08:07,027   adding 'pub_worm/impact_factor/__init__.py'
2025-05-31T16:08:07,029   adding 'pub_worm/impact_factor/impact_factor_lookup.py'
2025-05-31T16:08:07,234   adding 'pub_worm/impact_factor/data/2022_JCR_IF.csv'
2025-05-31T16:08:07,244   adding 'pub_worm/ncbi/__init__.py'
2025-05-31T16:08:07,247   adding 'pub_worm/ncbi/entreze_api.py'
2025-05-31T16:08:07,249   adding 'pub_worm/orcid/__init__.py'
2025-05-31T16:08:07,250   adding 'pub_worm/orcid/orcid_api.py'
2025-05-31T16:08:07,252   adding 'pub_worm/wormbase/__init__.py'
2025-05-31T16:08:07,253   adding 'pub_worm/wormbase/to_csv_helpers.py'
2025-05-31T16:08:07,255   adding 'pub_worm/wormbase/wormbase_api.py'
2025-05-31T16:08:07,257   adding 'pub_worm/wormbase/wormbase_util.py'
2025-05-31T16:08:07,259   adding 'pub_worm/wormbase/data/wormbase_field_gene.json'
2025-05-31T16:08:07,260   adding 'pub_worm/wormbase/data/wormbase_field_paper.json'
2025-05-31T16:08:07,261   adding 'pub_worm/wormbase/data/wormbase_widget_gene.json'
2025-05-31T16:08:07,264   adding 'tests/__init__.py'
2025-05-31T16:08:07,266   adding 'tests/impact_factor/__init__.py'
2025-05-31T16:08:07,267   adding 'tests/impact_factor/test_get_impact_factor.py'
2025-05-31T16:08:07,268   adding 'tests/ncbi/__init__.py'
2025-05-31T16:08:07,270   adding 'tests/ncbi/test_entreze_api.py'
2025-05-31T16:08:07,272   adding 'tests/orcid/__init__.py'
2025-05-31T16:08:07,273   adding 'tests/orcid/test_orcid_api.py'
2025-05-31T16:08:07,275   adding 'tests/wormbase/__init__.py'
2025-05-31T16:08:07,277   adding 'tests/wormbase/test_wormbase_api.py'
2025-05-31T16:08:07,278   adding 'pub_worm-0.3.9.dist-info/METADATA'
2025-05-31T16:08:07,279   adding 'pub_worm-0.3.9.dist-info/WHEEL'
2025-05-31T16:08:07,280   adding 'pub_worm-0.3.9.dist-info/top_level.txt'
2025-05-31T16:08:07,282   adding 'pub_worm-0.3.9.dist-info/RECORD'
2025-05-31T16:08:07,289   removing build/bdist.linux-armv7l/wheel
2025-05-31T16:08:07,305   error: [Errno 39] Directory not empty: 'data'
2025-05-31T16:08:07,415   ERROR: python setup.py bdist_wheel exited with 1
2025-05-31T16:08:07,429   [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c '
2025-05-31T16:08:07,429   exec(compile('"'"''"'"''"'"'
2025-05-31T16:08:07,429   # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
2025-05-31T16:08:07,429   #
2025-05-31T16:08:07,429   # - It imports setuptools before invoking setup.py, to enable projects that directly
2025-05-31T16:08:07,429   #   import from `distutils.core` to work with newer packaging standards.
2025-05-31T16:08:07,429   # - It provides a clear error message when setuptools is not installed.
2025-05-31T16:08:07,429   # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
2025-05-31T16:08:07,429   #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
2025-05-31T16:08:07,429   #     manifest_maker: standard file '"'"'-c'"'"' not found".
2025-05-31T16:08:07,429   # - It generates a shim setup.py, for handling setup.cfg-only projects.
2025-05-31T16:08:07,429   import os, sys, tokenize, traceback
2025-05-31T16:08:07,429   
2025-05-31T16:08:07,429   try:
2025-05-31T16:08:07,429       import setuptools
2025-05-31T16:08:07,429   except ImportError:
2025-05-31T16:08:07,429       print(
2025-05-31T16:08:07,429           "ERROR: Can not execute `setup.py` since setuptools failed to import in "
2025-05-31T16:08:07,429           "the build environment with exception:",
2025-05-31T16:08:07,429           file=sys.stderr,
2025-05-31T16:08:07,429       )
2025-05-31T16:08:07,429       traceback.print_exc()
2025-05-31T16:08:07,429       sys.exit(1)
2025-05-31T16:08:07,429   
2025-05-31T16:08:07,429   __file__ = %r
2025-05-31T16:08:07,429   sys.argv[0] = __file__
2025-05-31T16:08:07,429   
2025-05-31T16:08:07,429   if os.path.exists(__file__):
2025-05-31T16:08:07,429       filename = __file__
2025-05-31T16:08:07,429       with tokenize.open(__file__) as f:
2025-05-31T16:08:07,429           setup_py_code = f.read()
2025-05-31T16:08:07,429   else:
2025-05-31T16:08:07,429       filename = "<auto-generated setuptools caller>"
2025-05-31T16:08:07,429       setup_py_code = "from setuptools import setup; setup()"
2025-05-31T16:08:07,429   
2025-05-31T16:08:07,429   exec(compile(setup_py_code, filename, "exec"))
2025-05-31T16:08:07,429   '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-1jziwemt/pub-worm_311d590683194e29ab20ff3cbcb82004/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' bdist_wheel -d /tmp/pip-wheel-y7gf2qco[/]
2025-05-31T16:08:07,429   [bold magenta]cwd[/]: /tmp/pip-wheel-1jziwemt/pub-worm_311d590683194e29ab20ff3cbcb82004/
2025-05-31T16:08:07,430   Building wheel for pub-worm (setup.py): finished with status 'error'
2025-05-31T16:08:07,431   ERROR: Failed building wheel for pub-worm
2025-05-31T16:08:07,433   Running setup.py clean for pub-worm
2025-05-31T16:08:07,434   Running command python setup.py clean
2025-05-31T16:08:08,322   running clean
2025-05-31T16:08:08,376   removing 'build/lib' (and everything under it)
2025-05-31T16:08:08,388   removing 'build/bdist.linux-armv7l' (and everything under it)
2025-05-31T16:08:08,397   'build/scripts-3.11' does not exist -- can't clean it
2025-05-31T16:08:08,397   removing 'build'
2025-05-31T16:08:08,503 Failed to build pub-worm
2025-05-31T16:08:08,504 ERROR: Failed to build one or more wheels
2025-05-31T16:08:08,506 Exception information:
2025-05-31T16:08:08,506 Traceback (most recent call last):
2025-05-31T16:08:08,506   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 107, in _run_wrapper
2025-05-31T16:08:08,506     status = _inner_run()
2025-05-31T16:08:08,506              ^^^^^^^^^^^^
2025-05-31T16:08:08,506   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 98, in _inner_run
2025-05-31T16:08:08,506     return self.run(options, args)
2025-05-31T16:08:08,506            ^^^^^^^^^^^^^^^^^^^^^^^
2025-05-31T16:08:08,506   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 71, in wrapper
2025-05-31T16:08:08,506     return func(self, options, args)
2025-05-31T16:08:08,506            ^^^^^^^^^^^^^^^^^^^^^^^^^
2025-05-31T16:08:08,506   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 179, in run
2025-05-31T16:08:08,506     raise CommandError("Failed to build one or more wheels")
2025-05-31T16:08:08,506 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2025-05-31T16:08:08,509 Removed build tracker: '/tmp/pip-build-tracker-akxshrvn'