2025-06-11T09:08:39,764 Created temporary directory: /tmp/pip-build-tracker-7ihthd2y 2025-06-11T09:08:39,765 Initialized build tracking at /tmp/pip-build-tracker-7ihthd2y 2025-06-11T09:08:39,765 Created build tracker: /tmp/pip-build-tracker-7ihthd2y 2025-06-11T09:08:39,766 Entered build tracker: /tmp/pip-build-tracker-7ihthd2y 2025-06-11T09:08:39,767 Created temporary directory: /tmp/pip-wheel-a9wu6hv6 2025-06-11T09:08:39,771 Created temporary directory: /tmp/pip-ephem-wheel-cache-m8kom420 2025-06-11T09:08:39,820 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-11T09:08:39,823 2 location(s) to search for versions of pub-worm: 2025-06-11T09:08:39,823 * https://pypi.org/simple/pub-worm/ 2025-06-11T09:08:39,823 * https://www.piwheels.org/simple/pub-worm/ 2025-06-11T09:08:39,824 Fetching project page and analyzing links: https://pypi.org/simple/pub-worm/ 2025-06-11T09:08:39,824 Getting page https://pypi.org/simple/pub-worm/ 2025-06-11T09:08:39,826 Found index url https://pypi.org/simple/ 2025-06-11T09:08:39,979 Fetched page https://pypi.org/simple/pub-worm/ as application/vnd.pypi.simple.v1+json 2025-06-11T09:08:39,983 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 2025-06-11T09:08:39,984 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 2025-06-11T09:08:39,985 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 2025-06-11T09:08:39,985 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 2025-06-11T09:08:39,986 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 2025-06-11T09:08:39,987 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 2025-06-11T09:08:39,988 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 2025-06-11T09:08:39,988 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 2025-06-11T09:08:39,989 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 2025-06-11T09:08:39,990 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 2025-06-11T09:08:39,990 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 2025-06-11T09:08:39,991 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 2025-06-11T09:08:39,992 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 2025-06-11T09:08:39,992 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 2025-06-11T09:08:39,993 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 2025-06-11T09:08:39,994 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 2025-06-11T09:08:39,995 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 2025-06-11T09:08:39,995 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 2025-06-11T09:08:39,996 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 2025-06-11T09:08:39,996 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 2025-06-11T09:08:39,997 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 2025-06-11T09:08:39,998 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 2025-06-11T09:08:39,998 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 2025-06-11T09:08:39,999 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 2025-06-11T09:08:40,000 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 2025-06-11T09:08:40,000 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 2025-06-11T09:08:40,001 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 2025-06-11T09:08:40,002 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 2025-06-11T09:08:40,002 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 2025-06-11T09:08:40,003 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 2025-06-11T09:08:40,004 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 2025-06-11T09:08:40,004 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 2025-06-11T09:08:40,005 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 2025-06-11T09:08:40,006 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 2025-06-11T09:08:40,007 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 2025-06-11T09:08:40,007 Fetching project page and analyzing links: https://www.piwheels.org/simple/pub-worm/ 2025-06-11T09:08:40,008 Getting page https://www.piwheels.org/simple/pub-worm/ 2025-06-11T09:08:40,009 Found index url https://www.piwheels.org/simple/ 2025-06-11T09:08:40,177 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/ 2025-06-11T09:08:40,840 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/ 2025-06-11T09:08:41,996 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/ 2025-06-11T09:08:44,157 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/ 2025-06-11T09:08:48,314 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/ 2025-06-11T09:08:48,471 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 2025-06-11T09:08:48,472 Skipping link: not a file: https://www.piwheels.org/simple/pub-worm/ 2025-06-11T09:08:48,473 Skipping link: not a file: https://pypi.org/simple/pub-worm/ 2025-06-11T09:08:48,496 Given no hashes to check 1 links for project 'pub-worm': discarding no candidates 2025-06-11T09:08:48,499 Collecting pub-worm==0.3.11 2025-06-11T09:08:48,501 Created temporary directory: /tmp/pip-unpack-6xkh0g5o 2025-06-11T09:08:48,731 Downloading pub_worm-0.3.11.tar.gz (397 kB) 2025-06-11T09:08:48,962 Added pub-worm==0.3.11 from https://files.pythonhosted.org/packages/c9/7c/8ac6631b74eb781a27c88eed56ff3e592945f74bb73bc525319702534162/pub_worm-0.3.11.tar.gz to build tracker '/tmp/pip-build-tracker-7ihthd2y' 2025-06-11T09:08:48,965 Running setup.py (path:/tmp/pip-wheel-a9wu6hv6/pub-worm_dff6297b1fda48f681df1399c27f3333/setup.py) egg_info for package pub-worm 2025-06-11T09:08:48,966 Created temporary directory: /tmp/pip-pip-egg-info-63ampyjs 2025-06-11T09:08:48,966 Preparing metadata (setup.py): started 2025-06-11T09:08:48,968 Running command python setup.py egg_info 2025-06-11T09:08:49,932 running egg_info 2025-06-11T09:08:49,960 creating /tmp/pip-pip-egg-info-63ampyjs/pub_worm.egg-info 2025-06-11T09:08:49,961 writing /tmp/pip-pip-egg-info-63ampyjs/pub_worm.egg-info/PKG-INFO 2025-06-11T09:08:49,965 writing dependency_links to /tmp/pip-pip-egg-info-63ampyjs/pub_worm.egg-info/dependency_links.txt 2025-06-11T09:08:49,967 writing requirements to /tmp/pip-pip-egg-info-63ampyjs/pub_worm.egg-info/requires.txt 2025-06-11T09:08:49,968 writing top-level names to /tmp/pip-pip-egg-info-63ampyjs/pub_worm.egg-info/top_level.txt 2025-06-11T09:08:49,969 writing manifest file '/tmp/pip-pip-egg-info-63ampyjs/pub_worm.egg-info/SOURCES.txt' 2025-06-11T09:08:50,069 reading manifest file '/tmp/pip-pip-egg-info-63ampyjs/pub_worm.egg-info/SOURCES.txt' 2025-06-11T09:08:50,070 reading manifest template 'MANIFEST.in' 2025-06-11T09:08:50,072 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json' 2025-06-11T09:08:50,073 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json' 2025-06-11T09:08:50,073 warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json' 2025-06-11T09:08:50,076 writing manifest file '/tmp/pip-pip-egg-info-63ampyjs/pub_worm.egg-info/SOURCES.txt' 2025-06-11T09:08:50,187 Preparing metadata (setup.py): finished with status 'done' 2025-06-11T09:08:50,191 Source in /tmp/pip-wheel-a9wu6hv6/pub-worm_dff6297b1fda48f681df1399c27f3333 has version 0.3.11, which satisfies requirement pub-worm==0.3.11 from https://files.pythonhosted.org/packages/c9/7c/8ac6631b74eb781a27c88eed56ff3e592945f74bb73bc525319702534162/pub_worm-0.3.11.tar.gz 2025-06-11T09:08:50,192 Removed pub-worm==0.3.11 from https://files.pythonhosted.org/packages/c9/7c/8ac6631b74eb781a27c88eed56ff3e592945f74bb73bc525319702534162/pub_worm-0.3.11.tar.gz from build tracker '/tmp/pip-build-tracker-7ihthd2y' 2025-06-11T09:08:50,199 Created temporary directory: /tmp/pip-unpack-0b1ee1rm 2025-06-11T09:08:50,200 Created temporary directory: /tmp/pip-unpack-ayqokfcf 2025-06-11T09:08:50,200 Building wheels for collected packages: pub-worm 2025-06-11T09:08:50,204 Created temporary directory: /tmp/pip-wheel-skkuffeb 2025-06-11T09:08:50,205 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 2025-06-11T09:08:50,206 Building wheel for pub-worm (setup.py): started 2025-06-11T09:08:50,207 Destination directory: /tmp/pip-wheel-skkuffeb 2025-06-11T09:08:50,208 Running command python setup.py bdist_wheel 2025-06-11T09:08:51,053 running bdist_wheel 2025-06-11T09:08:51,187 running build 2025-06-11T09:08:51,188 running build_py 2025-06-11T09:08:51,218 creating build/lib/pub_worm 2025-06-11T09:08:51,221 copying pub_worm/__init__.py -> build/lib/pub_worm 2025-06-11T09:08:51,223 creating build/lib/tests 2025-06-11T09:08:51,224 copying tests/__init__.py -> build/lib/tests 2025-06-11T09:08:51,226 creating build/lib/pub_worm/impact_factor 2025-06-11T09:08:51,227 copying pub_worm/impact_factor/impact_factor_lookup.py -> build/lib/pub_worm/impact_factor 2025-06-11T09:08:51,229 copying pub_worm/impact_factor/__init__.py -> build/lib/pub_worm/impact_factor 2025-06-11T09:08:51,232 creating build/lib/pub_worm/orcid 2025-06-11T09:08:51,233 copying pub_worm/orcid/orcid_api.py -> build/lib/pub_worm/orcid 2025-06-11T09:08:51,235 copying pub_worm/orcid/__init__.py -> build/lib/pub_worm/orcid 2025-06-11T09:08:51,237 creating build/lib/pub_worm/ensembl 2025-06-11T09:08:51,238 copying pub_worm/ensembl/ensembl_api.py -> build/lib/pub_worm/ensembl 2025-06-11T09:08:51,241 copying pub_worm/ensembl/__init__.py -> build/lib/pub_worm/ensembl 2025-06-11T09:08:51,243 creating build/lib/pub_worm/wormbase 2025-06-11T09:08:51,244 copying pub_worm/wormbase/wormbase_util.py -> build/lib/pub_worm/wormbase 2025-06-11T09:08:51,246 copying pub_worm/wormbase/__init__.py -> build/lib/pub_worm/wormbase 2025-06-11T09:08:51,248 copying pub_worm/wormbase/to_csv_helpers.py -> build/lib/pub_worm/wormbase 2025-06-11T09:08:51,250 copying pub_worm/wormbase/wormbase_api.py -> build/lib/pub_worm/wormbase 2025-06-11T09:08:51,253 creating build/lib/pub_worm/biorxiv 2025-06-11T09:08:51,253 copying pub_worm/biorxiv/biorxiv_api.py -> build/lib/pub_worm/biorxiv 2025-06-11T09:08:51,256 copying pub_worm/biorxiv/__init__.py -> build/lib/pub_worm/biorxiv 2025-06-11T09:08:51,258 creating build/lib/pub_worm/ncbi 2025-06-11T09:08:51,259 copying pub_worm/ncbi/__init__.py -> build/lib/pub_worm/ncbi 2025-06-11T09:08:51,261 copying pub_worm/ncbi/entreze_api.py -> build/lib/pub_worm/ncbi 2025-06-11T09:08:51,264 creating build/lib/tests/impact_factor 2025-06-11T09:08:51,265 copying tests/impact_factor/__init__.py -> build/lib/tests/impact_factor 2025-06-11T09:08:51,266 copying tests/impact_factor/test_get_impact_factor.py -> build/lib/tests/impact_factor 2025-06-11T09:08:51,269 creating build/lib/tests/orcid 2025-06-11T09:08:51,270 copying tests/orcid/test_orcid_api.py -> build/lib/tests/orcid 2025-06-11T09:08:51,272 copying tests/orcid/__init__.py -> build/lib/tests/orcid 2025-06-11T09:08:51,274 creating build/lib/tests/wormbase 2025-06-11T09:08:51,275 copying tests/wormbase/__init__.py -> build/lib/tests/wormbase 2025-06-11T09:08:51,276 copying tests/wormbase/test_wormbase_api.py -> build/lib/tests/wormbase 2025-06-11T09:08:51,278 creating build/lib/tests/ncbi 2025-06-11T09:08:51,279 copying tests/ncbi/__init__.py -> build/lib/tests/ncbi 2025-06-11T09:08:51,281 copying tests/ncbi/test_entreze_api.py -> build/lib/tests/ncbi 2025-06-11T09:08:51,283 running egg_info 2025-06-11T09:08:51,312 writing pub_worm.egg-info/PKG-INFO 2025-06-11T09:08:51,315 writing dependency_links to pub_worm.egg-info/dependency_links.txt 2025-06-11T09:08:51,317 writing requirements to pub_worm.egg-info/requires.txt 2025-06-11T09:08:51,318 writing top-level names to pub_worm.egg-info/top_level.txt 2025-06-11T09:08:51,358 reading manifest file 'pub_worm.egg-info/SOURCES.txt' 2025-06-11T09:08:51,361 reading manifest template 'MANIFEST.in' 2025-06-11T09:08:51,363 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json' 2025-06-11T09:08:51,363 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json' 2025-06-11T09:08:51,364 warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json' 2025-06-11T09:08:51,367 writing manifest file 'pub_worm.egg-info/SOURCES.txt' 2025-06-11T09:08:51,370 /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. 2025-06-11T09:08:51,370 !! 2025-06-11T09:08:51,371 ******************************************************************************** 2025-06-11T09:08:51,372 ############################ 2025-06-11T09:08:51,372 # Package would be ignored # 2025-06-11T09:08:51,373 ############################ 2025-06-11T09:08:51,373 Python recognizes 'pub_worm.impact_factor.data' as an importable package[^1], 2025-06-11T09:08:51,374 but it is absent from setuptools' `packages` configuration. 2025-06-11T09:08:51,375 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T09:08:51,375 package, please make sure that 'pub_worm.impact_factor.data' is explicitly added 2025-06-11T09:08:51,376 to the `packages` configuration field. 2025-06-11T09:08:51,377 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T09:08:51,378 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T09:08:51,378 instead of `find_packages(...)`/`find:`). 2025-06-11T09:08:51,379 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T09:08:51,381 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T09:08:51,382 If you don't want 'pub_worm.impact_factor.data' to be distributed and are 2025-06-11T09:08:51,382 already explicitly excluding 'pub_worm.impact_factor.data' via 2025-06-11T09:08:51,383 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T09:08:51,383 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T09:08:51,384 combination with a more fine grained `package-data` configuration. 2025-06-11T09:08:51,384 You can read more about "package data files" on setuptools documentation page: 2025-06-11T09:08:51,385 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T09:08:51,387 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T09:08:51,395 even if it does not contain any `.py` files. 2025-06-11T09:08:51,399 On the other hand, currently there is no concept of package data 2025-06-11T09:08:51,401 directory, all directories are treated like packages. 2025-06-11T09:08:51,402 ******************************************************************************** 2025-06-11T09:08:51,403 !! 2025-06-11T09:08:51,403 check.warn(importable) 2025-06-11T09:08:51,404 /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. 2025-06-11T09:08:51,404 !! 2025-06-11T09:08:51,405 ******************************************************************************** 2025-06-11T09:08:51,406 ############################ 2025-06-11T09:08:51,406 # Package would be ignored # 2025-06-11T09:08:51,407 ############################ 2025-06-11T09:08:51,407 Python recognizes 'pub_worm.wormbase.data' as an importable package[^1], 2025-06-11T09:08:51,408 but it is absent from setuptools' `packages` configuration. 2025-06-11T09:08:51,409 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T09:08:51,409 package, please make sure that 'pub_worm.wormbase.data' is explicitly added 2025-06-11T09:08:51,410 to the `packages` configuration field. 2025-06-11T09:08:51,411 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T09:08:51,411 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T09:08:51,412 instead of `find_packages(...)`/`find:`). 2025-06-11T09:08:51,413 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T09:08:51,414 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T09:08:51,415 If you don't want 'pub_worm.wormbase.data' to be distributed and are 2025-06-11T09:08:51,415 already explicitly excluding 'pub_worm.wormbase.data' via 2025-06-11T09:08:51,416 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T09:08:51,417 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T09:08:51,417 combination with a more fine grained `package-data` configuration. 2025-06-11T09:08:51,418 You can read more about "package data files" on setuptools documentation page: 2025-06-11T09:08:51,419 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T09:08:51,421 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T09:08:51,422 even if it does not contain any `.py` files. 2025-06-11T09:08:51,422 On the other hand, currently there is no concept of package data 2025-06-11T09:08:51,423 directory, all directories are treated like packages. 2025-06-11T09:08:51,423 ******************************************************************************** 2025-06-11T09:08:51,425 !! 2025-06-11T09:08:51,425 check.warn(importable) 2025-06-11T09:08:51,426 creating build/lib/pub_worm/impact_factor/data 2025-06-11T09:08:51,426 copying pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/lib/pub_worm/impact_factor/data 2025-06-11T09:08:51,427 creating build/lib/pub_worm/wormbase/data 2025-06-11T09:08:51,427 copying pub_worm/wormbase/data/wormbase_field_gene.json -> build/lib/pub_worm/wormbase/data 2025-06-11T09:08:51,428 copying pub_worm/wormbase/data/wormbase_field_paper.json -> build/lib/pub_worm/wormbase/data 2025-06-11T09:08:51,428 copying pub_worm/wormbase/data/wormbase_widget_gene.json -> build/lib/pub_worm/wormbase/data 2025-06-11T09:08:51,448 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-11T09:08:51,448 !! 2025-06-11T09:08:51,449 ******************************************************************************** 2025-06-11T09:08:51,450 Please avoid running ``setup.py`` directly. 2025-06-11T09:08:51,450 Instead, use pypa/build, pypa/installer or other 2025-06-11T09:08:51,451 standards-based tools. 2025-06-11T09:08:51,452 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-11T09:08:51,452 or your builds will no longer be supported. 2025-06-11T09:08:51,453 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-11T09:08:51,454 ******************************************************************************** 2025-06-11T09:08:51,455 !! 2025-06-11T09:08:51,455 self.initialize_options() 2025-06-11T09:08:51,476 installing to build/bdist.linux-armv7l/wheel 2025-06-11T09:08:51,476 running install 2025-06-11T09:08:51,501 running install_lib 2025-06-11T09:08:51,529 creating build/bdist.linux-armv7l/wheel 2025-06-11T09:08:51,531 creating build/bdist.linux-armv7l/wheel/pub_worm 2025-06-11T09:08:51,533 creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor 2025-06-11T09:08:51,534 copying build/lib/pub_worm/impact_factor/impact_factor_lookup.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor 2025-06-11T09:08:51,536 copying build/lib/pub_worm/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor 2025-06-11T09:08:51,539 creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor/data 2025-06-11T09:08:51,540 copying build/lib/pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor/data 2025-06-11T09:08:51,566 creating build/bdist.linux-armv7l/wheel/pub_worm/orcid 2025-06-11T09:08:51,567 copying build/lib/pub_worm/orcid/orcid_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid 2025-06-11T09:08:51,569 copying build/lib/pub_worm/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid 2025-06-11T09:08:51,571 creating build/bdist.linux-armv7l/wheel/pub_worm/ensembl 2025-06-11T09:08:51,572 copying build/lib/pub_worm/ensembl/ensembl_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl 2025-06-11T09:08:51,574 copying build/lib/pub_worm/ensembl/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl 2025-06-11T09:08:51,576 creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase 2025-06-11T09:08:51,577 copying build/lib/pub_worm/wormbase/wormbase_util.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-11T09:08:51,580 copying build/lib/pub_worm/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-11T09:08:51,581 copying build/lib/pub_worm/wormbase/to_csv_helpers.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-11T09:08:51,584 creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase/data 2025-06-11T09:08:51,585 copying build/lib/pub_worm/wormbase/data/wormbase_widget_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data 2025-06-11T09:08:51,587 copying build/lib/pub_worm/wormbase/data/wormbase_field_paper.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data 2025-06-11T09:08:51,589 copying build/lib/pub_worm/wormbase/data/wormbase_field_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data 2025-06-11T09:08:51,591 copying build/lib/pub_worm/wormbase/wormbase_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-11T09:08:51,594 creating build/bdist.linux-armv7l/wheel/pub_worm/biorxiv 2025-06-11T09:08:51,595 copying build/lib/pub_worm/biorxiv/biorxiv_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv 2025-06-11T09:08:51,597 copying build/lib/pub_worm/biorxiv/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv 2025-06-11T09:08:51,598 copying build/lib/pub_worm/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm 2025-06-11T09:08:51,600 creating build/bdist.linux-armv7l/wheel/pub_worm/ncbi 2025-06-11T09:08:51,601 copying build/lib/pub_worm/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi 2025-06-11T09:08:51,603 copying build/lib/pub_worm/ncbi/entreze_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi 2025-06-11T09:08:51,606 creating build/bdist.linux-armv7l/wheel/tests 2025-06-11T09:08:51,608 creating build/bdist.linux-armv7l/wheel/tests/impact_factor 2025-06-11T09:08:51,609 copying build/lib/tests/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor 2025-06-11T09:08:51,610 copying build/lib/tests/impact_factor/test_get_impact_factor.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor 2025-06-11T09:08:51,613 creating build/bdist.linux-armv7l/wheel/tests/orcid 2025-06-11T09:08:51,614 copying build/lib/tests/orcid/test_orcid_api.py -> build/bdist.linux-armv7l/wheel/./tests/orcid 2025-06-11T09:08:51,616 copying build/lib/tests/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/orcid 2025-06-11T09:08:51,618 creating build/bdist.linux-armv7l/wheel/tests/wormbase 2025-06-11T09:08:51,619 copying build/lib/tests/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase 2025-06-11T09:08:51,620 copying build/lib/tests/wormbase/test_wormbase_api.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase 2025-06-11T09:08:51,622 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2025-06-11T09:08:51,625 creating build/bdist.linux-armv7l/wheel/tests/ncbi 2025-06-11T09:08:51,626 copying build/lib/tests/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi 2025-06-11T09:08:51,627 copying build/lib/tests/ncbi/test_entreze_api.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi 2025-06-11T09:08:51,630 running install_egg_info 2025-06-11T09:08:51,665 Copying pub_worm.egg-info to build/bdist.linux-armv7l/wheel/./pub_worm-0.3.11-py3.11.egg-info 2025-06-11T09:08:51,677 running install_scripts 2025-06-11T09:08:51,687 creating build/bdist.linux-armv7l/wheel/pub_worm-0.3.11.dist-info/WHEEL 2025-06-11T09:08:51,689 creating '/tmp/pip-wheel-skkuffeb/pub_worm-0.3.11-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-11T09:08:51,691 adding 'pub_worm/__init__.py' 2025-06-11T09:08:51,693 adding 'pub_worm/biorxiv/__init__.py' 2025-06-11T09:08:51,695 adding 'pub_worm/biorxiv/biorxiv_api.py' 2025-06-11T09:08:51,696 adding 'pub_worm/ensembl/__init__.py' 2025-06-11T09:08:51,698 adding 'pub_worm/ensembl/ensembl_api.py' 2025-06-11T09:08:51,700 adding 'pub_worm/impact_factor/__init__.py' 2025-06-11T09:08:51,701 adding 'pub_worm/impact_factor/impact_factor_lookup.py' 2025-06-11T09:08:51,869 adding 'pub_worm/impact_factor/data/2022_JCR_IF.csv' 2025-06-11T09:08:51,879 adding 'pub_worm/ncbi/__init__.py' 2025-06-11T09:08:51,882 adding 'pub_worm/ncbi/entreze_api.py' 2025-06-11T09:08:51,884 adding 'pub_worm/orcid/__init__.py' 2025-06-11T09:08:51,885 adding 'pub_worm/orcid/orcid_api.py' 2025-06-11T09:08:51,887 adding 'pub_worm/wormbase/__init__.py' 2025-06-11T09:08:51,888 adding 'pub_worm/wormbase/to_csv_helpers.py' 2025-06-11T09:08:51,890 adding 'pub_worm/wormbase/wormbase_api.py' 2025-06-11T09:08:51,892 adding 'pub_worm/wormbase/wormbase_util.py' 2025-06-11T09:08:51,894 adding 'pub_worm/wormbase/data/wormbase_field_gene.json' 2025-06-11T09:08:51,895 adding 'pub_worm/wormbase/data/wormbase_field_paper.json' 2025-06-11T09:08:51,896 adding 'pub_worm/wormbase/data/wormbase_widget_gene.json' 2025-06-11T09:08:51,898 adding 'tests/__init__.py' 2025-06-11T09:08:51,900 adding 'tests/impact_factor/__init__.py' 2025-06-11T09:08:51,901 adding 'tests/impact_factor/test_get_impact_factor.py' 2025-06-11T09:08:51,902 adding 'tests/ncbi/__init__.py' 2025-06-11T09:08:51,904 adding 'tests/ncbi/test_entreze_api.py' 2025-06-11T09:08:51,905 adding 'tests/orcid/__init__.py' 2025-06-11T09:08:51,906 adding 'tests/orcid/test_orcid_api.py' 2025-06-11T09:08:51,908 adding 'tests/wormbase/__init__.py' 2025-06-11T09:08:51,909 adding 'tests/wormbase/test_wormbase_api.py' 2025-06-11T09:08:51,910 adding 'pub_worm-0.3.11.dist-info/METADATA' 2025-06-11T09:08:51,911 adding 'pub_worm-0.3.11.dist-info/WHEEL' 2025-06-11T09:08:51,912 adding 'pub_worm-0.3.11.dist-info/top_level.txt' 2025-06-11T09:08:51,913 adding 'pub_worm-0.3.11.dist-info/RECORD' 2025-06-11T09:08:51,920 removing build/bdist.linux-armv7l/wheel 2025-06-11T09:08:52,047 Building wheel for pub-worm (setup.py): finished with status 'done' 2025-06-11T09:08:52,054 Created wheel for pub-worm: filename=pub_worm-0.3.11-py3-none-any.whl size=403505 sha256=3399bd8328d48c0469b14cd47a8ea66a6af6aba60d32f7fabe3459450c40a3a3 2025-06-11T09:08:52,055 Stored in directory: /tmp/pip-ephem-wheel-cache-m8kom420/wheels/02/b2/79/7f9e4e64e883ad6cbfed4d871ecb3ad019d925dd00921755e6 2025-06-11T09:08:52,067 Successfully built pub-worm 2025-06-11T09:08:52,082 Removed build tracker: '/tmp/pip-build-tracker-7ihthd2y'