2025-06-11T09:47:52,411 Created temporary directory: /tmp/pip-build-tracker-vjai9zzx 2025-06-11T09:47:52,412 Initialized build tracking at /tmp/pip-build-tracker-vjai9zzx 2025-06-11T09:47:52,413 Created build tracker: /tmp/pip-build-tracker-vjai9zzx 2025-06-11T09:47:52,413 Entered build tracker: /tmp/pip-build-tracker-vjai9zzx 2025-06-11T09:47:52,414 Created temporary directory: /tmp/pip-wheel-1qnkz_13 2025-06-11T09:47:52,419 Created temporary directory: /tmp/pip-ephem-wheel-cache-n1fd8gxf 2025-06-11T09:47:52,467 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-11T09:47:52,470 2 location(s) to search for versions of pub-worm: 2025-06-11T09:47:52,470 * https://pypi.org/simple/pub-worm/ 2025-06-11T09:47:52,470 * https://www.piwheels.org/simple/pub-worm/ 2025-06-11T09:47:52,470 Fetching project page and analyzing links: https://pypi.org/simple/pub-worm/ 2025-06-11T09:47:52,471 Getting page https://pypi.org/simple/pub-worm/ 2025-06-11T09:47:52,473 Found index url https://pypi.org/simple/ 2025-06-11T09:47:52,626 Fetched page https://pypi.org/simple/pub-worm/ as application/vnd.pypi.simple.v1+json 2025-06-11T09:47:52,630 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 2025-06-11T09:47:52,631 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 2025-06-11T09:47:52,632 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 2025-06-11T09:47:52,632 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 2025-06-11T09:47:52,633 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 2025-06-11T09:47:52,634 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 2025-06-11T09:47:52,635 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 2025-06-11T09:47:52,635 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 2025-06-11T09:47:52,636 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 2025-06-11T09:47:52,637 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 2025-06-11T09:47:52,638 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 2025-06-11T09:47:52,639 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 2025-06-11T09:47:52,639 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 2025-06-11T09:47:52,640 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 2025-06-11T09:47:52,641 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 2025-06-11T09:47:52,642 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 2025-06-11T09:47:52,642 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 2025-06-11T09:47:52,643 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 2025-06-11T09:47:52,644 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 2025-06-11T09:47:52,644 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 2025-06-11T09:47:52,645 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 2025-06-11T09:47:52,645 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 2025-06-11T09:47:52,646 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 2025-06-11T09:47:52,647 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 2025-06-11T09:47:52,648 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 2025-06-11T09:47:52,648 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 2025-06-11T09:47:52,649 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 2025-06-11T09:47:52,650 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 2025-06-11T09:47:52,651 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 2025-06-11T09:47:52,651 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 2025-06-11T09:47:52,652 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 2025-06-11T09:47:52,653 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 2025-06-11T09:47:52,654 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 2025-06-11T09:47:52,655 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 2025-06-11T09:47:52,655 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 2025-06-11T09:47:52,656 Fetching project page and analyzing links: https://www.piwheels.org/simple/pub-worm/ 2025-06-11T09:47:52,657 Getting page https://www.piwheels.org/simple/pub-worm/ 2025-06-11T09:47:52,658 Found index url https://www.piwheels.org/simple/ 2025-06-11T09:47:52,815 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/ 2025-06-11T09:47:53,473 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/ 2025-06-11T09:47:54,632 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/ 2025-06-11T09:47:56,792 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/ 2025-06-11T09:48:00,956 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/ 2025-06-11T09:48:01,118 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 2025-06-11T09:48:01,120 Skipping link: not a file: https://www.piwheels.org/simple/pub-worm/ 2025-06-11T09:48:01,121 Skipping link: not a file: https://pypi.org/simple/pub-worm/ 2025-06-11T09:48:01,142 Given no hashes to check 1 links for project 'pub-worm': discarding no candidates 2025-06-11T09:48:01,144 Collecting pub-worm==0.3.13 2025-06-11T09:48:01,146 Created temporary directory: /tmp/pip-unpack-ny99dpqh 2025-06-11T09:48:01,376 Downloading pub_worm-0.3.13.tar.gz (397 kB) 2025-06-11T09:48:01,603 Added pub-worm==0.3.13 from https://files.pythonhosted.org/packages/49/9a/b32f9d8d361b31f47f630f14ef510ade5abad9b93fc6c441686fb96d9fc6/pub_worm-0.3.13.tar.gz to build tracker '/tmp/pip-build-tracker-vjai9zzx' 2025-06-11T09:48:01,605 Running setup.py (path:/tmp/pip-wheel-1qnkz_13/pub-worm_03293ba6ea2643f88594ff48b8429a78/setup.py) egg_info for package pub-worm 2025-06-11T09:48:01,606 Created temporary directory: /tmp/pip-pip-egg-info-fp78j8qo 2025-06-11T09:48:01,607 Preparing metadata (setup.py): started 2025-06-11T09:48:01,608 Running command python setup.py egg_info 2025-06-11T09:48:02,491 running egg_info 2025-06-11T09:48:02,519 creating /tmp/pip-pip-egg-info-fp78j8qo/pub_worm.egg-info 2025-06-11T09:48:02,521 writing /tmp/pip-pip-egg-info-fp78j8qo/pub_worm.egg-info/PKG-INFO 2025-06-11T09:48:02,524 writing dependency_links to /tmp/pip-pip-egg-info-fp78j8qo/pub_worm.egg-info/dependency_links.txt 2025-06-11T09:48:02,527 writing requirements to /tmp/pip-pip-egg-info-fp78j8qo/pub_worm.egg-info/requires.txt 2025-06-11T09:48:02,528 writing top-level names to /tmp/pip-pip-egg-info-fp78j8qo/pub_worm.egg-info/top_level.txt 2025-06-11T09:48:02,529 writing manifest file '/tmp/pip-pip-egg-info-fp78j8qo/pub_worm.egg-info/SOURCES.txt' 2025-06-11T09:48:02,631 reading manifest file '/tmp/pip-pip-egg-info-fp78j8qo/pub_worm.egg-info/SOURCES.txt' 2025-06-11T09:48:02,632 reading manifest template 'MANIFEST.in' 2025-06-11T09:48:02,634 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json' 2025-06-11T09:48:02,635 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json' 2025-06-11T09:48:02,635 warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json' 2025-06-11T09:48:02,638 writing manifest file '/tmp/pip-pip-egg-info-fp78j8qo/pub_worm.egg-info/SOURCES.txt' 2025-06-11T09:48:02,749 Preparing metadata (setup.py): finished with status 'done' 2025-06-11T09:48:02,753 Source in /tmp/pip-wheel-1qnkz_13/pub-worm_03293ba6ea2643f88594ff48b8429a78 has version 0.3.13, which satisfies requirement pub-worm==0.3.13 from https://files.pythonhosted.org/packages/49/9a/b32f9d8d361b31f47f630f14ef510ade5abad9b93fc6c441686fb96d9fc6/pub_worm-0.3.13.tar.gz 2025-06-11T09:48:02,754 Removed pub-worm==0.3.13 from https://files.pythonhosted.org/packages/49/9a/b32f9d8d361b31f47f630f14ef510ade5abad9b93fc6c441686fb96d9fc6/pub_worm-0.3.13.tar.gz from build tracker '/tmp/pip-build-tracker-vjai9zzx' 2025-06-11T09:48:02,760 Created temporary directory: /tmp/pip-unpack-lh2m2nh6 2025-06-11T09:48:02,761 Created temporary directory: /tmp/pip-unpack-5z24t8kb 2025-06-11T09:48:02,762 Building wheels for collected packages: pub-worm 2025-06-11T09:48:02,766 Created temporary directory: /tmp/pip-wheel-p4glb0ev 2025-06-11T09:48:02,767 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 2025-06-11T09:48:02,768 Building wheel for pub-worm (setup.py): started 2025-06-11T09:48:02,770 Destination directory: /tmp/pip-wheel-p4glb0ev 2025-06-11T09:48:02,770 Running command python setup.py bdist_wheel 2025-06-11T09:48:03,626 running bdist_wheel 2025-06-11T09:48:03,763 running build 2025-06-11T09:48:03,763 running build_py 2025-06-11T09:48:03,794 creating build/lib/pub_worm 2025-06-11T09:48:03,796 copying pub_worm/__init__.py -> build/lib/pub_worm 2025-06-11T09:48:03,799 creating build/lib/tests 2025-06-11T09:48:03,800 copying tests/__init__.py -> build/lib/tests 2025-06-11T09:48:03,803 creating build/lib/pub_worm/impact_factor 2025-06-11T09:48:03,804 copying pub_worm/impact_factor/impact_factor_lookup.py -> build/lib/pub_worm/impact_factor 2025-06-11T09:48:03,806 copying pub_worm/impact_factor/__init__.py -> build/lib/pub_worm/impact_factor 2025-06-11T09:48:03,809 creating build/lib/pub_worm/orcid 2025-06-11T09:48:03,810 copying pub_worm/orcid/orcid_api.py -> build/lib/pub_worm/orcid 2025-06-11T09:48:03,812 copying pub_worm/orcid/__init__.py -> build/lib/pub_worm/orcid 2025-06-11T09:48:03,815 creating build/lib/pub_worm/ensembl 2025-06-11T09:48:03,816 copying pub_worm/ensembl/ensembl_api.py -> build/lib/pub_worm/ensembl 2025-06-11T09:48:03,819 copying pub_worm/ensembl/__init__.py -> build/lib/pub_worm/ensembl 2025-06-11T09:48:03,821 creating build/lib/pub_worm/wormbase 2025-06-11T09:48:03,822 copying pub_worm/wormbase/wormbase_util.py -> build/lib/pub_worm/wormbase 2025-06-11T09:48:03,825 copying pub_worm/wormbase/__init__.py -> build/lib/pub_worm/wormbase 2025-06-11T09:48:03,828 copying pub_worm/wormbase/to_csv_helpers.py -> build/lib/pub_worm/wormbase 2025-06-11T09:48:03,830 copying pub_worm/wormbase/wormbase_api.py -> build/lib/pub_worm/wormbase 2025-06-11T09:48:03,832 creating build/lib/pub_worm/biorxiv 2025-06-11T09:48:03,833 copying pub_worm/biorxiv/biorxiv_api.py -> build/lib/pub_worm/biorxiv 2025-06-11T09:48:03,836 copying pub_worm/biorxiv/__init__.py -> build/lib/pub_worm/biorxiv 2025-06-11T09:48:03,838 creating build/lib/pub_worm/ncbi 2025-06-11T09:48:03,839 copying pub_worm/ncbi/__init__.py -> build/lib/pub_worm/ncbi 2025-06-11T09:48:03,841 copying pub_worm/ncbi/entreze_api.py -> build/lib/pub_worm/ncbi 2025-06-11T09:48:03,844 creating build/lib/tests/impact_factor 2025-06-11T09:48:03,845 copying tests/impact_factor/__init__.py -> build/lib/tests/impact_factor 2025-06-11T09:48:03,847 copying tests/impact_factor/test_get_impact_factor.py -> build/lib/tests/impact_factor 2025-06-11T09:48:03,850 creating build/lib/tests/orcid 2025-06-11T09:48:03,851 copying tests/orcid/test_orcid_api.py -> build/lib/tests/orcid 2025-06-11T09:48:03,853 copying tests/orcid/__init__.py -> build/lib/tests/orcid 2025-06-11T09:48:03,855 creating build/lib/tests/wormbase 2025-06-11T09:48:03,856 copying tests/wormbase/__init__.py -> build/lib/tests/wormbase 2025-06-11T09:48:03,858 copying tests/wormbase/test_wormbase_api.py -> build/lib/tests/wormbase 2025-06-11T09:48:03,860 creating build/lib/tests/ncbi 2025-06-11T09:48:03,861 copying tests/ncbi/__init__.py -> build/lib/tests/ncbi 2025-06-11T09:48:03,863 copying tests/ncbi/test_entreze_api.py -> build/lib/tests/ncbi 2025-06-11T09:48:03,865 running egg_info 2025-06-11T09:48:03,894 writing pub_worm.egg-info/PKG-INFO 2025-06-11T09:48:03,897 writing dependency_links to pub_worm.egg-info/dependency_links.txt 2025-06-11T09:48:03,899 writing requirements to pub_worm.egg-info/requires.txt 2025-06-11T09:48:03,901 writing top-level names to pub_worm.egg-info/top_level.txt 2025-06-11T09:48:03,941 reading manifest file 'pub_worm.egg-info/SOURCES.txt' 2025-06-11T09:48:03,945 reading manifest template 'MANIFEST.in' 2025-06-11T09:48:03,946 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esummary.json' 2025-06-11T09:48:03,947 warning: no files found matching 'pub_worm/ncbi/data/ncbi_esearch.json' 2025-06-11T09:48:03,948 warning: no files found matching 'pub_worm/ncbi/data/ncbi_efetch.json' 2025-06-11T09:48:03,951 writing manifest file 'pub_worm.egg-info/SOURCES.txt' 2025-06-11T09:48:03,954 /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. 2025-06-11T09:48:03,954 !! 2025-06-11T09:48:03,956 ******************************************************************************** 2025-06-11T09:48:03,956 ############################ 2025-06-11T09:48:03,957 # Package would be ignored # 2025-06-11T09:48:03,957 ############################ 2025-06-11T09:48:03,958 Python recognizes 'pub_worm.impact_factor.data' as an importable package[^1], 2025-06-11T09:48:03,959 but it is absent from setuptools' `packages` configuration. 2025-06-11T09:48:03,960 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T09:48:03,961 package, please make sure that 'pub_worm.impact_factor.data' is explicitly added 2025-06-11T09:48:03,961 to the `packages` configuration field. 2025-06-11T09:48:03,963 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T09:48:03,963 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T09:48:03,964 instead of `find_packages(...)`/`find:`). 2025-06-11T09:48:03,965 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T09:48:03,966 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T09:48:03,967 If you don't want 'pub_worm.impact_factor.data' to be distributed and are 2025-06-11T09:48:03,968 already explicitly excluding 'pub_worm.impact_factor.data' via 2025-06-11T09:48:03,968 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T09:48:03,969 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T09:48:03,969 combination with a more fine grained `package-data` configuration. 2025-06-11T09:48:03,970 You can read more about "package data files" on setuptools documentation page: 2025-06-11T09:48:03,984 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T09:48:03,991 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T09:48:03,992 even if it does not contain any `.py` files. 2025-06-11T09:48:03,992 On the other hand, currently there is no concept of package data 2025-06-11T09:48:03,993 directory, all directories are treated like packages. 2025-06-11T09:48:03,994 ******************************************************************************** 2025-06-11T09:48:03,995 !! 2025-06-11T09:48:03,995 check.warn(importable) 2025-06-11T09:48:03,996 /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. 2025-06-11T09:48:03,997 !! 2025-06-11T09:48:03,998 ******************************************************************************** 2025-06-11T09:48:03,998 ############################ 2025-06-11T09:48:03,999 # Package would be ignored # 2025-06-11T09:48:03,999 ############################ 2025-06-11T09:48:04,000 Python recognizes 'pub_worm.wormbase.data' as an importable package[^1], 2025-06-11T09:48:04,000 but it is absent from setuptools' `packages` configuration. 2025-06-11T09:48:04,002 This leads to an ambiguous overall configuration. If you want to distribute this 2025-06-11T09:48:04,002 package, please make sure that 'pub_worm.wormbase.data' is explicitly added 2025-06-11T09:48:04,003 to the `packages` configuration field. 2025-06-11T09:48:04,004 Alternatively, you can also rely on setuptools' discovery methods 2025-06-11T09:48:04,004 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-06-11T09:48:04,005 instead of `find_packages(...)`/`find:`). 2025-06-11T09:48:04,006 You can read more about "package discovery" on setuptools documentation page: 2025-06-11T09:48:04,007 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-06-11T09:48:04,009 If you don't want 'pub_worm.wormbase.data' to be distributed and are 2025-06-11T09:48:04,009 already explicitly excluding 'pub_worm.wormbase.data' via 2025-06-11T09:48:04,010 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-06-11T09:48:04,010 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-06-11T09:48:04,011 combination with a more fine grained `package-data` configuration. 2025-06-11T09:48:04,012 You can read more about "package data files" on setuptools documentation page: 2025-06-11T09:48:04,013 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-06-11T09:48:04,015 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-06-11T09:48:04,016 even if it does not contain any `.py` files. 2025-06-11T09:48:04,016 On the other hand, currently there is no concept of package data 2025-06-11T09:48:04,017 directory, all directories are treated like packages. 2025-06-11T09:48:04,018 ******************************************************************************** 2025-06-11T09:48:04,019 !! 2025-06-11T09:48:04,020 check.warn(importable) 2025-06-11T09:48:04,020 creating build/lib/pub_worm/impact_factor/data 2025-06-11T09:48:04,021 copying pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/lib/pub_worm/impact_factor/data 2025-06-11T09:48:04,021 creating build/lib/pub_worm/wormbase/data 2025-06-11T09:48:04,022 copying pub_worm/wormbase/data/wormbase_field_gene.json -> build/lib/pub_worm/wormbase/data 2025-06-11T09:48:04,022 copying pub_worm/wormbase/data/wormbase_field_paper.json -> build/lib/pub_worm/wormbase/data 2025-06-11T09:48:04,023 copying pub_worm/wormbase/data/wormbase_widget_gene.json -> build/lib/pub_worm/wormbase/data 2025-06-11T09:48:04,037 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-11T09:48:04,038 !! 2025-06-11T09:48:04,039 ******************************************************************************** 2025-06-11T09:48:04,039 Please avoid running ``setup.py`` directly. 2025-06-11T09:48:04,040 Instead, use pypa/build, pypa/installer or other 2025-06-11T09:48:04,040 standards-based tools. 2025-06-11T09:48:04,041 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-11T09:48:04,042 or your builds will no longer be supported. 2025-06-11T09:48:04,043 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-11T09:48:04,043 ******************************************************************************** 2025-06-11T09:48:04,044 !! 2025-06-11T09:48:04,045 self.initialize_options() 2025-06-11T09:48:04,065 installing to build/bdist.linux-armv7l/wheel 2025-06-11T09:48:04,065 running install 2025-06-11T09:48:04,089 running install_lib 2025-06-11T09:48:04,117 creating build/bdist.linux-armv7l/wheel 2025-06-11T09:48:04,120 creating build/bdist.linux-armv7l/wheel/pub_worm 2025-06-11T09:48:04,122 creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor 2025-06-11T09:48:04,123 copying build/lib/pub_worm/impact_factor/impact_factor_lookup.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor 2025-06-11T09:48:04,125 copying build/lib/pub_worm/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor 2025-06-11T09:48:04,128 creating build/bdist.linux-armv7l/wheel/pub_worm/impact_factor/data 2025-06-11T09:48:04,129 copying build/lib/pub_worm/impact_factor/data/2022_JCR_IF.csv -> build/bdist.linux-armv7l/wheel/./pub_worm/impact_factor/data 2025-06-11T09:48:04,157 creating build/bdist.linux-armv7l/wheel/pub_worm/orcid 2025-06-11T09:48:04,158 copying build/lib/pub_worm/orcid/orcid_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid 2025-06-11T09:48:04,161 copying build/lib/pub_worm/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/orcid 2025-06-11T09:48:04,163 creating build/bdist.linux-armv7l/wheel/pub_worm/ensembl 2025-06-11T09:48:04,164 copying build/lib/pub_worm/ensembl/ensembl_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl 2025-06-11T09:48:04,166 copying build/lib/pub_worm/ensembl/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ensembl 2025-06-11T09:48:04,169 creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase 2025-06-11T09:48:04,170 copying build/lib/pub_worm/wormbase/wormbase_util.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-11T09:48:04,172 copying build/lib/pub_worm/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-11T09:48:04,174 copying build/lib/pub_worm/wormbase/to_csv_helpers.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-11T09:48:04,177 creating build/bdist.linux-armv7l/wheel/pub_worm/wormbase/data 2025-06-11T09:48:04,178 copying build/lib/pub_worm/wormbase/data/wormbase_widget_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data 2025-06-11T09:48:04,181 copying build/lib/pub_worm/wormbase/data/wormbase_field_paper.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data 2025-06-11T09:48:04,183 copying build/lib/pub_worm/wormbase/data/wormbase_field_gene.json -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase/data 2025-06-11T09:48:04,185 copying build/lib/pub_worm/wormbase/wormbase_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/wormbase 2025-06-11T09:48:04,188 creating build/bdist.linux-armv7l/wheel/pub_worm/biorxiv 2025-06-11T09:48:04,189 copying build/lib/pub_worm/biorxiv/biorxiv_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv 2025-06-11T09:48:04,191 copying build/lib/pub_worm/biorxiv/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/biorxiv 2025-06-11T09:48:04,193 copying build/lib/pub_worm/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm 2025-06-11T09:48:04,195 creating build/bdist.linux-armv7l/wheel/pub_worm/ncbi 2025-06-11T09:48:04,196 copying build/lib/pub_worm/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi 2025-06-11T09:48:04,198 copying build/lib/pub_worm/ncbi/entreze_api.py -> build/bdist.linux-armv7l/wheel/./pub_worm/ncbi 2025-06-11T09:48:04,202 creating build/bdist.linux-armv7l/wheel/tests 2025-06-11T09:48:04,203 creating build/bdist.linux-armv7l/wheel/tests/impact_factor 2025-06-11T09:48:04,205 copying build/lib/tests/impact_factor/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor 2025-06-11T09:48:04,206 copying build/lib/tests/impact_factor/test_get_impact_factor.py -> build/bdist.linux-armv7l/wheel/./tests/impact_factor 2025-06-11T09:48:04,209 creating build/bdist.linux-armv7l/wheel/tests/orcid 2025-06-11T09:48:04,210 copying build/lib/tests/orcid/test_orcid_api.py -> build/bdist.linux-armv7l/wheel/./tests/orcid 2025-06-11T09:48:04,212 copying build/lib/tests/orcid/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/orcid 2025-06-11T09:48:04,214 creating build/bdist.linux-armv7l/wheel/tests/wormbase 2025-06-11T09:48:04,215 copying build/lib/tests/wormbase/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase 2025-06-11T09:48:04,217 copying build/lib/tests/wormbase/test_wormbase_api.py -> build/bdist.linux-armv7l/wheel/./tests/wormbase 2025-06-11T09:48:04,219 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2025-06-11T09:48:04,221 creating build/bdist.linux-armv7l/wheel/tests/ncbi 2025-06-11T09:48:04,223 copying build/lib/tests/ncbi/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi 2025-06-11T09:48:04,224 copying build/lib/tests/ncbi/test_entreze_api.py -> build/bdist.linux-armv7l/wheel/./tests/ncbi 2025-06-11T09:48:04,226 running install_egg_info 2025-06-11T09:48:04,262 Copying pub_worm.egg-info to build/bdist.linux-armv7l/wheel/./pub_worm-0.3.13-py3.11.egg-info 2025-06-11T09:48:04,275 running install_scripts 2025-06-11T09:48:04,286 creating build/bdist.linux-armv7l/wheel/pub_worm-0.3.13.dist-info/WHEEL 2025-06-11T09:48:04,289 creating '/tmp/pip-wheel-p4glb0ev/pub_worm-0.3.13-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-11T09:48:04,291 adding 'pub_worm/__init__.py' 2025-06-11T09:48:04,293 adding 'pub_worm/biorxiv/__init__.py' 2025-06-11T09:48:04,295 adding 'pub_worm/biorxiv/biorxiv_api.py' 2025-06-11T09:48:04,297 adding 'pub_worm/ensembl/__init__.py' 2025-06-11T09:48:04,298 adding 'pub_worm/ensembl/ensembl_api.py' 2025-06-11T09:48:04,300 adding 'pub_worm/impact_factor/__init__.py' 2025-06-11T09:48:04,302 adding 'pub_worm/impact_factor/impact_factor_lookup.py' 2025-06-11T09:48:04,469 adding 'pub_worm/impact_factor/data/2022_JCR_IF.csv' 2025-06-11T09:48:04,480 adding 'pub_worm/ncbi/__init__.py' 2025-06-11T09:48:04,482 adding 'pub_worm/ncbi/entreze_api.py' 2025-06-11T09:48:04,484 adding 'pub_worm/orcid/__init__.py' 2025-06-11T09:48:04,486 adding 'pub_worm/orcid/orcid_api.py' 2025-06-11T09:48:04,488 adding 'pub_worm/wormbase/__init__.py' 2025-06-11T09:48:04,489 adding 'pub_worm/wormbase/to_csv_helpers.py' 2025-06-11T09:48:04,491 adding 'pub_worm/wormbase/wormbase_api.py' 2025-06-11T09:48:04,493 adding 'pub_worm/wormbase/wormbase_util.py' 2025-06-11T09:48:04,494 adding 'pub_worm/wormbase/data/wormbase_field_gene.json' 2025-06-11T09:48:04,496 adding 'pub_worm/wormbase/data/wormbase_field_paper.json' 2025-06-11T09:48:04,497 adding 'pub_worm/wormbase/data/wormbase_widget_gene.json' 2025-06-11T09:48:04,499 adding 'tests/__init__.py' 2025-06-11T09:48:04,501 adding 'tests/impact_factor/__init__.py' 2025-06-11T09:48:04,502 adding 'tests/impact_factor/test_get_impact_factor.py' 2025-06-11T09:48:04,503 adding 'tests/ncbi/__init__.py' 2025-06-11T09:48:04,505 adding 'tests/ncbi/test_entreze_api.py' 2025-06-11T09:48:04,507 adding 'tests/orcid/__init__.py' 2025-06-11T09:48:04,508 adding 'tests/orcid/test_orcid_api.py' 2025-06-11T09:48:04,510 adding 'tests/wormbase/__init__.py' 2025-06-11T09:48:04,511 adding 'tests/wormbase/test_wormbase_api.py' 2025-06-11T09:48:04,512 adding 'pub_worm-0.3.13.dist-info/METADATA' 2025-06-11T09:48:04,513 adding 'pub_worm-0.3.13.dist-info/WHEEL' 2025-06-11T09:48:04,514 adding 'pub_worm-0.3.13.dist-info/top_level.txt' 2025-06-11T09:48:04,515 adding 'pub_worm-0.3.13.dist-info/RECORD' 2025-06-11T09:48:04,522 removing build/bdist.linux-armv7l/wheel 2025-06-11T09:48:04,651 Building wheel for pub-worm (setup.py): finished with status 'done' 2025-06-11T09:48:04,657 Created wheel for pub-worm: filename=pub_worm-0.3.13-py3-none-any.whl size=403558 sha256=662157a72ce3c40f8c186cd29f430fe6259e65c0efa401d3b19c7c6d17fa3a5b 2025-06-11T09:48:04,659 Stored in directory: /tmp/pip-ephem-wheel-cache-n1fd8gxf/wheels/f6/5e/45/4996f66dbea347b7ddb952d9fcdd4d1464e8ee087023dd0f0b 2025-06-11T09:48:04,671 Successfully built pub-worm 2025-06-11T09:48:04,690 Removed build tracker: '/tmp/pip-build-tracker-vjai9zzx'