2025-05-31T14:35:37,800 Created temporary directory: /tmp/pip-build-tracker-t3n1l6s2 2025-05-31T14:35:37,801 Initialized build tracking at /tmp/pip-build-tracker-t3n1l6s2 2025-05-31T14:35:37,801 Created build tracker: /tmp/pip-build-tracker-t3n1l6s2 2025-05-31T14:35:37,802 Entered build tracker: /tmp/pip-build-tracker-t3n1l6s2 2025-05-31T14:35:37,803 Created temporary directory: /tmp/pip-wheel-fddgqs62 2025-05-31T14:35:37,807 Created temporary directory: /tmp/pip-ephem-wheel-cache-6_tcc7uu 2025-05-31T14:35:37,856 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-05-31T14:35:37,858 2 location(s) to search for versions of nmdc-runtime: 2025-05-31T14:35:37,858 * https://pypi.org/simple/nmdc-runtime/ 2025-05-31T14:35:37,858 * https://www.piwheels.org/simple/nmdc-runtime/ 2025-05-31T14:35:37,859 Fetching project page and analyzing links: https://pypi.org/simple/nmdc-runtime/ 2025-05-31T14:35:37,860 Getting page https://pypi.org/simple/nmdc-runtime/ 2025-05-31T14:35:37,862 Found index url https://pypi.org/simple/ 2025-05-31T14:35:38,173 Fetched page https://pypi.org/simple/nmdc-runtime/ as application/vnd.pypi.simple.v1+json 2025-05-31T14:35:38,195 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/ba/44/acaca01a3fdf26351a427b58ca793a2702c1157d5125d3101029e99d0ab0/nmdc_runtime-0.1.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.8) 2025-05-31T14:35:38,196 Found link https://files.pythonhosted.org/packages/3d/56/9ddca8b74ed798352aca6ba02e98c7bfbf232ccb237660b2488f7da8a39e/nmdc_runtime-0.1.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.8), version: 0.1.0 2025-05-31T14:35:38,197 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/38/59/cb99a0e180d0de57a68cdd118ed305b68d97561a7a82da80d48992236382/nmdc_runtime-0.1.1-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.8) 2025-05-31T14:35:38,198 Found link https://files.pythonhosted.org/packages/31/0d/353b462ef1bde0cdb4f4d36b943b19f4844070641e2ad25cf4b39e10154d/nmdc_runtime-0.1.1.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.8), version: 0.1.1 2025-05-31T14:35:38,198 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/c9/32/65aa3b8e7dae9e5c896fa1fcaf559fb1784d824759c78b4c89682c681275/nmdc_runtime-0.1.3-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.8) 2025-05-31T14:35:38,199 Found link https://files.pythonhosted.org/packages/f5/f9/e540bd39ae5b2f834f09138219ba5c9beab7797821f063b93e2f0cb48c30/nmdc_runtime-0.1.3.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.8), version: 0.1.3 2025-05-31T14:35:38,200 Skipping link: No binaries permitted for nmdc-runtime: 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version: 1.7.0 2025-05-31T14:35:38,229 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/7d/fc/35f5616c87cb148789b8c636a11333d71902cd218895c94acee56e5e7979/nmdc_runtime-1.8.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,230 Found link https://files.pythonhosted.org/packages/80/64/f0a15d5171e9242f322a0b4e4b9cb4e334fe2805aeccb8a21749575f2ca9/nmdc_runtime-1.8.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 1.8.0 2025-05-31T14:35:38,231 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/11/bd/7e4067469099c797692477f6fa617e65325676ae7c484c05dcce7091aecd/nmdc_runtime-1.9.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,231 Found link https://files.pythonhosted.org/packages/98/87/74b97999f1f5e4d99a6070375be390566455f4bc809b6743e2d9e1b42a29/nmdc_runtime-1.9.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 1.9.0 2025-05-31T14:35:38,232 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/f1/7f/31e1b514bb0ae76e5a4f693e61cc83327933db84148cff35f0c8b1dc9d5f/nmdc_runtime-1.10.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,233 Found link https://files.pythonhosted.org/packages/be/5a/48fb4b8d21dfe38218d374621a32854a9a93b97c558362a5c3fa63ef4da8/nmdc_runtime-1.10.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 1.10.0 2025-05-31T14:35:38,234 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/e5/a7/0ca2690a4c3d422a2d390b205cb298b5ebd892899f1d8ab6b4d1bca4943e/nmdc_runtime-2.0.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,234 Found link https://files.pythonhosted.org/packages/8e/d3/3c76090a49948ec21634124ce4ff6ff502149ceb2c0c9b7ce221d4567c69/nmdc_runtime-2.0.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.0.0 2025-05-31T14:35:38,235 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/0e/a2/0c6cf7c05813eb4ef23c97942e776613569e900ff1bf81b26e00034cc397/nmdc_runtime-2.0.1-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,235 Found link https://files.pythonhosted.org/packages/ec/0a/73e89df1d4c465949b8d7a5f90135ebf0f58e5b2bb72a5d2599006f3ddb6/nmdc_runtime-2.0.1.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.0.1 2025-05-31T14:35:38,236 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/50/b8/0442fe43927c849de58237d5ffa74a1b9aa0693e558afc15ecce2a53eb17/nmdc_runtime-2.1.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,237 Found link https://files.pythonhosted.org/packages/bb/19/6920c48bc4556225a6e8ae176ba72fe29db5547b9568708bdd5a1ab02485/nmdc_runtime-2.1.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.1.0 2025-05-31T14:35:38,237 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/7a/f2/a8c0f16a2b0307410507580b4553b162f2048c87b11699cb6d350fd74eaf/nmdc_runtime-2.1.1-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,238 Found link https://files.pythonhosted.org/packages/5f/76/3ef1e8c2d4513fbe14bf428d10d4129548c67ddf88f0302e4bd949941077/nmdc_runtime-2.1.1.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.1.1 2025-05-31T14:35:38,239 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/f5/fb/da758a76b77c8e36b83abd8fa3a21f82299a4c1e120e87bfa65c3ed9fabc/nmdc_runtime-2.2.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,239 Found link https://files.pythonhosted.org/packages/fe/9d/4f1ff1b5efc2975101441626d1bb0b8ae7f17b317272dc831b16c21cf95f/nmdc_runtime-2.2.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.2.0 2025-05-31T14:35:38,240 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/f2/aa/c95b6a90fd8f6e6b439e1569d75e31a38fe6da2b27f8801366b68b43203c/nmdc_runtime-2.2.1-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,241 Found link https://files.pythonhosted.org/packages/c2/a6/75b09e3bc678756f43137dfcae657309fa45c436bf7f43c3ae1f8ecb5d97/nmdc_runtime-2.2.1.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.2.1 2025-05-31T14:35:38,241 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/fb/af/9fb1bb5c2980b5c990505b543faf11ceda2e59d34cf8c3f90b5ffbc3d136/nmdc_runtime-2.3.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,242 Found link https://files.pythonhosted.org/packages/3a/8d/35b5968fd7efb05836fb23a9381f50cfdf2c44b364aa151fdc5be5cace60/nmdc_runtime-2.3.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.3.0 2025-05-31T14:35:38,243 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/9f/74/f5fea4dbd5d8204986550129833ac19ec6d22e93d96cff8cc6739529e6f8/nmdc_runtime-2.4.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,243 Found link https://files.pythonhosted.org/packages/26/75/241e268a408f69c3bf5e5c86bf47c69e972c1cf0916111df97d3ec7eeebe/nmdc_runtime-2.4.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.4.0 2025-05-31T14:35:38,244 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/50/74/8b7738310f28edfa5378c8df0fb8ef26bb28174e923eb1f76ea846489a25/nmdc_runtime-2.5.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,244 Found link https://files.pythonhosted.org/packages/f9/6a/5ae5128b6fc736cf57ac7044c6ad6d6dcd655cef3f1f0a9c8b8692c56bfd/nmdc_runtime-2.5.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.5.0 2025-05-31T14:35:38,245 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/73/00/ea0b216d37b0328463fd16b6dae03c2a35fc502fec97cca877de7c0636a5/nmdc_runtime-2.6.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,245 Found link https://files.pythonhosted.org/packages/15/37/b8410264d240e26310eb513f1fecd83a34831be30350e242607585fc324a/nmdc_runtime-2.6.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.6.0 2025-05-31T14:35:38,246 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/10/92/9cf041281ce14dd223bfff9da962f6491149e7822d287ae5867a4612528d/nmdc_runtime-2.7.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,247 Found link https://files.pythonhosted.org/packages/5e/6b/fbe817602d790668bd4f95b231f62916a831a4178cf100cf5ad28788b6d8/nmdc_runtime-2.7.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.7.0 2025-05-31T14:35:38,247 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/41/dc/631c817875f22b1bd523f84dcbc34feac1bf0e38ba498e4a2a7150fded50/nmdc_runtime-2.8.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,248 Found link https://files.pythonhosted.org/packages/b8/d2/5413b6998fee7bbfe9f4925739a534a2309a2006c0d2ff21d6aa501b9ee9/nmdc_runtime-2.8.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.8.0 2025-05-31T14:35:38,249 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/17/d9/503268a3fb3fc1fe636f4a94fa4f4c7bf03647ebb055f0aa294a72c6a6aa/nmdc_runtime-2.9.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,250 Found link https://files.pythonhosted.org/packages/6c/03/6ba8c1dfb1378ba58efb72f7917e92fa3b23381082fc49ceef93f735106b/nmdc_runtime-2.9.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.9.0 2025-05-31T14:35:38,250 Skipping link: No binaries permitted for nmdc-runtime: https://files.pythonhosted.org/packages/f3/fe/5624f6818201da35fafdca68204460d655a859a0e5cc6207474476173e7d/nmdc_runtime-2.10.0-py3-none-any.whl (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10) 2025-05-31T14:35:38,251 Found link https://files.pythonhosted.org/packages/6b/92/732825c6822d2922e552699f026909341d9e9cad790a07278a7bfeb97c83/nmdc_runtime-2.10.0.tar.gz (from https://pypi.org/simple/nmdc-runtime/) (requires-python:>=3.10), version: 2.10.0 2025-05-31T14:35:38,252 Fetching project page and analyzing links: https://www.piwheels.org/simple/nmdc-runtime/ 2025-05-31T14:35:38,253 Getting page https://www.piwheels.org/simple/nmdc-runtime/ 2025-05-31T14:35:38,254 Found index url https://www.piwheels.org/simple/ 2025-05-31T14:35:38,409 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/nmdc-runtime/ 2025-05-31T14:35:39,068 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/nmdc-runtime/ 2025-05-31T14:35:40,242 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/nmdc-runtime/ 2025-05-31T14:35:42,410 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/nmdc-runtime/ 2025-05-31T14:35:46,584 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/nmdc-runtime/ 2025-05-31T14:35:46,753 Could not fetch URL https://www.piwheels.org/simple/nmdc-runtime/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/nmdc-runtime/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping 2025-05-31T14:35:46,755 Skipping link: not a file: https://www.piwheels.org/simple/nmdc-runtime/ 2025-05-31T14:35:46,755 Skipping link: not a file: https://pypi.org/simple/nmdc-runtime/ 2025-05-31T14:35:46,782 Given no hashes to check 1 links for project 'nmdc-runtime': discarding no candidates 2025-05-31T14:35:46,784 Collecting nmdc-runtime==2.8.0 2025-05-31T14:35:46,787 Created temporary directory: /tmp/pip-unpack-we23n7cf 2025-05-31T14:35:47,274 Downloading nmdc_runtime-2.8.0.tar.gz (64.1 MB) 2025-05-31T14:36:00,188 Added nmdc-runtime==2.8.0 from https://files.pythonhosted.org/packages/b8/d2/5413b6998fee7bbfe9f4925739a534a2309a2006c0d2ff21d6aa501b9ee9/nmdc_runtime-2.8.0.tar.gz to build tracker '/tmp/pip-build-tracker-t3n1l6s2' 2025-05-31T14:36:00,191 Running setup.py (path:/tmp/pip-wheel-fddgqs62/nmdc-runtime_5f29c69c59384a7b860f226a0f3f88b7/setup.py) egg_info for package nmdc-runtime 2025-05-31T14:36:00,192 Created temporary directory: /tmp/pip-pip-egg-info-3j46sr1b 2025-05-31T14:36:00,192 Preparing metadata (setup.py): started 2025-05-31T14:36:00,194 Running command python setup.py egg_info 2025-05-31T14:36:00,836 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-05-31T14:36:00,837 !! 2025-05-31T14:36:00,838 ******************************************************************************** 2025-05-31T14:36:00,839 Requirements should be satisfied by a PEP 517 installer. 2025-05-31T14:36:00,839 If you are using pip, you can try `pip install --use-pep517`. 2025-05-31T14:36:00,841 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-05-31T14:36:00,841 or your builds will no longer be supported. 2025-05-31T14:36:00,842 ******************************************************************************** 2025-05-31T14:36:00,843 !! 2025-05-31T14:36:00,843 dist.fetch_build_eggs(dist.setup_requires) 2025-05-31T14:36:03,902 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-05-31T14:36:03,903 !! 2025-05-31T14:36:03,904 ******************************************************************************** 2025-05-31T14:36:03,904 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-05-31T14:36:03,905 License :: OSI Approved :: Apache Software License 2025-05-31T14:36:03,906 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-05-31T14:36:03,907 ******************************************************************************** 2025-05-31T14:36:03,908 !! 2025-05-31T14:36:03,908 self._finalize_license_expression() 2025-05-31T14:36:03,935 running egg_info 2025-05-31T14:36:03,966 creating /tmp/pip-pip-egg-info-3j46sr1b/nmdc_runtime.egg-info 2025-05-31T14:36:03,966 writing /tmp/pip-pip-egg-info-3j46sr1b/nmdc_runtime.egg-info/PKG-INFO 2025-05-31T14:36:03,970 writing dependency_links to /tmp/pip-pip-egg-info-3j46sr1b/nmdc_runtime.egg-info/dependency_links.txt 2025-05-31T14:36:03,971 writing entry points to /tmp/pip-pip-egg-info-3j46sr1b/nmdc_runtime.egg-info/entry_points.txt 2025-05-31T14:36:03,973 writing top-level names to /tmp/pip-pip-egg-info-3j46sr1b/nmdc_runtime.egg-info/top_level.txt 2025-05-31T14:36:03,974 writing manifest file '/tmp/pip-pip-egg-info-3j46sr1b/nmdc_runtime.egg-info/SOURCES.txt' 2025-05-31T14:36:04,188 listing git files failed - pretending there aren't any 2025-05-31T14:36:04,204 reading manifest file '/tmp/pip-pip-egg-info-3j46sr1b/nmdc_runtime.egg-info/SOURCES.txt' 2025-05-31T14:36:04,206 adding license file 'LICENSE' 2025-05-31T14:36:04,212 writing manifest file '/tmp/pip-pip-egg-info-3j46sr1b/nmdc_runtime.egg-info/SOURCES.txt' 2025-05-31T14:36:04,325 Preparing metadata (setup.py): finished with status 'done' 2025-05-31T14:36:04,329 Source in /tmp/pip-wheel-fddgqs62/nmdc-runtime_5f29c69c59384a7b860f226a0f3f88b7 has version 2.8.0, which satisfies requirement nmdc-runtime==2.8.0 from https://files.pythonhosted.org/packages/b8/d2/5413b6998fee7bbfe9f4925739a534a2309a2006c0d2ff21d6aa501b9ee9/nmdc_runtime-2.8.0.tar.gz 2025-05-31T14:36:04,330 Removed nmdc-runtime==2.8.0 from https://files.pythonhosted.org/packages/b8/d2/5413b6998fee7bbfe9f4925739a534a2309a2006c0d2ff21d6aa501b9ee9/nmdc_runtime-2.8.0.tar.gz from build tracker '/tmp/pip-build-tracker-t3n1l6s2' 2025-05-31T14:36:04,336 Created temporary directory: /tmp/pip-unpack-nni19jxj 2025-05-31T14:36:04,337 Created temporary directory: /tmp/pip-unpack-5kcuqcb5 2025-05-31T14:36:04,338 Building wheels for collected packages: nmdc-runtime 2025-05-31T14:36:04,342 Created temporary directory: /tmp/pip-wheel-4lootum_ 2025-05-31T14:36:04,343 DEPRECATION: Building 'nmdc-runtime' 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 'nmdc-runtime'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-05-31T14:36:04,345 Building wheel for nmdc-runtime (setup.py): started 2025-05-31T14:36:04,346 Destination directory: /tmp/pip-wheel-4lootum_ 2025-05-31T14:36:04,347 Running command python setup.py bdist_wheel 2025-05-31T14:36:04,940 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-05-31T14:36:04,940 !! 2025-05-31T14:36:04,941 ******************************************************************************** 2025-05-31T14:36:04,942 Requirements should be satisfied by a PEP 517 installer. 2025-05-31T14:36:04,942 If you are using pip, you can try `pip install --use-pep517`. 2025-05-31T14:36:04,943 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-05-31T14:36:04,943 or your builds will no longer be supported. 2025-05-31T14:36:04,944 ******************************************************************************** 2025-05-31T14:36:04,945 !! 2025-05-31T14:36:04,945 dist.fetch_build_eggs(dist.setup_requires) 2025-05-31T14:36:05,573 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-05-31T14:36:05,573 !! 2025-05-31T14:36:05,574 ******************************************************************************** 2025-05-31T14:36:05,575 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-05-31T14:36:05,576 License :: OSI Approved :: Apache Software License 2025-05-31T14:36:05,577 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-05-31T14:36:05,577 ******************************************************************************** 2025-05-31T14:36:05,578 !! 2025-05-31T14:36:05,579 self._finalize_license_expression() 2025-05-31T14:36:05,580 running bdist_wheel 2025-05-31T14:36:05,728 running build 2025-05-31T14:36:05,728 running build_py 2025-05-31T14:36:05,762 creating build/lib/nmdc_runtime 2025-05-31T14:36:05,765 copying nmdc_runtime/__init__.py -> build/lib/nmdc_runtime 2025-05-31T14:36:05,767 copying nmdc_runtime/mongo_util.py -> build/lib/nmdc_runtime 2025-05-31T14:36:05,769 copying nmdc_runtime/containers.py -> build/lib/nmdc_runtime 2025-05-31T14:36:05,771 copying nmdc_runtime/config.py -> build/lib/nmdc_runtime 2025-05-31T14:36:05,774 copying nmdc_runtime/util.py -> build/lib/nmdc_runtime 2025-05-31T14:36:05,777 copying nmdc_runtime/main.py -> build/lib/nmdc_runtime 2025-05-31T14:36:05,779 creating build/lib/nmdc_runtime/domain 2025-05-31T14:36:05,780 copying nmdc_runtime/domain/__init__.py -> build/lib/nmdc_runtime/domain 2025-05-31T14:36:05,782 creating build/lib/nmdc_runtime/lib 2025-05-31T14:36:05,783 copying nmdc_runtime/lib/extract_nmdc_data.py -> build/lib/nmdc_runtime/lib 2025-05-31T14:36:05,785 copying nmdc_runtime/lib/__init__.py -> build/lib/nmdc_runtime/lib 2025-05-31T14:36:05,787 copying nmdc_runtime/lib/nmdc_dataframes.py -> build/lib/nmdc_runtime/lib 2025-05-31T14:36:05,790 copying nmdc_runtime/lib/load_nmdc_data.py -> build/lib/nmdc_runtime/lib 2025-05-31T14:36:05,792 copying nmdc_runtime/lib/transform_nmdc_data.py -> build/lib/nmdc_runtime/lib 2025-05-31T14:36:05,795 copying nmdc_runtime/lib/nmdc_etl_class.py -> build/lib/nmdc_runtime/lib 2025-05-31T14:36:05,798 creating build/lib/nmdc_runtime/infrastructure 2025-05-31T14:36:05,800 copying nmdc_runtime/infrastructure/__init__.py -> build/lib/nmdc_runtime/infrastructure 2025-05-31T14:36:05,802 creating build/lib/nmdc_runtime/core 2025-05-31T14:36:05,803 copying nmdc_runtime/core/__init__.py -> build/lib/nmdc_runtime/core 2025-05-31T14:36:05,806 creating build/lib/nmdc_runtime/client 2025-05-31T14:36:05,807 copying nmdc_runtime/client/__init__.py -> build/lib/nmdc_runtime/client 2025-05-31T14:36:05,809 creating build/lib/nmdc_runtime/minter 2025-05-31T14:36:05,810 copying nmdc_runtime/minter/bootstrap.py -> build/lib/nmdc_runtime/minter 2025-05-31T14:36:05,813 copying nmdc_runtime/minter/__init__.py -> build/lib/nmdc_runtime/minter 2025-05-31T14:36:05,814 copying nmdc_runtime/minter/config.py -> build/lib/nmdc_runtime/minter 2025-05-31T14:36:05,817 creating build/lib/nmdc_runtime/site 2025-05-31T14:36:05,818 copying nmdc_runtime/site/resources.py -> build/lib/nmdc_runtime/site 2025-05-31T14:36:05,821 copying nmdc_runtime/site/__init__.py -> build/lib/nmdc_runtime/site 2025-05-31T14:36:05,823 copying nmdc_runtime/site/ops.py -> build/lib/nmdc_runtime/site 2025-05-31T14:36:05,827 copying nmdc_runtime/site/repository.py -> build/lib/nmdc_runtime/site 2025-05-31T14:36:05,830 copying nmdc_runtime/site/graphs.py -> build/lib/nmdc_runtime/site 2025-05-31T14:36:05,833 copying nmdc_runtime/site/util.py -> build/lib/nmdc_runtime/site 2025-05-31T14:36:05,836 creating build/lib/nmdc_runtime/domain/users 2025-05-31T14:36:05,837 copying nmdc_runtime/domain/users/__init__.py -> build/lib/nmdc_runtime/domain/users 2025-05-31T14:36:05,839 copying nmdc_runtime/domain/users/queriesInterface.py -> build/lib/nmdc_runtime/domain/users 2025-05-31T14:36:05,842 copying nmdc_runtime/domain/users/userService.py -> build/lib/nmdc_runtime/domain/users 2025-05-31T14:36:05,844 copying nmdc_runtime/domain/users/userSchema.py -> build/lib/nmdc_runtime/domain/users 2025-05-31T14:36:05,847 creating build/lib/nmdc_runtime/infrastructure/database 2025-05-31T14:36:05,848 copying nmdc_runtime/infrastructure/database/__init__.py -> build/lib/nmdc_runtime/infrastructure/database 2025-05-31T14:36:05,850 copying nmdc_runtime/infrastructure/database/db.py -> build/lib/nmdc_runtime/infrastructure/database 2025-05-31T14:36:05,853 creating build/lib/nmdc_runtime/infrastructure/database/models 2025-05-31T14:36:05,854 copying nmdc_runtime/infrastructure/database/models/__init__.py -> build/lib/nmdc_runtime/infrastructure/database/models 2025-05-31T14:36:05,856 copying nmdc_runtime/infrastructure/database/models/user.py -> build/lib/nmdc_runtime/infrastructure/database/models 2025-05-31T14:36:05,859 creating build/lib/nmdc_runtime/core/exceptions 2025-05-31T14:36:05,860 copying nmdc_runtime/core/exceptions/token.py -> build/lib/nmdc_runtime/core/exceptions 2025-05-31T14:36:05,863 copying nmdc_runtime/core/exceptions/base.py -> build/lib/nmdc_runtime/core/exceptions 2025-05-31T14:36:05,865 copying nmdc_runtime/core/exceptions/__init__.py -> build/lib/nmdc_runtime/core/exceptions 2025-05-31T14:36:05,868 creating build/lib/nmdc_runtime/core/db 2025-05-31T14:36:05,869 copying nmdc_runtime/core/db/__init__.py -> build/lib/nmdc_runtime/core/db 2025-05-31T14:36:05,871 copying nmdc_runtime/core/db/Database.py -> build/lib/nmdc_runtime/core/db 2025-05-31T14:36:05,873 creating build/lib/nmdc_runtime/minter/domain 2025-05-31T14:36:05,875 copying nmdc_runtime/minter/domain/__init__.py -> build/lib/nmdc_runtime/minter/domain 2025-05-31T14:36:05,877 copying nmdc_runtime/minter/domain/model.py -> build/lib/nmdc_runtime/minter/domain 2025-05-31T14:36:05,879 creating build/lib/nmdc_runtime/minter/adapters 2025-05-31T14:36:05,880 copying nmdc_runtime/minter/adapters/__init__.py -> build/lib/nmdc_runtime/minter/adapters 2025-05-31T14:36:05,882 copying nmdc_runtime/minter/adapters/repository.py -> build/lib/nmdc_runtime/minter/adapters 2025-05-31T14:36:05,885 creating build/lib/nmdc_runtime/minter/entrypoints 2025-05-31T14:36:05,887 copying nmdc_runtime/minter/entrypoints/__init__.py -> build/lib/nmdc_runtime/minter/entrypoints 2025-05-31T14:36:05,889 copying nmdc_runtime/minter/entrypoints/fastapi_app.py -> build/lib/nmdc_runtime/minter/entrypoints 2025-05-31T14:36:05,891 creating build/lib/nmdc_runtime/site/changesheets 2025-05-31T14:36:05,892 copying nmdc_runtime/site/changesheets/base.py -> build/lib/nmdc_runtime/site/changesheets 2025-05-31T14:36:05,895 copying nmdc_runtime/site/changesheets/__init__.py -> build/lib/nmdc_runtime/site/changesheets 2025-05-31T14:36:05,897 creating build/lib/nmdc_runtime/site/validation 2025-05-31T14:36:05,898 copying nmdc_runtime/site/validation/emsl.py -> build/lib/nmdc_runtime/site/validation 2025-05-31T14:36:05,900 copying nmdc_runtime/site/validation/__init__.py -> build/lib/nmdc_runtime/site/validation 2025-05-31T14:36:05,902 copying nmdc_runtime/site/validation/jgi.py -> build/lib/nmdc_runtime/site/validation 2025-05-31T14:36:05,904 copying nmdc_runtime/site/validation/gold.py -> build/lib/nmdc_runtime/site/validation 2025-05-31T14:36:05,906 copying nmdc_runtime/site/validation/util.py -> build/lib/nmdc_runtime/site/validation 2025-05-31T14:36:05,908 creating build/lib/nmdc_runtime/site/export 2025-05-31T14:36:05,909 copying nmdc_runtime/site/export/__init__.py -> build/lib/nmdc_runtime/site/export 2025-05-31T14:36:05,911 copying nmdc_runtime/site/export/ncbi_xml_utils.py -> build/lib/nmdc_runtime/site/export 2025-05-31T14:36:05,913 copying nmdc_runtime/site/export/ncbi_xml.py -> build/lib/nmdc_runtime/site/export 2025-05-31T14:36:05,916 copying nmdc_runtime/site/export/study_metadata.py -> build/lib/nmdc_runtime/site/export 2025-05-31T14:36:05,919 creating build/lib/nmdc_runtime/site/backup 2025-05-31T14:36:05,920 copying nmdc_runtime/site/backup/__init__.py -> build/lib/nmdc_runtime/site/backup 2025-05-31T14:36:05,922 copying nmdc_runtime/site/backup/nmdcdb_mongodump.py -> build/lib/nmdc_runtime/site/backup 2025-05-31T14:36:05,924 copying nmdc_runtime/site/backup/nmdcdb_mongoexport.py -> build/lib/nmdc_runtime/site/backup 2025-05-31T14:36:05,926 copying nmdc_runtime/site/backup/nmdcdb_mongoimport.py -> build/lib/nmdc_runtime/site/backup 2025-05-31T14:36:05,929 creating build/lib/nmdc_runtime/site/drsobjects 2025-05-31T14:36:05,930 copying nmdc_runtime/site/drsobjects/__init__.py -> build/lib/nmdc_runtime/site/drsobjects 2025-05-31T14:36:05,932 copying nmdc_runtime/site/drsobjects/ingest.py -> build/lib/nmdc_runtime/site/drsobjects 2025-05-31T14:36:05,934 copying nmdc_runtime/site/drsobjects/registration.py -> build/lib/nmdc_runtime/site/drsobjects 2025-05-31T14:36:05,936 creating build/lib/nmdc_runtime/site/repair 2025-05-31T14:36:05,937 copying nmdc_runtime/site/repair/__init__.py -> build/lib/nmdc_runtime/site/repair 2025-05-31T14:36:05,939 copying nmdc_runtime/site/repair/database_updater.py -> build/lib/nmdc_runtime/site/repair 2025-05-31T14:36:05,942 creating build/lib/nmdc_runtime/site/normalization 2025-05-31T14:36:05,943 copying nmdc_runtime/site/normalization/__init__.py -> build/lib/nmdc_runtime/site/normalization 2025-05-31T14:36:05,945 copying nmdc_runtime/site/normalization/gold.py -> build/lib/nmdc_runtime/site/normalization 2025-05-31T14:36:05,948 creating build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:05,949 copying nmdc_runtime/site/translation/emsl.py -> build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:05,952 copying nmdc_runtime/site/translation/__init__.py -> build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:05,953 copying nmdc_runtime/site/translation/submission_portal_translator.py -> build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:05,957 copying nmdc_runtime/site/translation/jgi.py -> build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:05,959 copying nmdc_runtime/site/translation/gold.py -> build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:05,961 copying nmdc_runtime/site/translation/neon_soil_translator.py -> build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:05,964 copying nmdc_runtime/site/translation/neon_surface_water_translator.py -> build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:05,967 copying nmdc_runtime/site/translation/neon_utils.py -> build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:05,970 copying nmdc_runtime/site/translation/translator.py -> build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:05,972 copying nmdc_runtime/site/translation/gold_translator.py -> build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:05,975 copying nmdc_runtime/site/translation/neon_benthic_translator.py -> build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:05,978 copying nmdc_runtime/site/translation/util.py -> build/lib/nmdc_runtime/site/translation 2025-05-31T14:36:06,037 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-05-31T14:36:06,038 !! 2025-05-31T14:36:06,039 ******************************************************************************** 2025-05-31T14:36:06,040 Please avoid running ``setup.py`` directly. 2025-05-31T14:36:06,040 Instead, use pypa/build, pypa/installer or other 2025-05-31T14:36:06,041 standards-based tools. 2025-05-31T14:36:06,042 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-05-31T14:36:06,042 or your builds will no longer be supported. 2025-05-31T14:36:06,043 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-05-31T14:36:06,044 ******************************************************************************** 2025-05-31T14:36:06,045 !! 2025-05-31T14:36:06,045 self.initialize_options() 2025-05-31T14:36:06,070 installing to build/bdist.linux-armv7l/wheel 2025-05-31T14:36:06,071 running install 2025-05-31T14:36:06,095 running install_lib 2025-05-31T14:36:06,126 creating build/bdist.linux-armv7l/wheel 2025-05-31T14:36:06,128 creating build/bdist.linux-armv7l/wheel/nmdc_runtime 2025-05-31T14:36:06,130 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/domain 2025-05-31T14:36:06,132 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/domain/users 2025-05-31T14:36:06,133 copying build/lib/nmdc_runtime/domain/users/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-05-31T14:36:06,135 copying build/lib/nmdc_runtime/domain/users/queriesInterface.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-05-31T14:36:06,137 copying build/lib/nmdc_runtime/domain/users/userService.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-05-31T14:36:06,139 copying build/lib/nmdc_runtime/domain/users/userSchema.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-05-31T14:36:06,142 copying build/lib/nmdc_runtime/domain/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain 2025-05-31T14:36:06,144 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/lib 2025-05-31T14:36:06,145 copying build/lib/nmdc_runtime/lib/extract_nmdc_data.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-05-31T14:36:06,148 copying build/lib/nmdc_runtime/lib/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-05-31T14:36:06,150 copying build/lib/nmdc_runtime/lib/nmdc_dataframes.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-05-31T14:36:06,154 copying build/lib/nmdc_runtime/lib/load_nmdc_data.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-05-31T14:36:06,156 copying build/lib/nmdc_runtime/lib/transform_nmdc_data.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-05-31T14:36:06,159 copying build/lib/nmdc_runtime/lib/nmdc_etl_class.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-05-31T14:36:06,162 copying build/lib/nmdc_runtime/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-05-31T14:36:06,164 copying build/lib/nmdc_runtime/mongo_util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-05-31T14:36:06,167 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/infrastructure 2025-05-31T14:36:06,168 copying build/lib/nmdc_runtime/infrastructure/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure 2025-05-31T14:36:06,171 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/infrastructure/database 2025-05-31T14:36:06,172 copying build/lib/nmdc_runtime/infrastructure/database/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database 2025-05-31T14:36:06,175 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/infrastructure/database/models 2025-05-31T14:36:06,176 copying build/lib/nmdc_runtime/infrastructure/database/models/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database/models 2025-05-31T14:36:06,178 copying build/lib/nmdc_runtime/infrastructure/database/models/user.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database/models 2025-05-31T14:36:06,181 copying build/lib/nmdc_runtime/infrastructure/database/db.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database 2025-05-31T14:36:06,183 copying build/lib/nmdc_runtime/containers.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-05-31T14:36:06,185 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/core 2025-05-31T14:36:06,187 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/core/exceptions 2025-05-31T14:36:06,188 copying build/lib/nmdc_runtime/core/exceptions/token.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/exceptions 2025-05-31T14:36:06,191 copying build/lib/nmdc_runtime/core/exceptions/base.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/exceptions 2025-05-31T14:36:06,193 copying build/lib/nmdc_runtime/core/exceptions/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/exceptions 2025-05-31T14:36:06,195 copying build/lib/nmdc_runtime/core/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core 2025-05-31T14:36:06,198 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/core/db 2025-05-31T14:36:06,199 copying build/lib/nmdc_runtime/core/db/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/db 2025-05-31T14:36:06,201 copying build/lib/nmdc_runtime/core/db/Database.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/db 2025-05-31T14:36:06,204 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/client 2025-05-31T14:36:06,205 copying build/lib/nmdc_runtime/client/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/client 2025-05-31T14:36:06,208 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter 2025-05-31T14:36:06,210 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter/domain 2025-05-31T14:36:06,212 copying build/lib/nmdc_runtime/minter/domain/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/domain 2025-05-31T14:36:06,214 copying build/lib/nmdc_runtime/minter/domain/model.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/domain 2025-05-31T14:36:06,216 copying build/lib/nmdc_runtime/minter/bootstrap.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter 2025-05-31T14:36:06,218 copying build/lib/nmdc_runtime/minter/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter 2025-05-31T14:36:06,220 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter/adapters 2025-05-31T14:36:06,222 copying build/lib/nmdc_runtime/minter/adapters/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/adapters 2025-05-31T14:36:06,224 copying build/lib/nmdc_runtime/minter/adapters/repository.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/adapters 2025-05-31T14:36:06,226 copying build/lib/nmdc_runtime/minter/config.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter 2025-05-31T14:36:06,229 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter/entrypoints 2025-05-31T14:36:06,231 copying build/lib/nmdc_runtime/minter/entrypoints/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/entrypoints 2025-05-31T14:36:06,233 copying build/lib/nmdc_runtime/minter/entrypoints/fastapi_app.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/entrypoints 2025-05-31T14:36:06,235 copying build/lib/nmdc_runtime/config.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-05-31T14:36:06,238 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site 2025-05-31T14:36:06,239 copying build/lib/nmdc_runtime/site/resources.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-05-31T14:36:06,242 copying build/lib/nmdc_runtime/site/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-05-31T14:36:06,245 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/changesheets 2025-05-31T14:36:06,246 copying build/lib/nmdc_runtime/site/changesheets/base.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/changesheets 2025-05-31T14:36:06,248 copying build/lib/nmdc_runtime/site/changesheets/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/changesheets 2025-05-31T14:36:06,251 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/validation 2025-05-31T14:36:06,252 copying build/lib/nmdc_runtime/site/validation/emsl.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-05-31T14:36:06,255 copying build/lib/nmdc_runtime/site/validation/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-05-31T14:36:06,257 copying build/lib/nmdc_runtime/site/validation/jgi.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-05-31T14:36:06,259 copying build/lib/nmdc_runtime/site/validation/gold.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-05-31T14:36:06,261 copying build/lib/nmdc_runtime/site/validation/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-05-31T14:36:06,263 copying build/lib/nmdc_runtime/site/ops.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-05-31T14:36:06,268 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/export 2025-05-31T14:36:06,269 copying build/lib/nmdc_runtime/site/export/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-05-31T14:36:06,272 copying build/lib/nmdc_runtime/site/export/ncbi_xml_utils.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-05-31T14:36:06,275 copying build/lib/nmdc_runtime/site/export/ncbi_xml.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-05-31T14:36:06,278 copying build/lib/nmdc_runtime/site/export/study_metadata.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-05-31T14:36:06,282 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/backup 2025-05-31T14:36:06,283 copying build/lib/nmdc_runtime/site/backup/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-05-31T14:36:06,285 copying build/lib/nmdc_runtime/site/backup/nmdcdb_mongodump.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-05-31T14:36:06,287 copying build/lib/nmdc_runtime/site/backup/nmdcdb_mongoexport.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-05-31T14:36:06,290 copying build/lib/nmdc_runtime/site/backup/nmdcdb_mongoimport.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-05-31T14:36:06,293 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/drsobjects 2025-05-31T14:36:06,294 copying build/lib/nmdc_runtime/site/drsobjects/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/drsobjects 2025-05-31T14:36:06,297 copying build/lib/nmdc_runtime/site/drsobjects/ingest.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/drsobjects 2025-05-31T14:36:06,299 copying build/lib/nmdc_runtime/site/drsobjects/registration.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/drsobjects 2025-05-31T14:36:06,302 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/repair 2025-05-31T14:36:06,304 copying build/lib/nmdc_runtime/site/repair/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/repair 2025-05-31T14:36:06,306 copying build/lib/nmdc_runtime/site/repair/database_updater.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/repair 2025-05-31T14:36:06,309 copying build/lib/nmdc_runtime/site/repository.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-05-31T14:36:06,313 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/normalization 2025-05-31T14:36:06,314 copying build/lib/nmdc_runtime/site/normalization/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/normalization 2025-05-31T14:36:06,317 copying build/lib/nmdc_runtime/site/normalization/gold.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/normalization 2025-05-31T14:36:06,319 copying build/lib/nmdc_runtime/site/graphs.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-05-31T14:36:06,322 copying build/lib/nmdc_runtime/site/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-05-31T14:36:06,325 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/translation 2025-05-31T14:36:06,326 copying build/lib/nmdc_runtime/site/translation/emsl.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-05-31T14:36:06,329 copying build/lib/nmdc_runtime/site/translation/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-05-31T14:36:06,330 copying build/lib/nmdc_runtime/site/translation/submission_portal_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-05-31T14:36:06,334 copying build/lib/nmdc_runtime/site/translation/jgi.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-05-31T14:36:06,336 copying build/lib/nmdc_runtime/site/translation/gold.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-05-31T14:36:06,339 copying build/lib/nmdc_runtime/site/translation/neon_soil_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-05-31T14:36:06,342 copying build/lib/nmdc_runtime/site/translation/neon_surface_water_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-05-31T14:36:06,345 copying build/lib/nmdc_runtime/site/translation/neon_utils.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-05-31T14:36:06,348 copying build/lib/nmdc_runtime/site/translation/translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-05-31T14:36:06,350 copying build/lib/nmdc_runtime/site/translation/gold_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-05-31T14:36:06,354 copying build/lib/nmdc_runtime/site/translation/neon_benthic_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-05-31T14:36:06,357 copying build/lib/nmdc_runtime/site/translation/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-05-31T14:36:06,360 copying build/lib/nmdc_runtime/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-05-31T14:36:06,363 copying build/lib/nmdc_runtime/main.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-05-31T14:36:06,365 running install_egg_info 2025-05-31T14:36:06,401 running egg_info 2025-05-31T14:36:06,434 writing nmdc_runtime.egg-info/PKG-INFO 2025-05-31T14:36:06,437 writing dependency_links to nmdc_runtime.egg-info/dependency_links.txt 2025-05-31T14:36:06,439 writing entry points to nmdc_runtime.egg-info/entry_points.txt 2025-05-31T14:36:06,441 writing top-level names to nmdc_runtime.egg-info/top_level.txt 2025-05-31T14:36:06,571 listing git files failed - pretending there aren't any 2025-05-31T14:36:06,576 reading manifest file 'nmdc_runtime.egg-info/SOURCES.txt' 2025-05-31T14:36:06,685 adding license file 'LICENSE' 2025-05-31T14:36:06,709 writing manifest file 'nmdc_runtime.egg-info/SOURCES.txt' 2025-05-31T14:36:06,711 Copying nmdc_runtime.egg-info to build/bdist.linux-armv7l/wheel/./nmdc_runtime-2.8.0-py3.11.egg-info 2025-05-31T14:36:06,724 running install_scripts 2025-05-31T14:36:06,741 creating build/bdist.linux-armv7l/wheel/nmdc_runtime-2.8.0.dist-info/WHEEL 2025-05-31T14:36:06,744 creating '/tmp/pip-wheel-4lootum_/nmdc_runtime-2.8.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-05-31T14:36:06,747 adding 'nmdc_runtime/__init__.py' 2025-05-31T14:36:06,748 adding 'nmdc_runtime/config.py' 2025-05-31T14:36:06,750 adding 'nmdc_runtime/containers.py' 2025-05-31T14:36:06,752 adding 'nmdc_runtime/main.py' 2025-05-31T14:36:06,753 adding 'nmdc_runtime/mongo_util.py' 2025-05-31T14:36:06,759 adding 'nmdc_runtime/util.py' 2025-05-31T14:36:06,761 adding 'nmdc_runtime/client/__init__.py' 2025-05-31T14:36:06,763 adding 'nmdc_runtime/core/__init__.py' 2025-05-31T14:36:06,765 adding 'nmdc_runtime/core/db/Database.py' 2025-05-31T14:36:06,766 adding 'nmdc_runtime/core/db/__init__.py' 2025-05-31T14:36:06,768 adding 'nmdc_runtime/core/exceptions/__init__.py' 2025-05-31T14:36:06,770 adding 'nmdc_runtime/core/exceptions/base.py' 2025-05-31T14:36:06,771 adding 'nmdc_runtime/core/exceptions/token.py' 2025-05-31T14:36:06,773 adding 'nmdc_runtime/domain/__init__.py' 2025-05-31T14:36:06,775 adding 'nmdc_runtime/domain/users/__init__.py' 2025-05-31T14:36:06,776 adding 'nmdc_runtime/domain/users/queriesInterface.py' 2025-05-31T14:36:06,777 adding 'nmdc_runtime/domain/users/userSchema.py' 2025-05-31T14:36:06,779 adding 'nmdc_runtime/domain/users/userService.py' 2025-05-31T14:36:06,780 adding 'nmdc_runtime/infrastructure/__init__.py' 2025-05-31T14:36:06,782 adding 'nmdc_runtime/infrastructure/database/__init__.py' 2025-05-31T14:36:06,783 adding 'nmdc_runtime/infrastructure/database/db.py' 2025-05-31T14:36:06,785 adding 'nmdc_runtime/infrastructure/database/models/__init__.py' 2025-05-31T14:36:06,786 adding 'nmdc_runtime/infrastructure/database/models/user.py' 2025-05-31T14:36:06,788 adding 'nmdc_runtime/lib/__init__.py' 2025-05-31T14:36:06,789 adding 'nmdc_runtime/lib/extract_nmdc_data.py' 2025-05-31T14:36:06,791 adding 'nmdc_runtime/lib/load_nmdc_data.py' 2025-05-31T14:36:06,794 adding 'nmdc_runtime/lib/nmdc_dataframes.py' 2025-05-31T14:36:06,796 adding 'nmdc_runtime/lib/nmdc_etl_class.py' 2025-05-31T14:36:06,802 adding 'nmdc_runtime/lib/transform_nmdc_data.py' 2025-05-31T14:36:06,805 adding 'nmdc_runtime/minter/__init__.py' 2025-05-31T14:36:06,806 adding 'nmdc_runtime/minter/bootstrap.py' 2025-05-31T14:36:06,807 adding 'nmdc_runtime/minter/config.py' 2025-05-31T14:36:06,809 adding 'nmdc_runtime/minter/adapters/__init__.py' 2025-05-31T14:36:06,811 adding 'nmdc_runtime/minter/adapters/repository.py' 2025-05-31T14:36:06,813 adding 'nmdc_runtime/minter/domain/__init__.py' 2025-05-31T14:36:06,814 adding 'nmdc_runtime/minter/domain/model.py' 2025-05-31T14:36:06,816 adding 'nmdc_runtime/minter/entrypoints/__init__.py' 2025-05-31T14:36:06,817 adding 'nmdc_runtime/minter/entrypoints/fastapi_app.py' 2025-05-31T14:36:06,819 adding 'nmdc_runtime/site/__init__.py' 2025-05-31T14:36:06,822 adding 'nmdc_runtime/site/graphs.py' 2025-05-31T14:36:06,830 adding 'nmdc_runtime/site/ops.py' 2025-05-31T14:36:06,834 adding 'nmdc_runtime/site/repository.py' 2025-05-31T14:36:06,837 adding 'nmdc_runtime/site/resources.py' 2025-05-31T14:36:06,839 adding 'nmdc_runtime/site/util.py' 2025-05-31T14:36:06,841 adding 'nmdc_runtime/site/backup/__init__.py' 2025-05-31T14:36:06,843 adding 'nmdc_runtime/site/backup/nmdcdb_mongodump.py' 2025-05-31T14:36:06,844 adding 'nmdc_runtime/site/backup/nmdcdb_mongoexport.py' 2025-05-31T14:36:06,846 adding 'nmdc_runtime/site/backup/nmdcdb_mongoimport.py' 2025-05-31T14:36:06,847 adding 'nmdc_runtime/site/changesheets/__init__.py' 2025-05-31T14:36:06,849 adding 'nmdc_runtime/site/changesheets/base.py' 2025-05-31T14:36:06,851 adding 'nmdc_runtime/site/drsobjects/__init__.py' 2025-05-31T14:36:06,853 adding 'nmdc_runtime/site/drsobjects/ingest.py' 2025-05-31T14:36:06,854 adding 'nmdc_runtime/site/drsobjects/registration.py' 2025-05-31T14:36:06,856 adding 'nmdc_runtime/site/export/__init__.py' 2025-05-31T14:36:06,859 adding 'nmdc_runtime/site/export/ncbi_xml.py' 2025-05-31T14:36:06,862 adding 'nmdc_runtime/site/export/ncbi_xml_utils.py' 2025-05-31T14:36:06,863 adding 'nmdc_runtime/site/export/study_metadata.py' 2025-05-31T14:36:06,865 adding 'nmdc_runtime/site/normalization/__init__.py' 2025-05-31T14:36:06,866 adding 'nmdc_runtime/site/normalization/gold.py' 2025-05-31T14:36:06,868 adding 'nmdc_runtime/site/repair/__init__.py' 2025-05-31T14:36:06,871 adding 'nmdc_runtime/site/repair/database_updater.py' 2025-05-31T14:36:06,873 adding 'nmdc_runtime/site/translation/__init__.py' 2025-05-31T14:36:06,874 adding 'nmdc_runtime/site/translation/emsl.py' 2025-05-31T14:36:06,876 adding 'nmdc_runtime/site/translation/gold.py' 2025-05-31T14:36:06,880 adding 'nmdc_runtime/site/translation/gold_translator.py' 2025-05-31T14:36:06,881 adding 'nmdc_runtime/site/translation/jgi.py' 2025-05-31T14:36:06,884 adding 'nmdc_runtime/site/translation/neon_benthic_translator.py' 2025-05-31T14:36:06,888 adding 'nmdc_runtime/site/translation/neon_soil_translator.py' 2025-05-31T14:36:06,892 adding 'nmdc_runtime/site/translation/neon_surface_water_translator.py' 2025-05-31T14:36:06,894 adding 'nmdc_runtime/site/translation/neon_utils.py' 2025-05-31T14:36:06,898 adding 'nmdc_runtime/site/translation/submission_portal_translator.py' 2025-05-31T14:36:06,900 adding 'nmdc_runtime/site/translation/translator.py' 2025-05-31T14:36:06,901 adding 'nmdc_runtime/site/translation/util.py' 2025-05-31T14:36:06,903 adding 'nmdc_runtime/site/validation/__init__.py' 2025-05-31T14:36:06,904 adding 'nmdc_runtime/site/validation/emsl.py' 2025-05-31T14:36:06,905 adding 'nmdc_runtime/site/validation/gold.py' 2025-05-31T14:36:06,906 adding 'nmdc_runtime/site/validation/jgi.py' 2025-05-31T14:36:06,908 adding 'nmdc_runtime/site/validation/util.py' 2025-05-31T14:36:06,911 adding 'nmdc_runtime-2.8.0.dist-info/licenses/LICENSE' 2025-05-31T14:36:06,912 adding 'nmdc_runtime-2.8.0.dist-info/METADATA' 2025-05-31T14:36:06,913 adding 'nmdc_runtime-2.8.0.dist-info/WHEEL' 2025-05-31T14:36:06,914 adding 'nmdc_runtime-2.8.0.dist-info/entry_points.txt' 2025-05-31T14:36:06,915 adding 'nmdc_runtime-2.8.0.dist-info/top_level.txt' 2025-05-31T14:36:06,917 adding 'nmdc_runtime-2.8.0.dist-info/RECORD' 2025-05-31T14:36:06,921 removing build/bdist.linux-armv7l/wheel 2025-05-31T14:36:07,064 Building wheel for nmdc-runtime (setup.py): finished with status 'done' 2025-05-31T14:36:07,068 Created wheel for nmdc-runtime: filename=nmdc_runtime-2.8.0-py3-none-any.whl size=149232 sha256=296830ccedc1bcce69e92e0f5838daa7ac298de7b5500f5689b80216b25e0fe0 2025-05-31T14:36:07,069 Stored in directory: /tmp/pip-ephem-wheel-cache-6_tcc7uu/wheels/d5/12/bc/50d4145c84dc11719dddbc3ab7231033e60316fe755f44f359 2025-05-31T14:36:07,087 Successfully built nmdc-runtime 2025-05-31T14:36:07,142 Removed build tracker: '/tmp/pip-build-tracker-t3n1l6s2'