2025-06-05T13:27:14,772 Created temporary directory: /tmp/pip-build-tracker-3s34k99p 2025-06-05T13:27:14,773 Initialized build tracking at /tmp/pip-build-tracker-3s34k99p 2025-06-05T13:27:14,774 Created build tracker: /tmp/pip-build-tracker-3s34k99p 2025-06-05T13:27:14,774 Entered build tracker: /tmp/pip-build-tracker-3s34k99p 2025-06-05T13:27:14,775 Created temporary directory: /tmp/pip-wheel-aqsiclnt 2025-06-05T13:27:14,779 Created temporary directory: /tmp/pip-ephem-wheel-cache-qack9t7c 2025-06-05T13:27:14,836 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-05T13:27:14,838 2 location(s) to search for versions of nmdc-runtime: 2025-06-05T13:27:14,838 * https://pypi.org/simple/nmdc-runtime/ 2025-06-05T13:27:14,838 * https://www.piwheels.org/simple/nmdc-runtime/ 2025-06-05T13:27:14,839 Fetching project page and analyzing links: https://pypi.org/simple/nmdc-runtime/ 2025-06-05T13:27:14,840 Getting page https://pypi.org/simple/nmdc-runtime/ 2025-06-05T13:27:14,841 Found index url https://pypi.org/simple/ 2025-06-05T13:27:15,069 Fetched page https://pypi.org/simple/nmdc-runtime/ as application/vnd.pypi.simple.v1+json 2025-06-05T13:27:15,090 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) 2025-06-05T13:27:15,092 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 2025-06-05T13:27:15,092 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) 2025-06-05T13:27:15,093 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 2025-06-05T13:27:15,094 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) 2025-06-05T13:27:15,094 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 2025-06-05T13:27:15,095 Skipping link: No binaries permitted for nmdc-runtime: 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version: 1.7.0 2025-06-05T13:27:15,128 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) 2025-06-05T13:27:15,128 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 2025-06-05T13:27:15,129 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) 2025-06-05T13:27:15,130 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 2025-06-05T13:27:15,131 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) 2025-06-05T13:27:15,132 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 2025-06-05T13:27:15,132 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) 2025-06-05T13:27:15,133 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 2025-06-05T13:27:15,134 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) 2025-06-05T13:27:15,134 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 2025-06-05T13:27:15,135 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) 2025-06-05T13:27:15,135 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 2025-06-05T13:27:15,136 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) 2025-06-05T13:27:15,137 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 2025-06-05T13:27:15,138 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) 2025-06-05T13:27:15,139 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 2025-06-05T13:27:15,139 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) 2025-06-05T13:27:15,140 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 2025-06-05T13:27:15,141 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) 2025-06-05T13:27:15,142 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 2025-06-05T13:27:15,143 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) 2025-06-05T13:27:15,143 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 2025-06-05T13:27:15,144 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) 2025-06-05T13:27:15,144 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 2025-06-05T13:27:15,145 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) 2025-06-05T13:27:15,146 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 2025-06-05T13:27:15,147 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) 2025-06-05T13:27:15,148 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 2025-06-05T13:27:15,149 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) 2025-06-05T13:27:15,150 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 2025-06-05T13:27:15,151 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) 2025-06-05T13:27:15,151 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 2025-06-05T13:27:15,152 Fetching project page and analyzing links: https://www.piwheels.org/simple/nmdc-runtime/ 2025-06-05T13:27:15,153 Getting page https://www.piwheels.org/simple/nmdc-runtime/ 2025-06-05T13:27:15,155 Found index url https://www.piwheels.org/simple/ 2025-06-05T13:27:15,317 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/ 2025-06-05T13:27:15,984 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/ 2025-06-05T13:27:17,150 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/ 2025-06-05T13:27:19,320 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/ 2025-06-05T13:27:23,509 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/ 2025-06-05T13:27:23,680 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 2025-06-05T13:27:23,682 Skipping link: not a file: https://www.piwheels.org/simple/nmdc-runtime/ 2025-06-05T13:27:23,683 Skipping link: not a file: https://pypi.org/simple/nmdc-runtime/ 2025-06-05T13:27:23,710 Given no hashes to check 1 links for project 'nmdc-runtime': discarding no candidates 2025-06-05T13:27:23,712 Collecting nmdc-runtime==2.6.0 2025-06-05T13:27:23,714 Created temporary directory: /tmp/pip-unpack-xjsgi1q9 2025-06-05T13:27:24,106 Downloading nmdc_runtime-2.6.0.tar.gz (63.9 MB) 2025-06-05T13:27:38,868 Added nmdc-runtime==2.6.0 from https://files.pythonhosted.org/packages/15/37/b8410264d240e26310eb513f1fecd83a34831be30350e242607585fc324a/nmdc_runtime-2.6.0.tar.gz to build tracker '/tmp/pip-build-tracker-3s34k99p' 2025-06-05T13:27:38,870 Running setup.py (path:/tmp/pip-wheel-aqsiclnt/nmdc-runtime_bea7290097bf45ac91d7f75218bec82d/setup.py) egg_info for package nmdc-runtime 2025-06-05T13:27:38,872 Created temporary directory: /tmp/pip-pip-egg-info-5ucdp3_i 2025-06-05T13:27:38,872 Preparing metadata (setup.py): started 2025-06-05T13:27:38,874 Running command python setup.py egg_info 2025-06-05T13:27:39,494 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-06-05T13:27:39,495 !! 2025-06-05T13:27:39,496 ******************************************************************************** 2025-06-05T13:27:39,496 Requirements should be satisfied by a PEP 517 installer. 2025-06-05T13:27:39,497 If you are using pip, you can try `pip install --use-pep517`. 2025-06-05T13:27:39,498 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-05T13:27:39,499 or your builds will no longer be supported. 2025-06-05T13:27:39,500 ******************************************************************************** 2025-06-05T13:27:39,501 !! 2025-06-05T13:27:39,502 dist.fetch_build_eggs(dist.setup_requires) 2025-06-05T13:27:42,447 WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section' 2025-06-05T13:27:42,448 Traceback (most recent call last): 2025-06-05T13:27:42,449 File "/tmp/pip-wheel-aqsiclnt/nmdc-runtime_bea7290097bf45ac91d7f75218bec82d/.eggs/setuptools_scm-8.3.1-py3.11.egg/setuptools_scm/_integration/pyproject_reading.py", line 36, in read_pyproject 2025-06-05T13:27:42,449 section = defn.get("tool", {})[tool_name] 2025-06-05T13:27:42,450 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 2025-06-05T13:27:42,450 KeyError: 'setuptools_scm' 2025-06-05T13:27:42,526 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-05T13:27:42,526 !! 2025-06-05T13:27:42,527 ******************************************************************************** 2025-06-05T13:27:42,528 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-05T13:27:42,529 License :: OSI Approved :: Apache Software License 2025-06-05T13:27:42,530 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-05T13:27:42,530 ******************************************************************************** 2025-06-05T13:27:42,531 !! 2025-06-05T13:27:42,532 self._finalize_license_expression() 2025-06-05T13:27:42,560 running egg_info 2025-06-05T13:27:42,592 creating /tmp/pip-pip-egg-info-5ucdp3_i/nmdc_runtime.egg-info 2025-06-05T13:27:42,593 writing /tmp/pip-pip-egg-info-5ucdp3_i/nmdc_runtime.egg-info/PKG-INFO 2025-06-05T13:27:42,596 writing dependency_links to /tmp/pip-pip-egg-info-5ucdp3_i/nmdc_runtime.egg-info/dependency_links.txt 2025-06-05T13:27:42,598 writing entry points to /tmp/pip-pip-egg-info-5ucdp3_i/nmdc_runtime.egg-info/entry_points.txt 2025-06-05T13:27:42,599 writing top-level names to /tmp/pip-pip-egg-info-5ucdp3_i/nmdc_runtime.egg-info/top_level.txt 2025-06-05T13:27:42,601 writing manifest file '/tmp/pip-pip-egg-info-5ucdp3_i/nmdc_runtime.egg-info/SOURCES.txt' 2025-06-05T13:27:42,827 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2025-06-05T13:27:42,833 reading manifest file '/tmp/pip-pip-egg-info-5ucdp3_i/nmdc_runtime.egg-info/SOURCES.txt' 2025-06-05T13:27:42,835 adding license file 'LICENSE' 2025-06-05T13:27:42,841 writing manifest file '/tmp/pip-pip-egg-info-5ucdp3_i/nmdc_runtime.egg-info/SOURCES.txt' 2025-06-05T13:27:42,954 Preparing metadata (setup.py): finished with status 'done' 2025-06-05T13:27:42,958 Source in /tmp/pip-wheel-aqsiclnt/nmdc-runtime_bea7290097bf45ac91d7f75218bec82d has version 2.6.0, which satisfies requirement nmdc-runtime==2.6.0 from https://files.pythonhosted.org/packages/15/37/b8410264d240e26310eb513f1fecd83a34831be30350e242607585fc324a/nmdc_runtime-2.6.0.tar.gz 2025-06-05T13:27:42,959 Removed nmdc-runtime==2.6.0 from https://files.pythonhosted.org/packages/15/37/b8410264d240e26310eb513f1fecd83a34831be30350e242607585fc324a/nmdc_runtime-2.6.0.tar.gz from build tracker '/tmp/pip-build-tracker-3s34k99p' 2025-06-05T13:27:42,965 Created temporary directory: /tmp/pip-unpack-99m_0ocu 2025-06-05T13:27:42,966 Created temporary directory: /tmp/pip-unpack-ib785j8e 2025-06-05T13:27:42,967 Building wheels for collected packages: nmdc-runtime 2025-06-05T13:27:42,972 Created temporary directory: /tmp/pip-wheel-p4ieamnl 2025-06-05T13:27:42,973 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 2025-06-05T13:27:42,974 Building wheel for nmdc-runtime (setup.py): started 2025-06-05T13:27:42,976 Destination directory: /tmp/pip-wheel-p4ieamnl 2025-06-05T13:27:42,977 Running command python setup.py bdist_wheel 2025-06-05T13:27:43,544 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-06-05T13:27:43,544 !! 2025-06-05T13:27:43,545 ******************************************************************************** 2025-06-05T13:27:43,545 Requirements should be satisfied by a PEP 517 installer. 2025-06-05T13:27:43,546 If you are using pip, you can try `pip install --use-pep517`. 2025-06-05T13:27:43,547 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-05T13:27:43,547 or your builds will no longer be supported. 2025-06-05T13:27:43,548 ******************************************************************************** 2025-06-05T13:27:43,548 !! 2025-06-05T13:27:43,549 dist.fetch_build_eggs(dist.setup_requires) 2025-06-05T13:27:44,089 WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section' 2025-06-05T13:27:44,089 Traceback (most recent call last): 2025-06-05T13:27:44,090 File "/tmp/pip-wheel-aqsiclnt/nmdc-runtime_bea7290097bf45ac91d7f75218bec82d/.eggs/setuptools_scm-8.3.1-py3.11.egg/setuptools_scm/_integration/pyproject_reading.py", line 36, in read_pyproject 2025-06-05T13:27:44,090 section = defn.get("tool", {})[tool_name] 2025-06-05T13:27:44,091 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 2025-06-05T13:27:44,091 KeyError: 'setuptools_scm' 2025-06-05T13:27:44,158 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-05T13:27:44,159 !! 2025-06-05T13:27:44,160 ******************************************************************************** 2025-06-05T13:27:44,161 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-05T13:27:44,162 License :: OSI Approved :: Apache Software License 2025-06-05T13:27:44,163 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-05T13:27:44,163 ******************************************************************************** 2025-06-05T13:27:44,165 !! 2025-06-05T13:27:44,165 self._finalize_license_expression() 2025-06-05T13:27:44,166 running bdist_wheel 2025-06-05T13:27:44,318 running build 2025-06-05T13:27:44,318 running build_py 2025-06-05T13:27:44,352 creating build/lib/nmdc_runtime 2025-06-05T13:27:44,355 copying nmdc_runtime/config.py -> build/lib/nmdc_runtime 2025-06-05T13:27:44,357 copying nmdc_runtime/__init__.py -> build/lib/nmdc_runtime 2025-06-05T13:27:44,359 copying nmdc_runtime/util.py -> build/lib/nmdc_runtime 2025-06-05T13:27:44,362 copying nmdc_runtime/containers.py -> build/lib/nmdc_runtime 2025-06-05T13:27:44,364 copying nmdc_runtime/main.py -> build/lib/nmdc_runtime 2025-06-05T13:27:44,367 creating build/lib/nmdc_runtime/lib 2025-06-05T13:27:44,368 copying nmdc_runtime/lib/nmdc_etl_class.py -> build/lib/nmdc_runtime/lib 2025-06-05T13:27:44,371 copying nmdc_runtime/lib/load_nmdc_data.py -> build/lib/nmdc_runtime/lib 2025-06-05T13:27:44,373 copying nmdc_runtime/lib/__init__.py -> build/lib/nmdc_runtime/lib 2025-06-05T13:27:44,376 copying nmdc_runtime/lib/extract_nmdc_data.py -> build/lib/nmdc_runtime/lib 2025-06-05T13:27:44,378 copying nmdc_runtime/lib/nmdc_dataframes.py -> build/lib/nmdc_runtime/lib 2025-06-05T13:27:44,381 copying nmdc_runtime/lib/transform_nmdc_data.py -> build/lib/nmdc_runtime/lib 2025-06-05T13:27:44,385 creating build/lib/nmdc_runtime/infrastructure 2025-06-05T13:27:44,386 copying nmdc_runtime/infrastructure/__init__.py -> build/lib/nmdc_runtime/infrastructure 2025-06-05T13:27:44,389 creating build/lib/nmdc_runtime/client 2025-06-05T13:27:44,390 copying nmdc_runtime/client/__init__.py -> build/lib/nmdc_runtime/client 2025-06-05T13:27:44,392 creating build/lib/nmdc_runtime/core 2025-06-05T13:27:44,394 copying nmdc_runtime/core/__init__.py -> build/lib/nmdc_runtime/core 2025-06-05T13:27:44,397 creating build/lib/nmdc_runtime/site 2025-06-05T13:27:44,398 copying nmdc_runtime/site/graphs.py -> build/lib/nmdc_runtime/site 2025-06-05T13:27:44,401 copying nmdc_runtime/site/resources.py -> build/lib/nmdc_runtime/site 2025-06-05T13:27:44,404 copying nmdc_runtime/site/__init__.py -> build/lib/nmdc_runtime/site 2025-06-05T13:27:44,405 copying nmdc_runtime/site/repository.py -> build/lib/nmdc_runtime/site 2025-06-05T13:27:44,409 copying nmdc_runtime/site/ops.py -> build/lib/nmdc_runtime/site 2025-06-05T13:27:44,412 copying nmdc_runtime/site/util.py -> build/lib/nmdc_runtime/site 2025-06-05T13:27:44,415 creating build/lib/nmdc_runtime/minter 2025-06-05T13:27:44,416 copying nmdc_runtime/minter/config.py -> build/lib/nmdc_runtime/minter 2025-06-05T13:27:44,418 copying nmdc_runtime/minter/__init__.py -> build/lib/nmdc_runtime/minter 2025-06-05T13:27:44,420 copying nmdc_runtime/minter/bootstrap.py -> build/lib/nmdc_runtime/minter 2025-06-05T13:27:44,423 creating build/lib/nmdc_runtime/domain 2025-06-05T13:27:44,424 copying nmdc_runtime/domain/__init__.py -> build/lib/nmdc_runtime/domain 2025-06-05T13:27:44,426 creating build/lib/nmdc_runtime/infrastructure/database 2025-06-05T13:27:44,428 copying nmdc_runtime/infrastructure/database/__init__.py -> build/lib/nmdc_runtime/infrastructure/database 2025-06-05T13:27:44,430 copying nmdc_runtime/infrastructure/database/db.py -> build/lib/nmdc_runtime/infrastructure/database 2025-06-05T13:27:44,433 creating build/lib/nmdc_runtime/infrastructure/database/models 2025-06-05T13:27:44,434 copying nmdc_runtime/infrastructure/database/models/user.py -> build/lib/nmdc_runtime/infrastructure/database/models 2025-06-05T13:27:44,436 copying nmdc_runtime/infrastructure/database/models/__init__.py -> build/lib/nmdc_runtime/infrastructure/database/models 2025-06-05T13:27:44,439 creating build/lib/nmdc_runtime/core/exceptions 2025-06-05T13:27:44,440 copying nmdc_runtime/core/exceptions/__init__.py -> build/lib/nmdc_runtime/core/exceptions 2025-06-05T13:27:44,442 copying nmdc_runtime/core/exceptions/token.py -> build/lib/nmdc_runtime/core/exceptions 2025-06-05T13:27:44,444 copying nmdc_runtime/core/exceptions/base.py -> build/lib/nmdc_runtime/core/exceptions 2025-06-05T13:27:44,447 creating build/lib/nmdc_runtime/core/db 2025-06-05T13:27:44,448 copying nmdc_runtime/core/db/__init__.py -> build/lib/nmdc_runtime/core/db 2025-06-05T13:27:44,450 copying nmdc_runtime/core/db/Database.py -> build/lib/nmdc_runtime/core/db 2025-06-05T13:27:44,453 creating build/lib/nmdc_runtime/site/validation 2025-06-05T13:27:44,454 copying nmdc_runtime/site/validation/jgi.py -> build/lib/nmdc_runtime/site/validation 2025-06-05T13:27:44,456 copying nmdc_runtime/site/validation/emsl.py -> build/lib/nmdc_runtime/site/validation 2025-06-05T13:27:44,458 copying nmdc_runtime/site/validation/__init__.py -> build/lib/nmdc_runtime/site/validation 2025-06-05T13:27:44,460 copying nmdc_runtime/site/validation/util.py -> build/lib/nmdc_runtime/site/validation 2025-06-05T13:27:44,462 copying nmdc_runtime/site/validation/gold.py -> build/lib/nmdc_runtime/site/validation 2025-06-05T13:27:44,465 creating build/lib/nmdc_runtime/site/normalization 2025-06-05T13:27:44,466 copying nmdc_runtime/site/normalization/__init__.py -> build/lib/nmdc_runtime/site/normalization 2025-06-05T13:27:44,468 copying nmdc_runtime/site/normalization/gold.py -> build/lib/nmdc_runtime/site/normalization 2025-06-05T13:27:44,471 creating build/lib/nmdc_runtime/site/drsobjects 2025-06-05T13:27:44,472 copying nmdc_runtime/site/drsobjects/__init__.py -> build/lib/nmdc_runtime/site/drsobjects 2025-06-05T13:27:44,474 copying nmdc_runtime/site/drsobjects/ingest.py -> build/lib/nmdc_runtime/site/drsobjects 2025-06-05T13:27:44,476 copying nmdc_runtime/site/drsobjects/registration.py -> build/lib/nmdc_runtime/site/drsobjects 2025-06-05T13:27:44,479 creating build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,481 copying nmdc_runtime/site/translation/jgi.py -> build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,483 copying nmdc_runtime/site/translation/emsl.py -> build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,485 copying nmdc_runtime/site/translation/neon_benthic_translator.py -> build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,488 copying nmdc_runtime/site/translation/neon_utils.py -> build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,490 copying nmdc_runtime/site/translation/gold_translator.py -> build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,493 copying nmdc_runtime/site/translation/__init__.py -> build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,495 copying nmdc_runtime/site/translation/neon_surface_water_translator.py -> build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,498 copying nmdc_runtime/site/translation/submission_portal_translator.py -> build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,502 copying nmdc_runtime/site/translation/translator.py -> build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,504 copying nmdc_runtime/site/translation/util.py -> build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,506 copying nmdc_runtime/site/translation/gold.py -> build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,509 copying nmdc_runtime/site/translation/neon_soil_translator.py -> build/lib/nmdc_runtime/site/translation 2025-06-05T13:27:44,513 creating build/lib/nmdc_runtime/site/changesheets 2025-06-05T13:27:44,515 copying nmdc_runtime/site/changesheets/__init__.py -> build/lib/nmdc_runtime/site/changesheets 2025-06-05T13:27:44,518 copying nmdc_runtime/site/changesheets/base.py -> build/lib/nmdc_runtime/site/changesheets 2025-06-05T13:27:44,521 creating build/lib/nmdc_runtime/site/repair 2025-06-05T13:27:44,523 copying nmdc_runtime/site/repair/database_updater.py -> build/lib/nmdc_runtime/site/repair 2025-06-05T13:27:44,526 copying nmdc_runtime/site/repair/__init__.py -> build/lib/nmdc_runtime/site/repair 2025-06-05T13:27:44,529 creating build/lib/nmdc_runtime/site/export 2025-06-05T13:27:44,530 copying nmdc_runtime/site/export/study_metadata.py -> build/lib/nmdc_runtime/site/export 2025-06-05T13:27:44,533 copying nmdc_runtime/site/export/__init__.py -> build/lib/nmdc_runtime/site/export 2025-06-05T13:27:44,535 copying nmdc_runtime/site/export/ncbi_xml.py -> build/lib/nmdc_runtime/site/export 2025-06-05T13:27:44,539 copying nmdc_runtime/site/export/ncbi_xml_utils.py -> build/lib/nmdc_runtime/site/export 2025-06-05T13:27:44,542 creating build/lib/nmdc_runtime/site/backup 2025-06-05T13:27:44,543 copying nmdc_runtime/site/backup/nmdcdb_mongoexport.py -> build/lib/nmdc_runtime/site/backup 2025-06-05T13:27:44,546 copying nmdc_runtime/site/backup/nmdcdb_mongoimport.py -> build/lib/nmdc_runtime/site/backup 2025-06-05T13:27:44,549 copying nmdc_runtime/site/backup/__init__.py -> build/lib/nmdc_runtime/site/backup 2025-06-05T13:27:44,551 copying nmdc_runtime/site/backup/nmdcdb_mongodump.py -> build/lib/nmdc_runtime/site/backup 2025-06-05T13:27:44,554 creating build/lib/nmdc_runtime/minter/adapters 2025-06-05T13:27:44,555 copying nmdc_runtime/minter/adapters/__init__.py -> build/lib/nmdc_runtime/minter/adapters 2025-06-05T13:27:44,557 copying nmdc_runtime/minter/adapters/repository.py -> build/lib/nmdc_runtime/minter/adapters 2025-06-05T13:27:44,560 creating build/lib/nmdc_runtime/minter/entrypoints 2025-06-05T13:27:44,562 copying nmdc_runtime/minter/entrypoints/__init__.py -> build/lib/nmdc_runtime/minter/entrypoints 2025-06-05T13:27:44,564 copying nmdc_runtime/minter/entrypoints/fastapi_app.py -> build/lib/nmdc_runtime/minter/entrypoints 2025-06-05T13:27:44,566 creating build/lib/nmdc_runtime/minter/domain 2025-06-05T13:27:44,568 copying nmdc_runtime/minter/domain/model.py -> build/lib/nmdc_runtime/minter/domain 2025-06-05T13:27:44,570 copying nmdc_runtime/minter/domain/__init__.py -> build/lib/nmdc_runtime/minter/domain 2025-06-05T13:27:44,573 creating build/lib/nmdc_runtime/domain/users 2025-06-05T13:27:44,574 copying nmdc_runtime/domain/users/__init__.py -> build/lib/nmdc_runtime/domain/users 2025-06-05T13:27:44,576 copying nmdc_runtime/domain/users/queriesInterface.py -> build/lib/nmdc_runtime/domain/users 2025-06-05T13:27:44,578 copying nmdc_runtime/domain/users/userService.py -> build/lib/nmdc_runtime/domain/users 2025-06-05T13:27:44,581 copying nmdc_runtime/domain/users/userSchema.py -> build/lib/nmdc_runtime/domain/users 2025-06-05T13:27:44,635 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-05T13:27:44,635 !! 2025-06-05T13:27:44,636 ******************************************************************************** 2025-06-05T13:27:44,637 Please avoid running ``setup.py`` directly. 2025-06-05T13:27:44,637 Instead, use pypa/build, pypa/installer or other 2025-06-05T13:27:44,638 standards-based tools. 2025-06-05T13:27:44,639 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-05T13:27:44,639 or your builds will no longer be supported. 2025-06-05T13:27:44,640 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-05T13:27:44,640 ******************************************************************************** 2025-06-05T13:27:44,641 !! 2025-06-05T13:27:44,642 self.initialize_options() 2025-06-05T13:27:44,669 installing to build/bdist.linux-armv7l/wheel 2025-06-05T13:27:44,670 running install 2025-06-05T13:27:44,696 running install_lib 2025-06-05T13:27:44,726 creating build/bdist.linux-armv7l/wheel 2025-06-05T13:27:44,729 creating build/bdist.linux-armv7l/wheel/nmdc_runtime 2025-06-05T13:27:44,731 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/lib 2025-06-05T13:27:44,733 copying build/lib/nmdc_runtime/lib/nmdc_etl_class.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-06-05T13:27:44,736 copying build/lib/nmdc_runtime/lib/load_nmdc_data.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-06-05T13:27:44,738 copying build/lib/nmdc_runtime/lib/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-06-05T13:27:44,741 copying build/lib/nmdc_runtime/lib/extract_nmdc_data.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-06-05T13:27:44,743 copying build/lib/nmdc_runtime/lib/nmdc_dataframes.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-06-05T13:27:44,746 copying build/lib/nmdc_runtime/lib/transform_nmdc_data.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-06-05T13:27:44,750 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/infrastructure 2025-06-05T13:27:44,752 copying build/lib/nmdc_runtime/infrastructure/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure 2025-06-05T13:27:44,755 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/infrastructure/database 2025-06-05T13:27:44,756 copying build/lib/nmdc_runtime/infrastructure/database/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database 2025-06-05T13:27:44,759 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/infrastructure/database/models 2025-06-05T13:27:44,761 copying build/lib/nmdc_runtime/infrastructure/database/models/user.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database/models 2025-06-05T13:27:44,764 copying build/lib/nmdc_runtime/infrastructure/database/models/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database/models 2025-06-05T13:27:44,766 copying build/lib/nmdc_runtime/infrastructure/database/db.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database 2025-06-05T13:27:44,768 copying build/lib/nmdc_runtime/config.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-06-05T13:27:44,771 copying build/lib/nmdc_runtime/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-06-05T13:27:44,774 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/client 2025-06-05T13:27:44,775 copying build/lib/nmdc_runtime/client/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/client 2025-06-05T13:27:44,778 copying build/lib/nmdc_runtime/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-06-05T13:27:44,781 copying build/lib/nmdc_runtime/containers.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-06-05T13:27:44,785 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/core 2025-06-05T13:27:44,787 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/core/exceptions 2025-06-05T13:27:44,789 copying build/lib/nmdc_runtime/core/exceptions/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/exceptions 2025-06-05T13:27:44,792 copying build/lib/nmdc_runtime/core/exceptions/token.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/exceptions 2025-06-05T13:27:44,794 copying build/lib/nmdc_runtime/core/exceptions/base.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/exceptions 2025-06-05T13:27:44,797 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/core/db 2025-06-05T13:27:44,799 copying build/lib/nmdc_runtime/core/db/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/db 2025-06-05T13:27:44,801 copying build/lib/nmdc_runtime/core/db/Database.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/db 2025-06-05T13:27:44,803 copying build/lib/nmdc_runtime/core/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core 2025-06-05T13:27:44,806 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site 2025-06-05T13:27:44,808 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/validation 2025-06-05T13:27:44,809 copying build/lib/nmdc_runtime/site/validation/jgi.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-06-05T13:27:44,812 copying build/lib/nmdc_runtime/site/validation/emsl.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-06-05T13:27:44,814 copying build/lib/nmdc_runtime/site/validation/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-06-05T13:27:44,816 copying build/lib/nmdc_runtime/site/validation/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-06-05T13:27:44,818 copying build/lib/nmdc_runtime/site/validation/gold.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-06-05T13:27:44,820 copying build/lib/nmdc_runtime/site/graphs.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-06-05T13:27:44,823 copying build/lib/nmdc_runtime/site/resources.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-06-05T13:27:44,827 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/normalization 2025-06-05T13:27:44,829 copying build/lib/nmdc_runtime/site/normalization/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/normalization 2025-06-05T13:27:44,831 copying build/lib/nmdc_runtime/site/normalization/gold.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/normalization 2025-06-05T13:27:44,833 copying build/lib/nmdc_runtime/site/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-06-05T13:27:44,836 copying build/lib/nmdc_runtime/site/repository.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-06-05T13:27:44,840 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/drsobjects 2025-06-05T13:27:44,841 copying build/lib/nmdc_runtime/site/drsobjects/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/drsobjects 2025-06-05T13:27:44,844 copying build/lib/nmdc_runtime/site/drsobjects/ingest.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/drsobjects 2025-06-05T13:27:44,846 copying build/lib/nmdc_runtime/site/drsobjects/registration.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/drsobjects 2025-06-05T13:27:44,849 copying build/lib/nmdc_runtime/site/ops.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-06-05T13:27:44,853 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/translation 2025-06-05T13:27:44,855 copying build/lib/nmdc_runtime/site/translation/jgi.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-05T13:27:44,858 copying build/lib/nmdc_runtime/site/translation/emsl.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-05T13:27:44,860 copying build/lib/nmdc_runtime/site/translation/neon_benthic_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-05T13:27:44,863 copying build/lib/nmdc_runtime/site/translation/neon_utils.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-05T13:27:44,866 copying build/lib/nmdc_runtime/site/translation/gold_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-05T13:27:44,869 copying build/lib/nmdc_runtime/site/translation/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-05T13:27:44,871 copying build/lib/nmdc_runtime/site/translation/neon_surface_water_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-05T13:27:44,876 copying build/lib/nmdc_runtime/site/translation/submission_portal_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-05T13:27:44,880 copying build/lib/nmdc_runtime/site/translation/translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-05T13:27:44,882 copying build/lib/nmdc_runtime/site/translation/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-05T13:27:44,885 copying build/lib/nmdc_runtime/site/translation/gold.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-05T13:27:44,887 copying build/lib/nmdc_runtime/site/translation/neon_soil_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-05T13:27:44,892 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/changesheets 2025-06-05T13:27:44,893 copying build/lib/nmdc_runtime/site/changesheets/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/changesheets 2025-06-05T13:27:44,895 copying build/lib/nmdc_runtime/site/changesheets/base.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/changesheets 2025-06-05T13:27:44,898 copying build/lib/nmdc_runtime/site/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-06-05T13:27:44,901 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/repair 2025-06-05T13:27:44,902 copying build/lib/nmdc_runtime/site/repair/database_updater.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/repair 2025-06-05T13:27:44,906 copying build/lib/nmdc_runtime/site/repair/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/repair 2025-06-05T13:27:44,908 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/export 2025-06-05T13:27:44,910 copying build/lib/nmdc_runtime/site/export/study_metadata.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-06-05T13:27:44,913 copying build/lib/nmdc_runtime/site/export/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-06-05T13:27:44,915 copying build/lib/nmdc_runtime/site/export/ncbi_xml.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-06-05T13:27:44,919 copying build/lib/nmdc_runtime/site/export/ncbi_xml_utils.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-06-05T13:27:44,922 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/backup 2025-06-05T13:27:44,924 copying build/lib/nmdc_runtime/site/backup/nmdcdb_mongoexport.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-06-05T13:27:44,927 copying build/lib/nmdc_runtime/site/backup/nmdcdb_mongoimport.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-06-05T13:27:44,930 copying build/lib/nmdc_runtime/site/backup/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-06-05T13:27:44,932 copying build/lib/nmdc_runtime/site/backup/nmdcdb_mongodump.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-06-05T13:27:44,935 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter 2025-06-05T13:27:44,937 copying build/lib/nmdc_runtime/minter/config.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter 2025-06-05T13:27:44,939 copying build/lib/nmdc_runtime/minter/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter 2025-06-05T13:27:44,941 copying build/lib/nmdc_runtime/minter/bootstrap.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter 2025-06-05T13:27:44,944 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter/adapters 2025-06-05T13:27:44,946 copying build/lib/nmdc_runtime/minter/adapters/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/adapters 2025-06-05T13:27:44,948 copying build/lib/nmdc_runtime/minter/adapters/repository.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/adapters 2025-06-05T13:27:44,951 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter/entrypoints 2025-06-05T13:27:44,953 copying build/lib/nmdc_runtime/minter/entrypoints/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/entrypoints 2025-06-05T13:27:44,955 copying build/lib/nmdc_runtime/minter/entrypoints/fastapi_app.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/entrypoints 2025-06-05T13:27:44,958 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter/domain 2025-06-05T13:27:44,960 copying build/lib/nmdc_runtime/minter/domain/model.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/domain 2025-06-05T13:27:44,962 copying build/lib/nmdc_runtime/minter/domain/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/domain 2025-06-05T13:27:44,964 copying build/lib/nmdc_runtime/main.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-06-05T13:27:44,967 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/domain 2025-06-05T13:27:44,968 copying build/lib/nmdc_runtime/domain/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain 2025-06-05T13:27:44,971 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/domain/users 2025-06-05T13:27:44,973 copying build/lib/nmdc_runtime/domain/users/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-06-05T13:27:44,975 copying build/lib/nmdc_runtime/domain/users/queriesInterface.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-06-05T13:27:44,977 copying build/lib/nmdc_runtime/domain/users/userService.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-06-05T13:27:44,979 copying build/lib/nmdc_runtime/domain/users/userSchema.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-06-05T13:27:44,981 running install_egg_info 2025-06-05T13:27:45,017 running egg_info 2025-06-05T13:27:45,049 writing nmdc_runtime.egg-info/PKG-INFO 2025-06-05T13:27:45,053 writing dependency_links to nmdc_runtime.egg-info/dependency_links.txt 2025-06-05T13:27:45,055 writing entry points to nmdc_runtime.egg-info/entry_points.txt 2025-06-05T13:27:45,057 writing top-level names to nmdc_runtime.egg-info/top_level.txt 2025-06-05T13:27:45,183 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2025-06-05T13:27:45,186 reading manifest file 'nmdc_runtime.egg-info/SOURCES.txt' 2025-06-05T13:27:45,295 adding license file 'LICENSE' 2025-06-05T13:27:45,319 writing manifest file 'nmdc_runtime.egg-info/SOURCES.txt' 2025-06-05T13:27:45,322 Copying nmdc_runtime.egg-info to build/bdist.linux-armv7l/wheel/./nmdc_runtime-2.6.0-py3.11.egg-info 2025-06-05T13:27:45,332 running install_scripts 2025-06-05T13:27:45,347 creating build/bdist.linux-armv7l/wheel/nmdc_runtime-2.6.0.dist-info/WHEEL 2025-06-05T13:27:45,350 creating '/tmp/pip-wheel-p4ieamnl/nmdc_runtime-2.6.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-05T13:27:45,353 adding 'nmdc_runtime/__init__.py' 2025-06-05T13:27:45,355 adding 'nmdc_runtime/config.py' 2025-06-05T13:27:45,357 adding 'nmdc_runtime/containers.py' 2025-06-05T13:27:45,359 adding 'nmdc_runtime/main.py' 2025-06-05T13:27:45,364 adding 'nmdc_runtime/util.py' 2025-06-05T13:27:45,366 adding 'nmdc_runtime/client/__init__.py' 2025-06-05T13:27:45,369 adding 'nmdc_runtime/core/__init__.py' 2025-06-05T13:27:45,371 adding 'nmdc_runtime/core/db/Database.py' 2025-06-05T13:27:45,373 adding 'nmdc_runtime/core/db/__init__.py' 2025-06-05T13:27:45,375 adding 'nmdc_runtime/core/exceptions/__init__.py' 2025-06-05T13:27:45,376 adding 'nmdc_runtime/core/exceptions/base.py' 2025-06-05T13:27:45,378 adding 'nmdc_runtime/core/exceptions/token.py' 2025-06-05T13:27:45,379 adding 'nmdc_runtime/domain/__init__.py' 2025-06-05T13:27:45,381 adding 'nmdc_runtime/domain/users/__init__.py' 2025-06-05T13:27:45,382 adding 'nmdc_runtime/domain/users/queriesInterface.py' 2025-06-05T13:27:45,384 adding 'nmdc_runtime/domain/users/userSchema.py' 2025-06-05T13:27:45,385 adding 'nmdc_runtime/domain/users/userService.py' 2025-06-05T13:27:45,386 adding 'nmdc_runtime/infrastructure/__init__.py' 2025-06-05T13:27:45,388 adding 'nmdc_runtime/infrastructure/database/__init__.py' 2025-06-05T13:27:45,389 adding 'nmdc_runtime/infrastructure/database/db.py' 2025-06-05T13:27:45,391 adding 'nmdc_runtime/infrastructure/database/models/__init__.py' 2025-06-05T13:27:45,392 adding 'nmdc_runtime/infrastructure/database/models/user.py' 2025-06-05T13:27:45,394 adding 'nmdc_runtime/lib/__init__.py' 2025-06-05T13:27:45,395 adding 'nmdc_runtime/lib/extract_nmdc_data.py' 2025-06-05T13:27:45,396 adding 'nmdc_runtime/lib/load_nmdc_data.py' 2025-06-05T13:27:45,400 adding 'nmdc_runtime/lib/nmdc_dataframes.py' 2025-06-05T13:27:45,402 adding 'nmdc_runtime/lib/nmdc_etl_class.py' 2025-06-05T13:27:45,408 adding 'nmdc_runtime/lib/transform_nmdc_data.py' 2025-06-05T13:27:45,410 adding 'nmdc_runtime/minter/__init__.py' 2025-06-05T13:27:45,411 adding 'nmdc_runtime/minter/bootstrap.py' 2025-06-05T13:27:45,413 adding 'nmdc_runtime/minter/config.py' 2025-06-05T13:27:45,414 adding 'nmdc_runtime/minter/adapters/__init__.py' 2025-06-05T13:27:45,416 adding 'nmdc_runtime/minter/adapters/repository.py' 2025-06-05T13:27:45,418 adding 'nmdc_runtime/minter/domain/__init__.py' 2025-06-05T13:27:45,419 adding 'nmdc_runtime/minter/domain/model.py' 2025-06-05T13:27:45,421 adding 'nmdc_runtime/minter/entrypoints/__init__.py' 2025-06-05T13:27:45,422 adding 'nmdc_runtime/minter/entrypoints/fastapi_app.py' 2025-06-05T13:27:45,424 adding 'nmdc_runtime/site/__init__.py' 2025-06-05T13:27:45,426 adding 'nmdc_runtime/site/graphs.py' 2025-06-05T13:27:45,433 adding 'nmdc_runtime/site/ops.py' 2025-06-05T13:27:45,436 adding 'nmdc_runtime/site/repository.py' 2025-06-05T13:27:45,439 adding 'nmdc_runtime/site/resources.py' 2025-06-05T13:27:45,441 adding 'nmdc_runtime/site/util.py' 2025-06-05T13:27:45,442 adding 'nmdc_runtime/site/backup/__init__.py' 2025-06-05T13:27:45,444 adding 'nmdc_runtime/site/backup/nmdcdb_mongodump.py' 2025-06-05T13:27:45,445 adding 'nmdc_runtime/site/backup/nmdcdb_mongoexport.py' 2025-06-05T13:27:45,447 adding 'nmdc_runtime/site/backup/nmdcdb_mongoimport.py' 2025-06-05T13:27:45,448 adding 'nmdc_runtime/site/changesheets/__init__.py' 2025-06-05T13:27:45,450 adding 'nmdc_runtime/site/changesheets/base.py' 2025-06-05T13:27:45,452 adding 'nmdc_runtime/site/drsobjects/__init__.py' 2025-06-05T13:27:45,453 adding 'nmdc_runtime/site/drsobjects/ingest.py' 2025-06-05T13:27:45,454 adding 'nmdc_runtime/site/drsobjects/registration.py' 2025-06-05T13:27:45,456 adding 'nmdc_runtime/site/export/__init__.py' 2025-06-05T13:27:45,459 adding 'nmdc_runtime/site/export/ncbi_xml.py' 2025-06-05T13:27:45,461 adding 'nmdc_runtime/site/export/ncbi_xml_utils.py' 2025-06-05T13:27:45,462 adding 'nmdc_runtime/site/export/study_metadata.py' 2025-06-05T13:27:45,464 adding 'nmdc_runtime/site/normalization/__init__.py' 2025-06-05T13:27:45,466 adding 'nmdc_runtime/site/normalization/gold.py' 2025-06-05T13:27:45,467 adding 'nmdc_runtime/site/repair/__init__.py' 2025-06-05T13:27:45,469 adding 'nmdc_runtime/site/repair/database_updater.py' 2025-06-05T13:27:45,471 adding 'nmdc_runtime/site/translation/__init__.py' 2025-06-05T13:27:45,473 adding 'nmdc_runtime/site/translation/emsl.py' 2025-06-05T13:27:45,474 adding 'nmdc_runtime/site/translation/gold.py' 2025-06-05T13:27:45,478 adding 'nmdc_runtime/site/translation/gold_translator.py' 2025-06-05T13:27:45,479 adding 'nmdc_runtime/site/translation/jgi.py' 2025-06-05T13:27:45,482 adding 'nmdc_runtime/site/translation/neon_benthic_translator.py' 2025-06-05T13:27:45,486 adding 'nmdc_runtime/site/translation/neon_soil_translator.py' 2025-06-05T13:27:45,489 adding 'nmdc_runtime/site/translation/neon_surface_water_translator.py' 2025-06-05T13:27:45,491 adding 'nmdc_runtime/site/translation/neon_utils.py' 2025-06-05T13:27:45,496 adding 'nmdc_runtime/site/translation/submission_portal_translator.py' 2025-06-05T13:27:45,498 adding 'nmdc_runtime/site/translation/translator.py' 2025-06-05T13:27:45,499 adding 'nmdc_runtime/site/translation/util.py' 2025-06-05T13:27:45,501 adding 'nmdc_runtime/site/validation/__init__.py' 2025-06-05T13:27:45,502 adding 'nmdc_runtime/site/validation/emsl.py' 2025-06-05T13:27:45,504 adding 'nmdc_runtime/site/validation/gold.py' 2025-06-05T13:27:45,505 adding 'nmdc_runtime/site/validation/jgi.py' 2025-06-05T13:27:45,506 adding 'nmdc_runtime/site/validation/util.py' 2025-06-05T13:27:45,509 adding 'nmdc_runtime-2.6.0.dist-info/licenses/LICENSE' 2025-06-05T13:27:45,510 adding 'nmdc_runtime-2.6.0.dist-info/METADATA' 2025-06-05T13:27:45,511 adding 'nmdc_runtime-2.6.0.dist-info/WHEEL' 2025-06-05T13:27:45,512 adding 'nmdc_runtime-2.6.0.dist-info/entry_points.txt' 2025-06-05T13:27:45,513 adding 'nmdc_runtime-2.6.0.dist-info/top_level.txt' 2025-06-05T13:27:45,515 adding 'nmdc_runtime-2.6.0.dist-info/RECORD' 2025-06-05T13:27:45,519 removing build/bdist.linux-armv7l/wheel 2025-06-05T13:27:45,662 Building wheel for nmdc-runtime (setup.py): finished with status 'done' 2025-06-05T13:27:45,666 Created wheel for nmdc-runtime: filename=nmdc_runtime-2.6.0-py3-none-any.whl size=138943 sha256=4c84d9aca5b971e2e1a2447f43e26e5a0d513df000d774ff2083477a315d73fe 2025-06-05T13:27:45,668 Stored in directory: /tmp/pip-ephem-wheel-cache-qack9t7c/wheels/25/39/c6/b8219fd589442582dc5e296de710072b2184da34158d8f55bc 2025-06-05T13:27:45,682 Successfully built nmdc-runtime 2025-06-05T13:27:45,690 Removed build tracker: '/tmp/pip-build-tracker-3s34k99p'