2025-06-09T01:35:08,200 Created temporary directory: /tmp/pip-build-tracker-5pm0efpc 2025-06-09T01:35:08,201 Initialized build tracking at /tmp/pip-build-tracker-5pm0efpc 2025-06-09T01:35:08,202 Created build tracker: /tmp/pip-build-tracker-5pm0efpc 2025-06-09T01:35:08,202 Entered build tracker: /tmp/pip-build-tracker-5pm0efpc 2025-06-09T01:35:08,203 Created temporary directory: /tmp/pip-wheel-qydatk4s 2025-06-09T01:35:08,207 Created temporary directory: /tmp/pip-ephem-wheel-cache-tltg54el 2025-06-09T01:35:08,255 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-09T01:35:08,257 2 location(s) to search for versions of nmdc-runtime: 2025-06-09T01:35:08,257 * https://pypi.org/simple/nmdc-runtime/ 2025-06-09T01:35:08,257 * https://www.piwheels.org/simple/nmdc-runtime/ 2025-06-09T01:35:08,258 Fetching project page and analyzing links: https://pypi.org/simple/nmdc-runtime/ 2025-06-09T01:35:08,259 Getting page https://pypi.org/simple/nmdc-runtime/ 2025-06-09T01:35:08,260 Found index url https://pypi.org/simple/ 2025-06-09T01:35:08,484 Fetched page https://pypi.org/simple/nmdc-runtime/ as application/vnd.pypi.simple.v1+json 2025-06-09T01:35:08,494 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) 2025-06-09T01:35:08,495 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 2025-06-09T01:35:08,495 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/) 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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 2025-06-09T01:35:08,531 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) 2025-06-09T01:35:08,532 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 2025-06-09T01:35:08,533 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) 2025-06-09T01:35:08,533 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 2025-06-09T01:35:08,534 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) 2025-06-09T01:35:08,534 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 2025-06-09T01:35:08,535 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) 2025-06-09T01:35:08,535 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 2025-06-09T01:35:08,536 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) 2025-06-09T01:35:08,536 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 2025-06-09T01:35:08,537 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) 2025-06-09T01:35:08,538 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 2025-06-09T01:35:08,539 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) 2025-06-09T01:35:08,539 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 2025-06-09T01:35:08,540 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) 2025-06-09T01:35:08,541 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 2025-06-09T01:35:08,542 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) 2025-06-09T01:35:08,542 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 2025-06-09T01:35:08,543 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) 2025-06-09T01:35:08,543 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 2025-06-09T01:35:08,544 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) 2025-06-09T01:35:08,544 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 2025-06-09T01:35:08,545 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) 2025-06-09T01:35:08,546 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 2025-06-09T01:35:08,546 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) 2025-06-09T01:35:08,547 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 2025-06-09T01:35:08,548 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) 2025-06-09T01:35:08,548 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 2025-06-09T01:35:08,549 Fetching project page and analyzing links: https://www.piwheels.org/simple/nmdc-runtime/ 2025-06-09T01:35:08,550 Getting page https://www.piwheels.org/simple/nmdc-runtime/ 2025-06-09T01:35:08,551 Found index url https://www.piwheels.org/simple/ 2025-06-09T01:35:08,699 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/ 2025-06-09T01:35:09,355 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/ 2025-06-09T01:35:10,512 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/ 2025-06-09T01:35:12,730 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/ 2025-06-09T01:35:16,922 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/ 2025-06-09T01:35:17,144 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 2025-06-09T01:35:17,146 Skipping link: not a file: https://www.piwheels.org/simple/nmdc-runtime/ 2025-06-09T01:35:17,146 Skipping link: not a file: https://pypi.org/simple/nmdc-runtime/ 2025-06-09T01:35:17,168 Given no hashes to check 1 links for project 'nmdc-runtime': discarding no candidates 2025-06-09T01:35:17,170 Collecting nmdc-runtime==2.7.0 2025-06-09T01:35:17,172 Created temporary directory: /tmp/pip-unpack-s943y0kx 2025-06-09T01:35:17,698 Downloading nmdc_runtime-2.7.0.tar.gz (64.1 MB) 2025-06-09T01:35:33,931 Added nmdc-runtime==2.7.0 from https://files.pythonhosted.org/packages/5e/6b/fbe817602d790668bd4f95b231f62916a831a4178cf100cf5ad28788b6d8/nmdc_runtime-2.7.0.tar.gz to build tracker '/tmp/pip-build-tracker-5pm0efpc' 2025-06-09T01:35:33,932 Running setup.py (path:/tmp/pip-wheel-qydatk4s/nmdc-runtime_d095fa8b844a445f86588a39b4a0141a/setup.py) egg_info for package nmdc-runtime 2025-06-09T01:35:33,933 Created temporary directory: /tmp/pip-pip-egg-info-y4hbf_67 2025-06-09T01:35:33,934 Preparing metadata (setup.py): started 2025-06-09T01:35:33,935 Running command python setup.py egg_info 2025-06-09T01:35:34,489 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-06-09T01:35:34,489 !! 2025-06-09T01:35:34,490 ******************************************************************************** 2025-06-09T01:35:34,491 Requirements should be satisfied by a PEP 517 installer. 2025-06-09T01:35:34,491 If you are using pip, you can try `pip install --use-pep517`. 2025-06-09T01:35:34,493 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-09T01:35:34,493 or your builds will no longer be supported. 2025-06-09T01:35:34,494 ******************************************************************************** 2025-06-09T01:35:34,495 !! 2025-06-09T01:35:34,496 dist.fetch_build_eggs(dist.setup_requires) 2025-06-09T01:35:37,490 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-09T01:35:37,491 !! 2025-06-09T01:35:37,492 ******************************************************************************** 2025-06-09T01:35:37,493 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-09T01:35:37,494 License :: OSI Approved :: Apache Software License 2025-06-09T01:35:37,495 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-09T01:35:37,495 ******************************************************************************** 2025-06-09T01:35:37,496 !! 2025-06-09T01:35:37,497 self._finalize_license_expression() 2025-06-09T01:35:37,524 running egg_info 2025-06-09T01:35:37,554 creating /tmp/pip-pip-egg-info-y4hbf_67/nmdc_runtime.egg-info 2025-06-09T01:35:37,555 writing /tmp/pip-pip-egg-info-y4hbf_67/nmdc_runtime.egg-info/PKG-INFO 2025-06-09T01:35:37,559 writing dependency_links to /tmp/pip-pip-egg-info-y4hbf_67/nmdc_runtime.egg-info/dependency_links.txt 2025-06-09T01:35:37,560 writing entry points to /tmp/pip-pip-egg-info-y4hbf_67/nmdc_runtime.egg-info/entry_points.txt 2025-06-09T01:35:37,562 writing top-level names to /tmp/pip-pip-egg-info-y4hbf_67/nmdc_runtime.egg-info/top_level.txt 2025-06-09T01:35:37,563 writing manifest file '/tmp/pip-pip-egg-info-y4hbf_67/nmdc_runtime.egg-info/SOURCES.txt' 2025-06-09T01:35:37,777 listing git files failed - pretending there aren't any 2025-06-09T01:35:37,792 reading manifest file '/tmp/pip-pip-egg-info-y4hbf_67/nmdc_runtime.egg-info/SOURCES.txt' 2025-06-09T01:35:37,794 adding license file 'LICENSE' 2025-06-09T01:35:37,799 writing manifest file '/tmp/pip-pip-egg-info-y4hbf_67/nmdc_runtime.egg-info/SOURCES.txt' 2025-06-09T01:35:37,912 Preparing metadata (setup.py): finished with status 'done' 2025-06-09T01:35:37,916 Source in /tmp/pip-wheel-qydatk4s/nmdc-runtime_d095fa8b844a445f86588a39b4a0141a has version 2.7.0, which satisfies requirement nmdc-runtime==2.7.0 from https://files.pythonhosted.org/packages/5e/6b/fbe817602d790668bd4f95b231f62916a831a4178cf100cf5ad28788b6d8/nmdc_runtime-2.7.0.tar.gz 2025-06-09T01:35:37,917 Removed nmdc-runtime==2.7.0 from https://files.pythonhosted.org/packages/5e/6b/fbe817602d790668bd4f95b231f62916a831a4178cf100cf5ad28788b6d8/nmdc_runtime-2.7.0.tar.gz from build tracker '/tmp/pip-build-tracker-5pm0efpc' 2025-06-09T01:35:37,923 Created temporary directory: /tmp/pip-unpack-m1qjxha9 2025-06-09T01:35:37,924 Created temporary directory: /tmp/pip-unpack-ezhndwpx 2025-06-09T01:35:37,924 Building wheels for collected packages: nmdc-runtime 2025-06-09T01:35:37,928 Created temporary directory: /tmp/pip-wheel-00oiplqb 2025-06-09T01:35:37,929 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 2025-06-09T01:35:37,931 Building wheel for nmdc-runtime (setup.py): started 2025-06-09T01:35:37,932 Destination directory: /tmp/pip-wheel-00oiplqb 2025-06-09T01:35:37,932 Running command python setup.py bdist_wheel 2025-06-09T01:35:38,480 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-06-09T01:35:38,481 !! 2025-06-09T01:35:38,482 ******************************************************************************** 2025-06-09T01:35:38,482 Requirements should be satisfied by a PEP 517 installer. 2025-06-09T01:35:38,483 If you are using pip, you can try `pip install --use-pep517`. 2025-06-09T01:35:38,484 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-09T01:35:38,485 or your builds will no longer be supported. 2025-06-09T01:35:38,486 ******************************************************************************** 2025-06-09T01:35:38,487 !! 2025-06-09T01:35:38,487 dist.fetch_build_eggs(dist.setup_requires) 2025-06-09T01:35:39,116 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-09T01:35:39,116 !! 2025-06-09T01:35:39,117 ******************************************************************************** 2025-06-09T01:35:39,117 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-09T01:35:39,118 License :: OSI Approved :: Apache Software License 2025-06-09T01:35:39,119 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-09T01:35:39,120 ******************************************************************************** 2025-06-09T01:35:39,121 !! 2025-06-09T01:35:39,121 self._finalize_license_expression() 2025-06-09T01:35:39,122 running bdist_wheel 2025-06-09T01:35:39,270 running build 2025-06-09T01:35:39,271 running build_py 2025-06-09T01:35:39,304 creating build/lib/nmdc_runtime 2025-06-09T01:35:39,306 copying nmdc_runtime/config.py -> build/lib/nmdc_runtime 2025-06-09T01:35:39,309 copying nmdc_runtime/__init__.py -> build/lib/nmdc_runtime 2025-06-09T01:35:39,310 copying nmdc_runtime/main.py -> build/lib/nmdc_runtime 2025-06-09T01:35:39,312 copying nmdc_runtime/containers.py -> build/lib/nmdc_runtime 2025-06-09T01:35:39,314 copying nmdc_runtime/util.py -> build/lib/nmdc_runtime 2025-06-09T01:35:39,317 creating build/lib/nmdc_runtime/site 2025-06-09T01:35:39,318 copying nmdc_runtime/site/repository.py -> build/lib/nmdc_runtime/site 2025-06-09T01:35:39,321 copying nmdc_runtime/site/resources.py -> build/lib/nmdc_runtime/site 2025-06-09T01:35:39,324 copying nmdc_runtime/site/__init__.py -> build/lib/nmdc_runtime/site 2025-06-09T01:35:39,326 copying nmdc_runtime/site/ops.py -> build/lib/nmdc_runtime/site 2025-06-09T01:35:39,329 copying nmdc_runtime/site/graphs.py -> build/lib/nmdc_runtime/site 2025-06-09T01:35:39,331 copying nmdc_runtime/site/util.py -> build/lib/nmdc_runtime/site 2025-06-09T01:35:39,334 creating build/lib/nmdc_runtime/domain 2025-06-09T01:35:39,335 copying nmdc_runtime/domain/__init__.py -> build/lib/nmdc_runtime/domain 2025-06-09T01:35:39,337 creating build/lib/nmdc_runtime/core 2025-06-09T01:35:39,338 copying nmdc_runtime/core/__init__.py -> build/lib/nmdc_runtime/core 2025-06-09T01:35:39,340 creating build/lib/nmdc_runtime/client 2025-06-09T01:35:39,341 copying nmdc_runtime/client/__init__.py -> build/lib/nmdc_runtime/client 2025-06-09T01:35:39,343 creating build/lib/nmdc_runtime/lib 2025-06-09T01:35:39,344 copying nmdc_runtime/lib/nmdc_dataframes.py -> build/lib/nmdc_runtime/lib 2025-06-09T01:35:39,347 copying nmdc_runtime/lib/extract_nmdc_data.py -> build/lib/nmdc_runtime/lib 2025-06-09T01:35:39,349 copying nmdc_runtime/lib/transform_nmdc_data.py -> build/lib/nmdc_runtime/lib 2025-06-09T01:35:39,352 copying nmdc_runtime/lib/load_nmdc_data.py -> build/lib/nmdc_runtime/lib 2025-06-09T01:35:39,354 copying nmdc_runtime/lib/nmdc_etl_class.py -> build/lib/nmdc_runtime/lib 2025-06-09T01:35:39,356 copying nmdc_runtime/lib/__init__.py -> build/lib/nmdc_runtime/lib 2025-06-09T01:35:39,359 creating build/lib/nmdc_runtime/infrastructure 2025-06-09T01:35:39,360 copying nmdc_runtime/infrastructure/__init__.py -> build/lib/nmdc_runtime/infrastructure 2025-06-09T01:35:39,362 creating build/lib/nmdc_runtime/minter 2025-06-09T01:35:39,363 copying nmdc_runtime/minter/config.py -> build/lib/nmdc_runtime/minter 2025-06-09T01:35:39,365 copying nmdc_runtime/minter/__init__.py -> build/lib/nmdc_runtime/minter 2025-06-09T01:35:39,366 copying nmdc_runtime/minter/bootstrap.py -> build/lib/nmdc_runtime/minter 2025-06-09T01:35:39,369 creating build/lib/nmdc_runtime/site/backup 2025-06-09T01:35:39,370 copying nmdc_runtime/site/backup/nmdcdb_mongodump.py -> build/lib/nmdc_runtime/site/backup 2025-06-09T01:35:39,372 copying nmdc_runtime/site/backup/nmdcdb_mongoexport.py -> build/lib/nmdc_runtime/site/backup 2025-06-09T01:35:39,374 copying nmdc_runtime/site/backup/__init__.py -> build/lib/nmdc_runtime/site/backup 2025-06-09T01:35:39,375 copying nmdc_runtime/site/backup/nmdcdb_mongoimport.py -> build/lib/nmdc_runtime/site/backup 2025-06-09T01:35:39,378 creating build/lib/nmdc_runtime/site/export 2025-06-09T01:35:39,379 copying nmdc_runtime/site/export/study_metadata.py -> build/lib/nmdc_runtime/site/export 2025-06-09T01:35:39,381 copying nmdc_runtime/site/export/ncbi_xml_utils.py -> build/lib/nmdc_runtime/site/export 2025-06-09T01:35:39,383 copying nmdc_runtime/site/export/__init__.py -> build/lib/nmdc_runtime/site/export 2025-06-09T01:35:39,385 copying nmdc_runtime/site/export/ncbi_xml.py -> build/lib/nmdc_runtime/site/export 2025-06-09T01:35:39,388 creating build/lib/nmdc_runtime/site/changesheets 2025-06-09T01:35:39,389 copying nmdc_runtime/site/changesheets/__init__.py -> build/lib/nmdc_runtime/site/changesheets 2025-06-09T01:35:39,391 copying nmdc_runtime/site/changesheets/base.py -> build/lib/nmdc_runtime/site/changesheets 2025-06-09T01:35:39,393 creating build/lib/nmdc_runtime/site/validation 2025-06-09T01:35:39,394 copying nmdc_runtime/site/validation/gold.py -> build/lib/nmdc_runtime/site/validation 2025-06-09T01:35:39,396 copying nmdc_runtime/site/validation/emsl.py -> build/lib/nmdc_runtime/site/validation 2025-06-09T01:35:39,398 copying nmdc_runtime/site/validation/__init__.py -> build/lib/nmdc_runtime/site/validation 2025-06-09T01:35:39,400 copying nmdc_runtime/site/validation/jgi.py -> build/lib/nmdc_runtime/site/validation 2025-06-09T01:35:39,402 copying nmdc_runtime/site/validation/util.py -> build/lib/nmdc_runtime/site/validation 2025-06-09T01:35:39,404 creating build/lib/nmdc_runtime/site/repair 2025-06-09T01:35:39,405 copying nmdc_runtime/site/repair/database_updater.py -> build/lib/nmdc_runtime/site/repair 2025-06-09T01:35:39,408 copying nmdc_runtime/site/repair/__init__.py -> build/lib/nmdc_runtime/site/repair 2025-06-09T01:35:39,410 creating build/lib/nmdc_runtime/site/drsobjects 2025-06-09T01:35:39,411 copying nmdc_runtime/site/drsobjects/registration.py -> build/lib/nmdc_runtime/site/drsobjects 2025-06-09T01:35:39,413 copying nmdc_runtime/site/drsobjects/ingest.py -> build/lib/nmdc_runtime/site/drsobjects 2025-06-09T01:35:39,415 copying nmdc_runtime/site/drsobjects/__init__.py -> build/lib/nmdc_runtime/site/drsobjects 2025-06-09T01:35:39,417 creating build/lib/nmdc_runtime/site/normalization 2025-06-09T01:35:39,418 copying nmdc_runtime/site/normalization/gold.py -> build/lib/nmdc_runtime/site/normalization 2025-06-09T01:35:39,420 copying nmdc_runtime/site/normalization/__init__.py -> build/lib/nmdc_runtime/site/normalization 2025-06-09T01:35:39,423 creating build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,424 copying nmdc_runtime/site/translation/neon_surface_water_translator.py -> build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,427 copying nmdc_runtime/site/translation/gold.py -> build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,429 copying nmdc_runtime/site/translation/gold_translator.py -> build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,432 copying nmdc_runtime/site/translation/emsl.py -> build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,434 copying nmdc_runtime/site/translation/neon_utils.py -> build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,437 copying nmdc_runtime/site/translation/__init__.py -> build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,438 copying nmdc_runtime/site/translation/submission_portal_translator.py -> build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,442 copying nmdc_runtime/site/translation/neon_soil_translator.py -> build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,445 copying nmdc_runtime/site/translation/jgi.py -> build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,447 copying nmdc_runtime/site/translation/translator.py -> build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,448 copying nmdc_runtime/site/translation/util.py -> build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,451 copying nmdc_runtime/site/translation/neon_benthic_translator.py -> build/lib/nmdc_runtime/site/translation 2025-06-09T01:35:39,454 creating build/lib/nmdc_runtime/domain/users 2025-06-09T01:35:39,455 copying nmdc_runtime/domain/users/queriesInterface.py -> build/lib/nmdc_runtime/domain/users 2025-06-09T01:35:39,457 copying nmdc_runtime/domain/users/__init__.py -> build/lib/nmdc_runtime/domain/users 2025-06-09T01:35:39,459 copying nmdc_runtime/domain/users/userService.py -> build/lib/nmdc_runtime/domain/users 2025-06-09T01:35:39,460 copying nmdc_runtime/domain/users/userSchema.py -> build/lib/nmdc_runtime/domain/users 2025-06-09T01:35:39,463 creating build/lib/nmdc_runtime/core/exceptions 2025-06-09T01:35:39,464 copying nmdc_runtime/core/exceptions/token.py -> build/lib/nmdc_runtime/core/exceptions 2025-06-09T01:35:39,466 copying nmdc_runtime/core/exceptions/__init__.py -> build/lib/nmdc_runtime/core/exceptions 2025-06-09T01:35:39,468 copying nmdc_runtime/core/exceptions/base.py -> build/lib/nmdc_runtime/core/exceptions 2025-06-09T01:35:39,470 creating build/lib/nmdc_runtime/core/db 2025-06-09T01:35:39,471 copying nmdc_runtime/core/db/__init__.py -> build/lib/nmdc_runtime/core/db 2025-06-09T01:35:39,473 copying nmdc_runtime/core/db/Database.py -> build/lib/nmdc_runtime/core/db 2025-06-09T01:35:39,475 creating build/lib/nmdc_runtime/infrastructure/database 2025-06-09T01:35:39,476 copying nmdc_runtime/infrastructure/database/db.py -> build/lib/nmdc_runtime/infrastructure/database 2025-06-09T01:35:39,478 copying nmdc_runtime/infrastructure/database/__init__.py -> build/lib/nmdc_runtime/infrastructure/database 2025-06-09T01:35:39,480 creating build/lib/nmdc_runtime/infrastructure/database/models 2025-06-09T01:35:39,481 copying nmdc_runtime/infrastructure/database/models/__init__.py -> build/lib/nmdc_runtime/infrastructure/database/models 2025-06-09T01:35:39,482 copying nmdc_runtime/infrastructure/database/models/user.py -> build/lib/nmdc_runtime/infrastructure/database/models 2025-06-09T01:35:39,485 creating build/lib/nmdc_runtime/minter/entrypoints 2025-06-09T01:35:39,486 copying nmdc_runtime/minter/entrypoints/fastapi_app.py -> build/lib/nmdc_runtime/minter/entrypoints 2025-06-09T01:35:39,488 copying nmdc_runtime/minter/entrypoints/__init__.py -> build/lib/nmdc_runtime/minter/entrypoints 2025-06-09T01:35:39,490 creating build/lib/nmdc_runtime/minter/domain 2025-06-09T01:35:39,491 copying nmdc_runtime/minter/domain/__init__.py -> build/lib/nmdc_runtime/minter/domain 2025-06-09T01:35:39,493 copying nmdc_runtime/minter/domain/model.py -> build/lib/nmdc_runtime/minter/domain 2025-06-09T01:35:39,495 creating build/lib/nmdc_runtime/minter/adapters 2025-06-09T01:35:39,496 copying nmdc_runtime/minter/adapters/repository.py -> build/lib/nmdc_runtime/minter/adapters 2025-06-09T01:35:39,499 copying nmdc_runtime/minter/adapters/__init__.py -> build/lib/nmdc_runtime/minter/adapters 2025-06-09T01:35:39,552 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-09T01:35:39,553 !! 2025-06-09T01:35:39,554 ******************************************************************************** 2025-06-09T01:35:39,555 Please avoid running ``setup.py`` directly. 2025-06-09T01:35:39,555 Instead, use pypa/build, pypa/installer or other 2025-06-09T01:35:39,556 standards-based tools. 2025-06-09T01:35:39,557 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-09T01:35:39,558 or your builds will no longer be supported. 2025-06-09T01:35:39,559 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-09T01:35:39,560 ******************************************************************************** 2025-06-09T01:35:39,561 !! 2025-06-09T01:35:39,562 self.initialize_options() 2025-06-09T01:35:39,584 installing to build/bdist.linux-armv7l/wheel 2025-06-09T01:35:39,585 running install 2025-06-09T01:35:39,608 running install_lib 2025-06-09T01:35:39,639 creating build/bdist.linux-armv7l/wheel 2025-06-09T01:35:39,641 creating build/bdist.linux-armv7l/wheel/nmdc_runtime 2025-06-09T01:35:39,643 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site 2025-06-09T01:35:39,645 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/backup 2025-06-09T01:35:39,646 copying build/lib/nmdc_runtime/site/backup/nmdcdb_mongodump.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-06-09T01:35:39,648 copying build/lib/nmdc_runtime/site/backup/nmdcdb_mongoexport.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-06-09T01:35:39,651 copying build/lib/nmdc_runtime/site/backup/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-06-09T01:35:39,653 copying build/lib/nmdc_runtime/site/backup/nmdcdb_mongoimport.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/backup 2025-06-09T01:35:39,655 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/export 2025-06-09T01:35:39,656 copying build/lib/nmdc_runtime/site/export/study_metadata.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-06-09T01:35:39,659 copying build/lib/nmdc_runtime/site/export/ncbi_xml_utils.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-06-09T01:35:39,661 copying build/lib/nmdc_runtime/site/export/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-06-09T01:35:39,663 copying build/lib/nmdc_runtime/site/export/ncbi_xml.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/export 2025-06-09T01:35:39,666 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/changesheets 2025-06-09T01:35:39,667 copying build/lib/nmdc_runtime/site/changesheets/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/changesheets 2025-06-09T01:35:39,669 copying build/lib/nmdc_runtime/site/changesheets/base.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/changesheets 2025-06-09T01:35:39,671 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/validation 2025-06-09T01:35:39,672 copying build/lib/nmdc_runtime/site/validation/gold.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-06-09T01:35:39,674 copying build/lib/nmdc_runtime/site/validation/emsl.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-06-09T01:35:39,676 copying build/lib/nmdc_runtime/site/validation/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-06-09T01:35:39,678 copying build/lib/nmdc_runtime/site/validation/jgi.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-06-09T01:35:39,680 copying build/lib/nmdc_runtime/site/validation/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/validation 2025-06-09T01:35:39,682 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/repair 2025-06-09T01:35:39,683 copying build/lib/nmdc_runtime/site/repair/database_updater.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/repair 2025-06-09T01:35:39,686 copying build/lib/nmdc_runtime/site/repair/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/repair 2025-06-09T01:35:39,688 copying build/lib/nmdc_runtime/site/repository.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-06-09T01:35:39,691 copying build/lib/nmdc_runtime/site/resources.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-06-09T01:35:39,694 copying build/lib/nmdc_runtime/site/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-06-09T01:35:39,695 copying build/lib/nmdc_runtime/site/ops.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-06-09T01:35:39,699 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/drsobjects 2025-06-09T01:35:39,700 copying build/lib/nmdc_runtime/site/drsobjects/registration.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/drsobjects 2025-06-09T01:35:39,702 copying build/lib/nmdc_runtime/site/drsobjects/ingest.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/drsobjects 2025-06-09T01:35:39,704 copying build/lib/nmdc_runtime/site/drsobjects/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/drsobjects 2025-06-09T01:35:39,706 copying build/lib/nmdc_runtime/site/graphs.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-06-09T01:35:39,708 copying build/lib/nmdc_runtime/site/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site 2025-06-09T01:35:39,711 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/normalization 2025-06-09T01:35:39,712 copying build/lib/nmdc_runtime/site/normalization/gold.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/normalization 2025-06-09T01:35:39,714 copying build/lib/nmdc_runtime/site/normalization/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/normalization 2025-06-09T01:35:39,716 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/site/translation 2025-06-09T01:35:39,717 copying build/lib/nmdc_runtime/site/translation/neon_surface_water_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-09T01:35:39,720 copying build/lib/nmdc_runtime/site/translation/gold.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-09T01:35:39,722 copying build/lib/nmdc_runtime/site/translation/gold_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-09T01:35:39,724 copying build/lib/nmdc_runtime/site/translation/emsl.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-09T01:35:39,726 copying build/lib/nmdc_runtime/site/translation/neon_utils.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-09T01:35:39,728 copying build/lib/nmdc_runtime/site/translation/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-09T01:35:39,730 copying build/lib/nmdc_runtime/site/translation/submission_portal_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-09T01:35:39,733 copying build/lib/nmdc_runtime/site/translation/neon_soil_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-09T01:35:39,736 copying build/lib/nmdc_runtime/site/translation/jgi.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-09T01:35:39,738 copying build/lib/nmdc_runtime/site/translation/translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-09T01:35:39,740 copying build/lib/nmdc_runtime/site/translation/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-09T01:35:39,742 copying build/lib/nmdc_runtime/site/translation/neon_benthic_translator.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/site/translation 2025-06-09T01:35:39,746 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/domain 2025-06-09T01:35:39,747 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/domain/users 2025-06-09T01:35:39,748 copying build/lib/nmdc_runtime/domain/users/queriesInterface.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-06-09T01:35:39,750 copying build/lib/nmdc_runtime/domain/users/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-06-09T01:35:39,752 copying build/lib/nmdc_runtime/domain/users/userService.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-06-09T01:35:39,754 copying build/lib/nmdc_runtime/domain/users/userSchema.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain/users 2025-06-09T01:35:39,756 copying build/lib/nmdc_runtime/domain/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/domain 2025-06-09T01:35:39,758 copying build/lib/nmdc_runtime/config.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-06-09T01:35:39,760 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/core 2025-06-09T01:35:39,762 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/core/exceptions 2025-06-09T01:35:39,763 copying build/lib/nmdc_runtime/core/exceptions/token.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/exceptions 2025-06-09T01:35:39,765 copying build/lib/nmdc_runtime/core/exceptions/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/exceptions 2025-06-09T01:35:39,766 copying build/lib/nmdc_runtime/core/exceptions/base.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/exceptions 2025-06-09T01:35:39,769 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/core/db 2025-06-09T01:35:39,770 copying build/lib/nmdc_runtime/core/db/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/db 2025-06-09T01:35:39,771 copying build/lib/nmdc_runtime/core/db/Database.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core/db 2025-06-09T01:35:39,773 copying build/lib/nmdc_runtime/core/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/core 2025-06-09T01:35:39,775 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/client 2025-06-09T01:35:39,776 copying build/lib/nmdc_runtime/client/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/client 2025-06-09T01:35:39,778 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/lib 2025-06-09T01:35:39,779 copying build/lib/nmdc_runtime/lib/nmdc_dataframes.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-06-09T01:35:39,782 copying build/lib/nmdc_runtime/lib/extract_nmdc_data.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-06-09T01:35:39,784 copying build/lib/nmdc_runtime/lib/transform_nmdc_data.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-06-09T01:35:39,787 copying build/lib/nmdc_runtime/lib/load_nmdc_data.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-06-09T01:35:39,789 copying build/lib/nmdc_runtime/lib/nmdc_etl_class.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-06-09T01:35:39,791 copying build/lib/nmdc_runtime/lib/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/lib 2025-06-09T01:35:39,793 copying build/lib/nmdc_runtime/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-06-09T01:35:39,794 copying build/lib/nmdc_runtime/main.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-06-09T01:35:39,796 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/infrastructure 2025-06-09T01:35:39,798 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/infrastructure/database 2025-06-09T01:35:39,799 copying build/lib/nmdc_runtime/infrastructure/database/db.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database 2025-06-09T01:35:39,801 copying build/lib/nmdc_runtime/infrastructure/database/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database 2025-06-09T01:35:39,804 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/infrastructure/database/models 2025-06-09T01:35:39,805 copying build/lib/nmdc_runtime/infrastructure/database/models/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database/models 2025-06-09T01:35:39,806 copying build/lib/nmdc_runtime/infrastructure/database/models/user.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure/database/models 2025-06-09T01:35:39,808 copying build/lib/nmdc_runtime/infrastructure/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/infrastructure 2025-06-09T01:35:39,810 copying build/lib/nmdc_runtime/containers.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-06-09T01:35:39,812 copying build/lib/nmdc_runtime/util.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime 2025-06-09T01:35:39,815 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter 2025-06-09T01:35:39,817 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter/entrypoints 2025-06-09T01:35:39,818 copying build/lib/nmdc_runtime/minter/entrypoints/fastapi_app.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/entrypoints 2025-06-09T01:35:39,820 copying build/lib/nmdc_runtime/minter/entrypoints/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/entrypoints 2025-06-09T01:35:39,822 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter/domain 2025-06-09T01:35:39,823 copying build/lib/nmdc_runtime/minter/domain/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/domain 2025-06-09T01:35:39,825 copying build/lib/nmdc_runtime/minter/domain/model.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/domain 2025-06-09T01:35:39,827 copying build/lib/nmdc_runtime/minter/config.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter 2025-06-09T01:35:39,829 creating build/bdist.linux-armv7l/wheel/nmdc_runtime/minter/adapters 2025-06-09T01:35:39,830 copying build/lib/nmdc_runtime/minter/adapters/repository.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/adapters 2025-06-09T01:35:39,833 copying build/lib/nmdc_runtime/minter/adapters/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter/adapters 2025-06-09T01:35:39,835 copying build/lib/nmdc_runtime/minter/__init__.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter 2025-06-09T01:35:39,836 copying build/lib/nmdc_runtime/minter/bootstrap.py -> build/bdist.linux-armv7l/wheel/./nmdc_runtime/minter 2025-06-09T01:35:39,838 running install_egg_info 2025-06-09T01:35:39,870 running egg_info 2025-06-09T01:35:39,900 writing nmdc_runtime.egg-info/PKG-INFO 2025-06-09T01:35:39,904 writing dependency_links to nmdc_runtime.egg-info/dependency_links.txt 2025-06-09T01:35:39,906 writing entry points to nmdc_runtime.egg-info/entry_points.txt 2025-06-09T01:35:39,908 writing top-level names to nmdc_runtime.egg-info/top_level.txt 2025-06-09T01:35:40,028 listing git files failed - pretending there aren't any 2025-06-09T01:35:40,033 reading manifest file 'nmdc_runtime.egg-info/SOURCES.txt' 2025-06-09T01:35:40,127 adding license file 'LICENSE' 2025-06-09T01:35:40,146 writing manifest file 'nmdc_runtime.egg-info/SOURCES.txt' 2025-06-09T01:35:40,148 Copying nmdc_runtime.egg-info to build/bdist.linux-armv7l/wheel/./nmdc_runtime-2.7.0-py3.11.egg-info 2025-06-09T01:35:40,160 running install_scripts 2025-06-09T01:35:40,174 creating build/bdist.linux-armv7l/wheel/nmdc_runtime-2.7.0.dist-info/WHEEL 2025-06-09T01:35:40,176 creating '/tmp/pip-wheel-00oiplqb/nmdc_runtime-2.7.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-09T01:35:40,178 adding 'nmdc_runtime/__init__.py' 2025-06-09T01:35:40,179 adding 'nmdc_runtime/config.py' 2025-06-09T01:35:40,181 adding 'nmdc_runtime/containers.py' 2025-06-09T01:35:40,182 adding 'nmdc_runtime/main.py' 2025-06-09T01:35:40,187 adding 'nmdc_runtime/util.py' 2025-06-09T01:35:40,189 adding 'nmdc_runtime/client/__init__.py' 2025-06-09T01:35:40,190 adding 'nmdc_runtime/core/__init__.py' 2025-06-09T01:35:40,192 adding 'nmdc_runtime/core/db/Database.py' 2025-06-09T01:35:40,194 adding 'nmdc_runtime/core/db/__init__.py' 2025-06-09T01:35:40,195 adding 'nmdc_runtime/core/exceptions/__init__.py' 2025-06-09T01:35:40,197 adding 'nmdc_runtime/core/exceptions/base.py' 2025-06-09T01:35:40,198 adding 'nmdc_runtime/core/exceptions/token.py' 2025-06-09T01:35:40,200 adding 'nmdc_runtime/domain/__init__.py' 2025-06-09T01:35:40,202 adding 'nmdc_runtime/domain/users/__init__.py' 2025-06-09T01:35:40,203 adding 'nmdc_runtime/domain/users/queriesInterface.py' 2025-06-09T01:35:40,204 adding 'nmdc_runtime/domain/users/userSchema.py' 2025-06-09T01:35:40,205 adding 'nmdc_runtime/domain/users/userService.py' 2025-06-09T01:35:40,207 adding 'nmdc_runtime/infrastructure/__init__.py' 2025-06-09T01:35:40,209 adding 'nmdc_runtime/infrastructure/database/__init__.py' 2025-06-09T01:35:40,210 adding 'nmdc_runtime/infrastructure/database/db.py' 2025-06-09T01:35:40,212 adding 'nmdc_runtime/infrastructure/database/models/__init__.py' 2025-06-09T01:35:40,213 adding 'nmdc_runtime/infrastructure/database/models/user.py' 2025-06-09T01:35:40,215 adding 'nmdc_runtime/lib/__init__.py' 2025-06-09T01:35:40,216 adding 'nmdc_runtime/lib/extract_nmdc_data.py' 2025-06-09T01:35:40,217 adding 'nmdc_runtime/lib/load_nmdc_data.py' 2025-06-09T01:35:40,221 adding 'nmdc_runtime/lib/nmdc_dataframes.py' 2025-06-09T01:35:40,223 adding 'nmdc_runtime/lib/nmdc_etl_class.py' 2025-06-09T01:35:40,228 adding 'nmdc_runtime/lib/transform_nmdc_data.py' 2025-06-09T01:35:40,230 adding 'nmdc_runtime/minter/__init__.py' 2025-06-09T01:35:40,231 adding 'nmdc_runtime/minter/bootstrap.py' 2025-06-09T01:35:40,232 adding 'nmdc_runtime/minter/config.py' 2025-06-09T01:35:40,234 adding 'nmdc_runtime/minter/adapters/__init__.py' 2025-06-09T01:35:40,235 adding 'nmdc_runtime/minter/adapters/repository.py' 2025-06-09T01:35:40,237 adding 'nmdc_runtime/minter/domain/__init__.py' 2025-06-09T01:35:40,238 adding 'nmdc_runtime/minter/domain/model.py' 2025-06-09T01:35:40,240 adding 'nmdc_runtime/minter/entrypoints/__init__.py' 2025-06-09T01:35:40,241 adding 'nmdc_runtime/minter/entrypoints/fastapi_app.py' 2025-06-09T01:35:40,243 adding 'nmdc_runtime/site/__init__.py' 2025-06-09T01:35:40,245 adding 'nmdc_runtime/site/graphs.py' 2025-06-09T01:35:40,250 adding 'nmdc_runtime/site/ops.py' 2025-06-09T01:35:40,254 adding 'nmdc_runtime/site/repository.py' 2025-06-09T01:35:40,256 adding 'nmdc_runtime/site/resources.py' 2025-06-09T01:35:40,258 adding 'nmdc_runtime/site/util.py' 2025-06-09T01:35:40,260 adding 'nmdc_runtime/site/backup/__init__.py' 2025-06-09T01:35:40,261 adding 'nmdc_runtime/site/backup/nmdcdb_mongodump.py' 2025-06-09T01:35:40,262 adding 'nmdc_runtime/site/backup/nmdcdb_mongoexport.py' 2025-06-09T01:35:40,263 adding 'nmdc_runtime/site/backup/nmdcdb_mongoimport.py' 2025-06-09T01:35:40,265 adding 'nmdc_runtime/site/changesheets/__init__.py' 2025-06-09T01:35:40,267 adding 'nmdc_runtime/site/changesheets/base.py' 2025-06-09T01:35:40,268 adding 'nmdc_runtime/site/drsobjects/__init__.py' 2025-06-09T01:35:40,270 adding 'nmdc_runtime/site/drsobjects/ingest.py' 2025-06-09T01:35:40,271 adding 'nmdc_runtime/site/drsobjects/registration.py' 2025-06-09T01:35:40,273 adding 'nmdc_runtime/site/export/__init__.py' 2025-06-09T01:35:40,275 adding 'nmdc_runtime/site/export/ncbi_xml.py' 2025-06-09T01:35:40,277 adding 'nmdc_runtime/site/export/ncbi_xml_utils.py' 2025-06-09T01:35:40,279 adding 'nmdc_runtime/site/export/study_metadata.py' 2025-06-09T01:35:40,280 adding 'nmdc_runtime/site/normalization/__init__.py' 2025-06-09T01:35:40,282 adding 'nmdc_runtime/site/normalization/gold.py' 2025-06-09T01:35:40,283 adding 'nmdc_runtime/site/repair/__init__.py' 2025-06-09T01:35:40,285 adding 'nmdc_runtime/site/repair/database_updater.py' 2025-06-09T01:35:40,287 adding 'nmdc_runtime/site/translation/__init__.py' 2025-06-09T01:35:40,288 adding 'nmdc_runtime/site/translation/emsl.py' 2025-06-09T01:35:40,290 adding 'nmdc_runtime/site/translation/gold.py' 2025-06-09T01:35:40,293 adding 'nmdc_runtime/site/translation/gold_translator.py' 2025-06-09T01:35:40,295 adding 'nmdc_runtime/site/translation/jgi.py' 2025-06-09T01:35:40,297 adding 'nmdc_runtime/site/translation/neon_benthic_translator.py' 2025-06-09T01:35:40,301 adding 'nmdc_runtime/site/translation/neon_soil_translator.py' 2025-06-09T01:35:40,305 adding 'nmdc_runtime/site/translation/neon_surface_water_translator.py' 2025-06-09T01:35:40,306 adding 'nmdc_runtime/site/translation/neon_utils.py' 2025-06-09T01:35:40,311 adding 'nmdc_runtime/site/translation/submission_portal_translator.py' 2025-06-09T01:35:40,313 adding 'nmdc_runtime/site/translation/translator.py' 2025-06-09T01:35:40,314 adding 'nmdc_runtime/site/translation/util.py' 2025-06-09T01:35:40,316 adding 'nmdc_runtime/site/validation/__init__.py' 2025-06-09T01:35:40,317 adding 'nmdc_runtime/site/validation/emsl.py' 2025-06-09T01:35:40,318 adding 'nmdc_runtime/site/validation/gold.py' 2025-06-09T01:35:40,320 adding 'nmdc_runtime/site/validation/jgi.py' 2025-06-09T01:35:40,321 adding 'nmdc_runtime/site/validation/util.py' 2025-06-09T01:35:40,324 adding 'nmdc_runtime-2.7.0.dist-info/licenses/LICENSE' 2025-06-09T01:35:40,325 adding 'nmdc_runtime-2.7.0.dist-info/METADATA' 2025-06-09T01:35:40,326 adding 'nmdc_runtime-2.7.0.dist-info/WHEEL' 2025-06-09T01:35:40,327 adding 'nmdc_runtime-2.7.0.dist-info/entry_points.txt' 2025-06-09T01:35:40,328 adding 'nmdc_runtime-2.7.0.dist-info/top_level.txt' 2025-06-09T01:35:40,330 adding 'nmdc_runtime-2.7.0.dist-info/RECORD' 2025-06-09T01:35:40,333 removing build/bdist.linux-armv7l/wheel 2025-06-09T01:35:40,479 Building wheel for nmdc-runtime (setup.py): finished with status 'done' 2025-06-09T01:35:40,483 Created wheel for nmdc-runtime: filename=nmdc_runtime-2.7.0-py3-none-any.whl size=138945 sha256=b335c515ce58079cf8a7787f28f7d6f15d316f6c92ab4d7a9555f0b4e37b4496 2025-06-09T01:35:40,484 Stored in directory: /tmp/pip-ephem-wheel-cache-tltg54el/wheels/e3/b7/8a/40567978e7fa829f2399a6e83f28e1bb56a1f97ea8c3dee29d 2025-06-09T01:35:40,498 Successfully built nmdc-runtime 2025-06-09T01:35:40,504 Removed build tracker: '/tmp/pip-build-tracker-5pm0efpc'