2025-06-04T21:21:38,263 Created temporary directory: /tmp/pip-build-tracker-_5ax6wgp 2025-06-04T21:21:38,264 Initialized build tracking at /tmp/pip-build-tracker-_5ax6wgp 2025-06-04T21:21:38,264 Created build tracker: /tmp/pip-build-tracker-_5ax6wgp 2025-06-04T21:21:38,265 Entered build tracker: /tmp/pip-build-tracker-_5ax6wgp 2025-06-04T21:21:38,266 Created temporary directory: /tmp/pip-wheel-1jpx135i 2025-06-04T21:21:38,270 Created temporary directory: /tmp/pip-ephem-wheel-cache-z2xauny5 2025-06-04T21:21:38,325 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-04T21:21:38,327 2 location(s) to search for versions of concord-sc: 2025-06-04T21:21:38,327 * https://pypi.org/simple/concord-sc/ 2025-06-04T21:21:38,327 * https://www.piwheels.org/simple/concord-sc/ 2025-06-04T21:21:38,328 Fetching project page and analyzing links: https://pypi.org/simple/concord-sc/ 2025-06-04T21:21:38,329 Getting page https://pypi.org/simple/concord-sc/ 2025-06-04T21:21:38,330 Found index url https://pypi.org/simple/ 2025-06-04T21:21:38,560 Fetched page https://pypi.org/simple/concord-sc/ as application/vnd.pypi.simple.v1+json 2025-06-04T21:21:38,567 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/8e/ae/22e0b7b29b9c9c1a4ba16c91c5017059a7e48367aa4aaa9568e5cb525092/concord_sc-0.9.0-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-06-04T21:21:38,569 Found link https://files.pythonhosted.org/packages/10/58/79f4033f7fbc06d0c2c0a78ddb77debf2bee47eb6f914cadb8a00095e429/concord_sc-0.9.0.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 0.9.0 2025-06-04T21:21:38,570 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/4d/ab/8b89e30462620a4338e2337127525d69413ed90b969bcc61264c0b547e96/concord_sc-0.9.1-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-06-04T21:21:38,571 Found link https://files.pythonhosted.org/packages/0e/90/5ef728a9d2568db1d7e36c9df7af98b5b9d6e8b6a98bf1d3cd3d344ea449/concord_sc-0.9.1.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 0.9.1 2025-06-04T21:21:38,572 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/39/b3/6918c9ca5f3046e2bba415b978bc22d537cfd9c2a908b2489e4e3048d776/concord_sc-0.9.2-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-06-04T21:21:38,573 Found link https://files.pythonhosted.org/packages/55/01/1c16f7a11b80cc77bee4e5ed0827137b4e2e074a9668c0b44150d48afe74/concord_sc-0.9.2.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 0.9.2 2025-06-04T21:21:38,574 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/fb/f3/a0d8a696c17ad8aa9d3b89416e1938a05fe1d476d9a157a1ca88671d6bb1/concord_sc-0.9.3-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-06-04T21:21:38,575 Found link https://files.pythonhosted.org/packages/5b/40/2ec491724912d89c649155e8dbf06c4828fc6153a1b4fc56632e34302715/concord_sc-0.9.3.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 0.9.3 2025-06-04T21:21:38,576 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/96/12/bfb5abf4ec0594cc3daf5b0b9db10357910a9d0547fd15532c22903e12b0/concord_sc-0.9.4-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-06-04T21:21:38,577 Found link https://files.pythonhosted.org/packages/9f/90/29e1b0a7797b75f332fe4883b847795fb78af3640b3257acd83387e84724/concord_sc-0.9.4.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 0.9.4 2025-06-04T21:21:38,578 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/8d/aa/04363b0f0a4e002a8690a96bed9f60aee04f4708a23be499ec43afe27720/concord_sc-0.9.5-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-06-04T21:21:38,579 Found link https://files.pythonhosted.org/packages/d8/f0/b8974243a19b799f97589ac5853c40426cc2fd261969d4950880df87f562/concord_sc-0.9.5.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 0.9.5 2025-06-04T21:21:38,580 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/a0/d6/b26a330d21b190f3bdaaa9e9195e8ac508c60fdf7657626db96405b9537a/concord_sc-0.9.6-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-06-04T21:21:38,581 Found link https://files.pythonhosted.org/packages/33/18/cd335e73418d60425aff93ac3cb6ba4d62a16040636d7481744194582416/concord_sc-0.9.6.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 0.9.6 2025-06-04T21:21:38,581 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/7f/c8/887aee9b43aca00279f9a2c2c6944b32f6341d8ac1ef297a04773e3d5061/concord_sc-0.9.7-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-06-04T21:21:38,582 Found link https://files.pythonhosted.org/packages/7b/7e/afc7826dc853c736974af065a5092ff6256f1718222a4eb91d403cc4d52c/concord_sc-0.9.7.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 0.9.7 2025-06-04T21:21:38,582 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/cd/f7/af72936bff2f1163633b39db5272466d262b339c759197266e0af33784c9/concord_sc-1.0.0-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-06-04T21:21:38,583 Found link https://files.pythonhosted.org/packages/63/85/ee633bc44868c73f1a70b7d84c23b359c820e1b2f2fd9d9d39269788ad49/concord_sc-1.0.0.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 1.0.0 2025-06-04T21:21:38,583 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/8b/d2/4d4b677de88c93bb08a7c0f78ddedceaab3fc2033de2dbc57f0e6f4431a0/concord_sc-1.0.4-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-06-04T21:21:38,584 Found link https://files.pythonhosted.org/packages/99/e1/07eba0da0f26e2cd1dfd7ebb52a0b39dd22bbdf6be5a9056e1a84b42cbc2/concord_sc-1.0.4.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 1.0.4 2025-06-04T21:21:38,585 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/db/d3/b0becbdc0f0aa362fe40bcf7917ed655d22d1009ed20651b6219bc3e5f61/concord_sc-1.0.6-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-06-04T21:21:38,585 Found link https://files.pythonhosted.org/packages/33/e9/77bcf0dcd825519e077b67e53a201dd2d1ad87e1ec55d0207adcd960d37c/concord_sc-1.0.6.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 1.0.6 2025-06-04T21:21:38,586 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/f8/d8/42a1cf823c0a3e4ab6b5de3e8c2bd846385b526538424e4abc52154c14cd/concord_sc-1.0.7-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-06-04T21:21:38,587 Found link https://files.pythonhosted.org/packages/ab/d0/12581f7b36e31b10b2301f87bde00115c774b47fbf025d25b1e1437993e3/concord_sc-1.0.7.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 1.0.7 2025-06-04T21:21:38,588 Fetching project page and analyzing links: https://www.piwheels.org/simple/concord-sc/ 2025-06-04T21:21:38,588 Getting page https://www.piwheels.org/simple/concord-sc/ 2025-06-04T21:21:38,590 Found index url https://www.piwheels.org/simple/ 2025-06-04T21:21:38,765 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/concord-sc/ 2025-06-04T21:21:39,603 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/concord-sc/ 2025-06-04T21:21:40,767 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/concord-sc/ 2025-06-04T21:21:42,940 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/concord-sc/ 2025-06-04T21:21:47,115 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/concord-sc/ 2025-06-04T21:21:47,285 Could not fetch URL https://www.piwheels.org/simple/concord-sc/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/concord-sc/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping 2025-06-04T21:21:47,287 Skipping link: not a file: https://www.piwheels.org/simple/concord-sc/ 2025-06-04T21:21:47,288 Skipping link: not a file: https://pypi.org/simple/concord-sc/ 2025-06-04T21:21:47,310 Given no hashes to check 1 links for project 'concord-sc': discarding no candidates 2025-06-04T21:21:47,312 Collecting concord-sc==0.9.6 2025-06-04T21:21:47,314 Created temporary directory: /tmp/pip-unpack-y3ov9nd3 2025-06-04T21:21:47,557 Downloading concord_sc-0.9.6.tar.gz (123 kB) 2025-06-04T21:21:47,800 Added concord-sc==0.9.6 from https://files.pythonhosted.org/packages/33/18/cd335e73418d60425aff93ac3cb6ba4d62a16040636d7481744194582416/concord_sc-0.9.6.tar.gz to build tracker '/tmp/pip-build-tracker-_5ax6wgp' 2025-06-04T21:21:47,803 Running setup.py (path:/tmp/pip-wheel-1jpx135i/concord-sc_9aee5a07d9e14dcbb96bc97638f3567b/setup.py) egg_info for package concord-sc 2025-06-04T21:21:47,804 Created temporary directory: /tmp/pip-pip-egg-info-_x07enr2 2025-06-04T21:21:47,804 Preparing metadata (setup.py): started 2025-06-04T21:21:47,806 Running command python setup.py egg_info 2025-06-04T21:21:48,691 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-04T21:21:48,691 !! 2025-06-04T21:21:48,692 ******************************************************************************** 2025-06-04T21:21:48,693 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-04T21:21:48,694 License :: OSI Approved :: MIT License 2025-06-04T21:21:48,695 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-04T21:21:48,696 ******************************************************************************** 2025-06-04T21:21:48,697 !! 2025-06-04T21:21:48,698 self._finalize_license_expression() 2025-06-04T21:21:48,721 running egg_info 2025-06-04T21:21:48,750 creating /tmp/pip-pip-egg-info-_x07enr2/concord_sc.egg-info 2025-06-04T21:21:48,751 writing /tmp/pip-pip-egg-info-_x07enr2/concord_sc.egg-info/PKG-INFO 2025-06-04T21:21:48,757 writing dependency_links to /tmp/pip-pip-egg-info-_x07enr2/concord_sc.egg-info/dependency_links.txt 2025-06-04T21:21:48,761 writing requirements to /tmp/pip-pip-egg-info-_x07enr2/concord_sc.egg-info/requires.txt 2025-06-04T21:21:48,762 writing top-level names to /tmp/pip-pip-egg-info-_x07enr2/concord_sc.egg-info/top_level.txt 2025-06-04T21:21:48,764 writing manifest file '/tmp/pip-pip-egg-info-_x07enr2/concord_sc.egg-info/SOURCES.txt' 2025-06-04T21:21:48,860 reading manifest file '/tmp/pip-pip-egg-info-_x07enr2/concord_sc.egg-info/SOURCES.txt' 2025-06-04T21:21:48,862 adding license file 'LICENSE.md' 2025-06-04T21:21:48,866 writing manifest file '/tmp/pip-pip-egg-info-_x07enr2/concord_sc.egg-info/SOURCES.txt' 2025-06-04T21:21:48,972 Preparing metadata (setup.py): finished with status 'done' 2025-06-04T21:21:48,976 Source in /tmp/pip-wheel-1jpx135i/concord-sc_9aee5a07d9e14dcbb96bc97638f3567b has version 0.9.6, which satisfies requirement concord-sc==0.9.6 from https://files.pythonhosted.org/packages/33/18/cd335e73418d60425aff93ac3cb6ba4d62a16040636d7481744194582416/concord_sc-0.9.6.tar.gz 2025-06-04T21:21:48,977 Removed concord-sc==0.9.6 from https://files.pythonhosted.org/packages/33/18/cd335e73418d60425aff93ac3cb6ba4d62a16040636d7481744194582416/concord_sc-0.9.6.tar.gz from build tracker '/tmp/pip-build-tracker-_5ax6wgp' 2025-06-04T21:21:48,989 Created temporary directory: /tmp/pip-unpack-9nslc7ug 2025-06-04T21:21:48,990 Created temporary directory: /tmp/pip-unpack-o3c3cbre 2025-06-04T21:21:48,990 Building wheels for collected packages: concord-sc 2025-06-04T21:21:48,995 Created temporary directory: /tmp/pip-wheel-wpjmdmy4 2025-06-04T21:21:48,996 DEPRECATION: Building 'concord-sc' 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 'concord-sc'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-06-04T21:21:48,997 Building wheel for concord-sc (setup.py): started 2025-06-04T21:21:48,999 Destination directory: /tmp/pip-wheel-wpjmdmy4 2025-06-04T21:21:48,999 Running command python setup.py bdist_wheel 2025-06-04T21:21:49,864 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-04T21:21:49,865 !! 2025-06-04T21:21:49,866 ******************************************************************************** 2025-06-04T21:21:49,866 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-04T21:21:49,868 License :: OSI Approved :: MIT License 2025-06-04T21:21:49,869 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-04T21:21:49,870 ******************************************************************************** 2025-06-04T21:21:49,871 !! 2025-06-04T21:21:49,871 self._finalize_license_expression() 2025-06-04T21:21:49,872 running bdist_wheel 2025-06-04T21:21:50,009 running build 2025-06-04T21:21:50,009 running build_py 2025-06-04T21:21:50,041 creating build/lib/concord 2025-06-04T21:21:50,043 copying src/concord/pl.py -> build/lib/concord 2025-06-04T21:21:50,045 copying src/concord/ml.py -> build/lib/concord 2025-06-04T21:21:50,047 copying src/concord/__init__.py -> build/lib/concord 2025-06-04T21:21:50,049 copying src/concord/concord.py -> build/lib/concord 2025-06-04T21:21:50,052 copying src/concord/ul.py -> build/lib/concord 2025-06-04T21:21:50,055 creating build/lib/concord/model 2025-06-04T21:21:50,056 copying src/concord/model/trainer.py -> build/lib/concord/model 2025-06-04T21:21:50,059 copying src/concord/model/knn.py -> build/lib/concord/model 2025-06-04T21:21:50,062 copying src/concord/model/chunkloader.py -> build/lib/concord/model 2025-06-04T21:21:50,065 copying src/concord/model/__init__.py -> build/lib/concord/model 2025-06-04T21:21:50,067 copying src/concord/model/loss.py -> build/lib/concord/model 2025-06-04T21:21:50,070 copying src/concord/model/dataloader.py -> build/lib/concord/model 2025-06-04T21:21:50,073 copying src/concord/model/build_layer.py -> build/lib/concord/model 2025-06-04T21:21:50,075 copying src/concord/model/model.py -> build/lib/concord/model 2025-06-04T21:21:50,078 copying src/concord/model/sampler.py -> build/lib/concord/model 2025-06-04T21:21:50,081 copying src/concord/model/anndataset.py -> build/lib/concord/model 2025-06-04T21:21:50,084 creating build/lib/concord/plotting 2025-06-04T21:21:50,085 copying src/concord/plotting/pl_path.py -> build/lib/concord/plotting 2025-06-04T21:21:50,088 copying src/concord/plotting/pl_geometry.py -> build/lib/concord/plotting 2025-06-04T21:21:50,090 copying src/concord/plotting/pl_heatmap.py -> build/lib/concord/plotting 2025-06-04T21:21:50,093 copying src/concord/plotting/pl_general.py -> build/lib/concord/plotting 2025-06-04T21:21:50,095 copying src/concord/plotting/pl_datacoverage.py -> build/lib/concord/plotting 2025-06-04T21:21:50,098 copying src/concord/plotting/pl_embedding.py -> build/lib/concord/plotting 2025-06-04T21:21:50,103 copying src/concord/plotting/pl_model.py -> build/lib/concord/plotting 2025-06-04T21:21:50,106 copying src/concord/plotting/pl_enrichment.py -> build/lib/concord/plotting 2025-06-04T21:21:50,109 copying src/concord/plotting/__init__.py -> build/lib/concord/plotting 2025-06-04T21:21:50,112 copying src/concord/plotting/pl_benchmark.py -> build/lib/concord/plotting 2025-06-04T21:21:50,114 copying src/concord/plotting/palettes.py -> build/lib/concord/plotting 2025-06-04T21:21:50,117 copying src/concord/plotting/pl_tda.py -> build/lib/concord/plotting 2025-06-04T21:21:50,120 copying src/concord/plotting/pl_graph.py -> build/lib/concord/plotting 2025-06-04T21:21:50,124 copying src/concord/plotting/pl_batch.py -> build/lib/concord/plotting 2025-06-04T21:21:50,127 creating build/lib/concord/utils 2025-06-04T21:21:50,129 copying src/concord/utils/run_dim_reduction.py -> build/lib/concord/utils 2025-06-04T21:21:50,132 copying src/concord/utils/estimate_aug_mask_prob.py -> build/lib/concord/utils 2025-06-04T21:21:50,134 copying src/concord/utils/Hs_Mm_conversion.py -> build/lib/concord/utils 2025-06-04T21:21:50,137 copying src/concord/utils/doublet_utils.py -> build/lib/concord/utils 2025-06-04T21:21:50,139 copying src/concord/utils/benchmark.py -> build/lib/concord/utils 2025-06-04T21:21:50,143 copying src/concord/utils/io.py -> build/lib/concord/utils 2025-06-04T21:21:50,145 copying src/concord/utils/timer.py -> build/lib/concord/utils 2025-06-04T21:21:50,148 copying src/concord/utils/feature_selector.py -> build/lib/concord/utils 2025-06-04T21:21:50,151 copying src/concord/utils/__init__.py -> build/lib/concord/utils 2025-06-04T21:21:50,154 copying src/concord/utils/coverage_estimator.py -> build/lib/concord/utils 2025-06-04T21:21:50,156 copying src/concord/utils/anndata_utils.py -> build/lib/concord/utils 2025-06-04T21:21:50,159 copying src/concord/utils/simulation.py -> build/lib/concord/utils 2025-06-04T21:21:50,162 copying src/concord/utils/geometry.py -> build/lib/concord/utils 2025-06-04T21:21:50,166 copying src/concord/utils/other_util.py -> build/lib/concord/utils 2025-06-04T21:21:50,168 copying src/concord/utils/run_integration_methods.py -> build/lib/concord/utils 2025-06-04T21:21:50,171 copying src/concord/utils/sparsity.py -> build/lib/concord/utils 2025-06-04T21:21:50,174 copying src/concord/utils/cellxgene.py -> build/lib/concord/utils 2025-06-04T21:21:50,176 copying src/concord/utils/path_analysis.py -> build/lib/concord/utils 2025-06-04T21:21:50,179 copying src/concord/utils/visCello.py -> build/lib/concord/utils 2025-06-04T21:21:50,182 copying src/concord/utils/preprocessor.py -> build/lib/concord/utils 2025-06-04T21:21:50,185 copying src/concord/utils/enrichment_analysis.py -> build/lib/concord/utils 2025-06-04T21:21:50,187 copying src/concord/utils/cell_cycle.py -> build/lib/concord/utils 2025-06-04T21:21:50,190 copying src/concord/utils/tda.py -> build/lib/concord/utils 2025-06-04T21:21:50,193 copying src/concord/utils/evaluator.py -> build/lib/concord/utils 2025-06-04T21:21:50,195 copying src/concord/utils/importance_analysis.py -> build/lib/concord/utils 2025-06-04T21:21:50,198 copying src/concord/utils/value_check.py -> build/lib/concord/utils 2025-06-04T21:21:50,200 copying src/concord/utils/batch_analysis.py -> build/lib/concord/utils 2025-06-04T21:21:50,240 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-04T21:21:50,240 !! 2025-06-04T21:21:50,241 ******************************************************************************** 2025-06-04T21:21:50,242 Please avoid running ``setup.py`` directly. 2025-06-04T21:21:50,242 Instead, use pypa/build, pypa/installer or other 2025-06-04T21:21:50,243 standards-based tools. 2025-06-04T21:21:50,244 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-04T21:21:50,244 or your builds will no longer be supported. 2025-06-04T21:21:50,245 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-04T21:21:50,246 ******************************************************************************** 2025-06-04T21:21:50,247 !! 2025-06-04T21:21:50,247 self.initialize_options() 2025-06-04T21:21:50,269 installing to build/bdist.linux-armv7l/wheel 2025-06-04T21:21:50,269 running install 2025-06-04T21:21:50,295 running install_lib 2025-06-04T21:21:50,323 creating build/bdist.linux-armv7l/wheel 2025-06-04T21:21:50,326 creating build/bdist.linux-armv7l/wheel/concord 2025-06-04T21:21:50,327 copying build/lib/concord/pl.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-04T21:21:50,331 creating build/bdist.linux-armv7l/wheel/concord/model 2025-06-04T21:21:50,333 copying build/lib/concord/model/trainer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-04T21:21:50,337 copying build/lib/concord/model/knn.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-04T21:21:50,340 copying build/lib/concord/model/chunkloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-04T21:21:50,344 copying build/lib/concord/model/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-04T21:21:50,347 copying build/lib/concord/model/loss.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-04T21:21:50,350 copying build/lib/concord/model/dataloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-04T21:21:50,354 copying build/lib/concord/model/build_layer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-04T21:21:50,356 copying build/lib/concord/model/model.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-04T21:21:50,359 copying build/lib/concord/model/sampler.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-04T21:21:50,362 copying build/lib/concord/model/anndataset.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-04T21:21:50,365 copying build/lib/concord/ml.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-04T21:21:50,368 copying build/lib/concord/__init__.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-04T21:21:50,371 copying build/lib/concord/concord.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-04T21:21:50,374 copying build/lib/concord/ul.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-04T21:21:50,377 creating build/bdist.linux-armv7l/wheel/concord/plotting 2025-06-04T21:21:50,378 copying build/lib/concord/plotting/pl_path.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,381 copying build/lib/concord/plotting/pl_geometry.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,383 copying build/lib/concord/plotting/pl_heatmap.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,387 copying build/lib/concord/plotting/pl_general.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,389 copying build/lib/concord/plotting/pl_datacoverage.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,391 copying build/lib/concord/plotting/pl_embedding.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,397 copying build/lib/concord/plotting/pl_model.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,400 copying build/lib/concord/plotting/pl_enrichment.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,403 copying build/lib/concord/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,405 copying build/lib/concord/plotting/pl_benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,408 copying build/lib/concord/plotting/palettes.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,412 copying build/lib/concord/plotting/pl_tda.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,416 copying build/lib/concord/plotting/pl_graph.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,420 copying build/lib/concord/plotting/pl_batch.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-04T21:21:50,424 creating build/bdist.linux-armv7l/wheel/concord/utils 2025-06-04T21:21:50,425 copying build/lib/concord/utils/run_dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,428 copying build/lib/concord/utils/estimate_aug_mask_prob.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,430 copying build/lib/concord/utils/Hs_Mm_conversion.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,433 copying build/lib/concord/utils/doublet_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,435 copying build/lib/concord/utils/benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,438 copying build/lib/concord/utils/io.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,441 copying build/lib/concord/utils/timer.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,443 copying build/lib/concord/utils/feature_selector.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,446 copying build/lib/concord/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,448 copying build/lib/concord/utils/coverage_estimator.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,451 copying build/lib/concord/utils/anndata_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,453 copying build/lib/concord/utils/simulation.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,458 copying build/lib/concord/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,461 copying build/lib/concord/utils/other_util.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,464 copying build/lib/concord/utils/run_integration_methods.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,466 copying build/lib/concord/utils/sparsity.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,468 copying build/lib/concord/utils/cellxgene.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,471 copying build/lib/concord/utils/path_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,473 copying build/lib/concord/utils/visCello.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,477 copying build/lib/concord/utils/preprocessor.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,479 copying build/lib/concord/utils/enrichment_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,483 copying build/lib/concord/utils/cell_cycle.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,487 copying build/lib/concord/utils/tda.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,492 copying build/lib/concord/utils/evaluator.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,495 copying build/lib/concord/utils/importance_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,498 copying build/lib/concord/utils/value_check.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,501 copying build/lib/concord/utils/batch_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-04T21:21:50,503 running install_egg_info 2025-06-04T21:21:50,545 running egg_info 2025-06-04T21:21:50,578 writing src/concord_sc.egg-info/PKG-INFO 2025-06-04T21:21:50,585 writing dependency_links to src/concord_sc.egg-info/dependency_links.txt 2025-06-04T21:21:50,590 writing requirements to src/concord_sc.egg-info/requires.txt 2025-06-04T21:21:50,591 writing top-level names to src/concord_sc.egg-info/top_level.txt 2025-06-04T21:21:50,635 reading manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-06-04T21:21:50,641 adding license file 'LICENSE.md' 2025-06-04T21:21:50,646 writing manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-06-04T21:21:50,647 Copying src/concord_sc.egg-info to build/bdist.linux-armv7l/wheel/./concord_sc-0.9.6-py3.11.egg-info 2025-06-04T21:21:50,660 running install_scripts 2025-06-04T21:21:50,678 creating build/bdist.linux-armv7l/wheel/concord_sc-0.9.6.dist-info/WHEEL 2025-06-04T21:21:50,681 creating '/tmp/pip-wheel-wpjmdmy4/concord_sc-0.9.6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-04T21:21:50,684 adding 'concord/__init__.py' 2025-06-04T21:21:50,691 adding 'concord/concord.py' 2025-06-04T21:21:50,693 adding 'concord/ml.py' 2025-06-04T21:21:50,695 adding 'concord/pl.py' 2025-06-04T21:21:50,696 adding 'concord/ul.py' 2025-06-04T21:21:50,698 adding 'concord/model/__init__.py' 2025-06-04T21:21:50,700 adding 'concord/model/anndataset.py' 2025-06-04T21:21:50,702 adding 'concord/model/build_layer.py' 2025-06-04T21:21:50,704 adding 'concord/model/chunkloader.py' 2025-06-04T21:21:50,706 adding 'concord/model/dataloader.py' 2025-06-04T21:21:50,709 adding 'concord/model/knn.py' 2025-06-04T21:21:50,710 adding 'concord/model/loss.py' 2025-06-04T21:21:50,713 adding 'concord/model/model.py' 2025-06-04T21:21:50,715 adding 'concord/model/sampler.py' 2025-06-04T21:21:50,717 adding 'concord/model/trainer.py' 2025-06-04T21:21:50,719 adding 'concord/plotting/__init__.py' 2025-06-04T21:21:50,721 adding 'concord/plotting/palettes.py' 2025-06-04T21:21:50,722 adding 'concord/plotting/pl_batch.py' 2025-06-04T21:21:50,724 adding 'concord/plotting/pl_benchmark.py' 2025-06-04T21:21:50,725 adding 'concord/plotting/pl_datacoverage.py' 2025-06-04T21:21:50,732 adding 'concord/plotting/pl_embedding.py' 2025-06-04T21:21:50,734 adding 'concord/plotting/pl_enrichment.py' 2025-06-04T21:21:50,735 adding 'concord/plotting/pl_general.py' 2025-06-04T21:21:50,737 adding 'concord/plotting/pl_geometry.py' 2025-06-04T21:21:50,740 adding 'concord/plotting/pl_graph.py' 2025-06-04T21:21:50,742 adding 'concord/plotting/pl_heatmap.py' 2025-06-04T21:21:50,744 adding 'concord/plotting/pl_model.py' 2025-06-04T21:21:50,745 adding 'concord/plotting/pl_path.py' 2025-06-04T21:21:50,748 adding 'concord/plotting/pl_tda.py' 2025-06-04T21:21:50,751 adding 'concord/utils/Hs_Mm_conversion.py' 2025-06-04T21:21:50,752 adding 'concord/utils/__init__.py' 2025-06-04T21:21:50,754 adding 'concord/utils/anndata_utils.py' 2025-06-04T21:21:50,755 adding 'concord/utils/batch_analysis.py' 2025-06-04T21:21:50,759 adding 'concord/utils/benchmark.py' 2025-06-04T21:21:50,761 adding 'concord/utils/cell_cycle.py' 2025-06-04T21:21:50,762 adding 'concord/utils/cellxgene.py' 2025-06-04T21:21:50,764 adding 'concord/utils/coverage_estimator.py' 2025-06-04T21:21:50,765 adding 'concord/utils/doublet_utils.py' 2025-06-04T21:21:50,767 adding 'concord/utils/enrichment_analysis.py' 2025-06-04T21:21:50,769 adding 'concord/utils/estimate_aug_mask_prob.py' 2025-06-04T21:21:50,770 adding 'concord/utils/evaluator.py' 2025-06-04T21:21:50,772 adding 'concord/utils/feature_selector.py' 2025-06-04T21:21:50,774 adding 'concord/utils/geometry.py' 2025-06-04T21:21:50,776 adding 'concord/utils/importance_analysis.py' 2025-06-04T21:21:50,777 adding 'concord/utils/io.py' 2025-06-04T21:21:50,779 adding 'concord/utils/other_util.py' 2025-06-04T21:21:50,780 adding 'concord/utils/path_analysis.py' 2025-06-04T21:21:50,782 adding 'concord/utils/preprocessor.py' 2025-06-04T21:21:50,784 adding 'concord/utils/run_dim_reduction.py' 2025-06-04T21:21:50,786 adding 'concord/utils/run_integration_methods.py' 2025-06-04T21:21:50,792 adding 'concord/utils/simulation.py' 2025-06-04T21:21:50,794 adding 'concord/utils/sparsity.py' 2025-06-04T21:21:50,796 adding 'concord/utils/tda.py' 2025-06-04T21:21:50,797 adding 'concord/utils/timer.py' 2025-06-04T21:21:50,798 adding 'concord/utils/value_check.py' 2025-06-04T21:21:50,800 adding 'concord/utils/visCello.py' 2025-06-04T21:21:50,803 adding 'concord_sc-0.9.6.dist-info/licenses/LICENSE.md' 2025-06-04T21:21:50,805 adding 'concord_sc-0.9.6.dist-info/METADATA' 2025-06-04T21:21:50,806 adding 'concord_sc-0.9.6.dist-info/WHEEL' 2025-06-04T21:21:50,807 adding 'concord_sc-0.9.6.dist-info/top_level.txt' 2025-06-04T21:21:50,808 adding 'concord_sc-0.9.6.dist-info/RECORD' 2025-06-04T21:21:50,812 removing build/bdist.linux-armv7l/wheel 2025-06-04T21:21:50,939 Building wheel for concord-sc (setup.py): finished with status 'done' 2025-06-04T21:21:50,943 Created wheel for concord-sc: filename=concord_sc-0.9.6-py3-none-any.whl size=140977 sha256=f1901b2404d6ddebb76cb5b640d0adc977b292f605f2fc39befac054a91dfc6d 2025-06-04T21:21:50,945 Stored in directory: /tmp/pip-ephem-wheel-cache-z2xauny5/wheels/1f/ad/bd/7c65c73337da9249a9759e640249e31eaa1d37ba765f0b4a62 2025-06-04T21:21:50,959 Successfully built concord-sc 2025-06-04T21:21:50,968 Removed build tracker: '/tmp/pip-build-tracker-_5ax6wgp'