2025-06-02T00:43:42,528 Created temporary directory: /tmp/pip-build-tracker-9u66u89g 2025-06-02T00:43:42,529 Initialized build tracking at /tmp/pip-build-tracker-9u66u89g 2025-06-02T00:43:42,530 Created build tracker: /tmp/pip-build-tracker-9u66u89g 2025-06-02T00:43:42,530 Entered build tracker: /tmp/pip-build-tracker-9u66u89g 2025-06-02T00:43:42,531 Created temporary directory: /tmp/pip-wheel-24r1yrp7 2025-06-02T00:43:42,535 Created temporary directory: /tmp/pip-ephem-wheel-cache-lzm56xe4 2025-06-02T00:43:42,581 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-02T00:43:42,584 2 location(s) to search for versions of concord-sc: 2025-06-02T00:43:42,584 * https://pypi.org/simple/concord-sc/ 2025-06-02T00:43:42,584 * https://www.piwheels.org/simple/concord-sc/ 2025-06-02T00:43:42,585 Fetching project page and analyzing links: https://pypi.org/simple/concord-sc/ 2025-06-02T00:43:42,586 Getting page https://pypi.org/simple/concord-sc/ 2025-06-02T00:43:42,587 Found index url https://pypi.org/simple/ 2025-06-02T00:43:42,807 Fetched page https://pypi.org/simple/concord-sc/ as application/vnd.pypi.simple.v1+json 2025-06-02T00:43:42,811 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) 2025-06-02T00:43:42,812 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 2025-06-02T00:43:42,812 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) 2025-06-02T00:43:42,813 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 2025-06-02T00:43:42,814 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) 2025-06-02T00:43:42,814 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 2025-06-02T00:43:42,815 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) 2025-06-02T00:43:42,816 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 2025-06-02T00:43:42,817 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) 2025-06-02T00:43:42,817 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 2025-06-02T00:43:42,818 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) 2025-06-02T00:43:42,819 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 2025-06-02T00:43:42,820 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) 2025-06-02T00:43:42,820 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 2025-06-02T00:43:42,821 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) 2025-06-02T00:43:42,821 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 2025-06-02T00:43:42,822 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) 2025-06-02T00:43:42,822 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 2025-06-02T00:43:42,823 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) 2025-06-02T00:43:42,823 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 2025-06-02T00:43:42,824 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) 2025-06-02T00:43:42,824 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 2025-06-02T00:43:42,825 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) 2025-06-02T00:43:42,826 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 2025-06-02T00:43:42,827 Fetching project page and analyzing links: https://www.piwheels.org/simple/concord-sc/ 2025-06-02T00:43:42,827 Getting page https://www.piwheels.org/simple/concord-sc/ 2025-06-02T00:43:42,829 Found index url https://www.piwheels.org/simple/ 2025-06-02T00:43:42,982 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/ 2025-06-02T00:43:43,657 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/ 2025-06-02T00:43:44,823 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/ 2025-06-02T00:43:47,008 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/ 2025-06-02T00:43:51,210 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/ 2025-06-02T00:43:51,418 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 2025-06-02T00:43:51,420 Skipping link: not a file: https://www.piwheels.org/simple/concord-sc/ 2025-06-02T00:43:51,420 Skipping link: not a file: https://pypi.org/simple/concord-sc/ 2025-06-02T00:43:51,439 Given no hashes to check 1 links for project 'concord-sc': discarding no candidates 2025-06-02T00:43:51,441 Collecting concord-sc==0.9.4 2025-06-02T00:43:51,443 Created temporary directory: /tmp/pip-unpack-3mh9zeve 2025-06-02T00:43:51,673 Downloading concord_sc-0.9.4.tar.gz (123 kB) 2025-06-02T00:43:51,874 Added concord-sc==0.9.4 from https://files.pythonhosted.org/packages/9f/90/29e1b0a7797b75f332fe4883b847795fb78af3640b3257acd83387e84724/concord_sc-0.9.4.tar.gz to build tracker '/tmp/pip-build-tracker-9u66u89g' 2025-06-02T00:43:51,876 Running setup.py (path:/tmp/pip-wheel-24r1yrp7/concord-sc_db90b029c78f4781864bffbb53870ab3/setup.py) egg_info for package concord-sc 2025-06-02T00:43:51,877 Created temporary directory: /tmp/pip-pip-egg-info-_z1uc3q2 2025-06-02T00:43:51,877 Preparing metadata (setup.py): started 2025-06-02T00:43:51,878 Running command python setup.py egg_info 2025-06-02T00:43:52,727 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-02T00:43:52,727 !! 2025-06-02T00:43:52,729 ******************************************************************************** 2025-06-02T00:43:52,729 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-02T00:43:52,730 License :: OSI Approved :: MIT License 2025-06-02T00:43:52,731 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-02T00:43:52,732 ******************************************************************************** 2025-06-02T00:43:52,733 !! 2025-06-02T00:43:52,734 self._finalize_license_expression() 2025-06-02T00:43:52,757 running egg_info 2025-06-02T00:43:52,783 creating /tmp/pip-pip-egg-info-_z1uc3q2/concord_sc.egg-info 2025-06-02T00:43:52,784 writing /tmp/pip-pip-egg-info-_z1uc3q2/concord_sc.egg-info/PKG-INFO 2025-06-02T00:43:52,790 writing dependency_links to /tmp/pip-pip-egg-info-_z1uc3q2/concord_sc.egg-info/dependency_links.txt 2025-06-02T00:43:52,794 writing requirements to /tmp/pip-pip-egg-info-_z1uc3q2/concord_sc.egg-info/requires.txt 2025-06-02T00:43:52,795 writing top-level names to /tmp/pip-pip-egg-info-_z1uc3q2/concord_sc.egg-info/top_level.txt 2025-06-02T00:43:52,796 writing manifest file '/tmp/pip-pip-egg-info-_z1uc3q2/concord_sc.egg-info/SOURCES.txt' 2025-06-02T00:43:52,886 reading manifest file '/tmp/pip-pip-egg-info-_z1uc3q2/concord_sc.egg-info/SOURCES.txt' 2025-06-02T00:43:52,888 adding license file 'LICENSE.md' 2025-06-02T00:43:52,892 writing manifest file '/tmp/pip-pip-egg-info-_z1uc3q2/concord_sc.egg-info/SOURCES.txt' 2025-06-02T00:43:52,997 Preparing metadata (setup.py): finished with status 'done' 2025-06-02T00:43:53,001 Source in /tmp/pip-wheel-24r1yrp7/concord-sc_db90b029c78f4781864bffbb53870ab3 has version 0.9.4, which satisfies requirement concord-sc==0.9.4 from https://files.pythonhosted.org/packages/9f/90/29e1b0a7797b75f332fe4883b847795fb78af3640b3257acd83387e84724/concord_sc-0.9.4.tar.gz 2025-06-02T00:43:53,002 Removed concord-sc==0.9.4 from https://files.pythonhosted.org/packages/9f/90/29e1b0a7797b75f332fe4883b847795fb78af3640b3257acd83387e84724/concord_sc-0.9.4.tar.gz from build tracker '/tmp/pip-build-tracker-9u66u89g' 2025-06-02T00:43:53,013 Created temporary directory: /tmp/pip-unpack-49rljpp1 2025-06-02T00:43:53,014 Created temporary directory: /tmp/pip-unpack-ejirz06y 2025-06-02T00:43:53,015 Building wheels for collected packages: concord-sc 2025-06-02T00:43:53,018 Created temporary directory: /tmp/pip-wheel-s_if8gs5 2025-06-02T00:43:53,019 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 2025-06-02T00:43:53,020 Building wheel for concord-sc (setup.py): started 2025-06-02T00:43:53,021 Destination directory: /tmp/pip-wheel-s_if8gs5 2025-06-02T00:43:53,022 Running command python setup.py bdist_wheel 2025-06-02T00:43:53,847 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-02T00:43:53,847 !! 2025-06-02T00:43:53,848 ******************************************************************************** 2025-06-02T00:43:53,848 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-02T00:43:53,850 License :: OSI Approved :: MIT License 2025-06-02T00:43:53,851 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-02T00:43:53,851 ******************************************************************************** 2025-06-02T00:43:53,853 !! 2025-06-02T00:43:53,853 self._finalize_license_expression() 2025-06-02T00:43:53,854 running bdist_wheel 2025-06-02T00:43:53,980 running build 2025-06-02T00:43:53,980 running build_py 2025-06-02T00:43:54,009 creating build/lib/concord 2025-06-02T00:43:54,011 copying src/concord/__init__.py -> build/lib/concord 2025-06-02T00:43:54,014 copying src/concord/concord.py -> build/lib/concord 2025-06-02T00:43:54,016 copying src/concord/ul.py -> build/lib/concord 2025-06-02T00:43:54,019 copying src/concord/ml.py -> build/lib/concord 2025-06-02T00:43:54,021 copying src/concord/pl.py -> build/lib/concord 2025-06-02T00:43:54,024 creating build/lib/concord/utils 2025-06-02T00:43:54,025 copying src/concord/utils/evaluator.py -> build/lib/concord/utils 2025-06-02T00:43:54,027 copying src/concord/utils/run_integration_methods.py -> build/lib/concord/utils 2025-06-02T00:43:54,030 copying src/concord/utils/other_util.py -> build/lib/concord/utils 2025-06-02T00:43:54,033 copying src/concord/utils/value_check.py -> build/lib/concord/utils 2025-06-02T00:43:54,036 copying src/concord/utils/Hs_Mm_conversion.py -> build/lib/concord/utils 2025-06-02T00:43:54,039 copying src/concord/utils/path_analysis.py -> build/lib/concord/utils 2025-06-02T00:43:54,042 copying src/concord/utils/preprocessor.py -> build/lib/concord/utils 2025-06-02T00:43:54,045 copying src/concord/utils/enrichment_analysis.py -> build/lib/concord/utils 2025-06-02T00:43:54,048 copying src/concord/utils/run_dim_reduction.py -> build/lib/concord/utils 2025-06-02T00:43:54,050 copying src/concord/utils/coverage_estimator.py -> build/lib/concord/utils 2025-06-02T00:43:54,053 copying src/concord/utils/batch_analysis.py -> build/lib/concord/utils 2025-06-02T00:43:54,055 copying src/concord/utils/sparsity.py -> build/lib/concord/utils 2025-06-02T00:43:54,058 copying src/concord/utils/io.py -> build/lib/concord/utils 2025-06-02T00:43:54,059 copying src/concord/utils/__init__.py -> build/lib/concord/utils 2025-06-02T00:43:54,061 copying src/concord/utils/feature_selector.py -> build/lib/concord/utils 2025-06-02T00:43:54,064 copying src/concord/utils/simulation.py -> build/lib/concord/utils 2025-06-02T00:43:54,066 copying src/concord/utils/cellxgene.py -> build/lib/concord/utils 2025-06-02T00:43:54,068 copying src/concord/utils/timer.py -> build/lib/concord/utils 2025-06-02T00:43:54,070 copying src/concord/utils/geometry.py -> build/lib/concord/utils 2025-06-02T00:43:54,072 copying src/concord/utils/benchmark.py -> build/lib/concord/utils 2025-06-02T00:43:54,075 copying src/concord/utils/tda.py -> build/lib/concord/utils 2025-06-02T00:43:54,077 copying src/concord/utils/cell_cycle.py -> build/lib/concord/utils 2025-06-02T00:43:54,079 copying src/concord/utils/visCello.py -> build/lib/concord/utils 2025-06-02T00:43:54,081 copying src/concord/utils/doublet_utils.py -> build/lib/concord/utils 2025-06-02T00:43:54,083 copying src/concord/utils/estimate_aug_mask_prob.py -> build/lib/concord/utils 2025-06-02T00:43:54,085 copying src/concord/utils/importance_analysis.py -> build/lib/concord/utils 2025-06-02T00:43:54,087 copying src/concord/utils/anndata_utils.py -> build/lib/concord/utils 2025-06-02T00:43:54,090 creating build/lib/concord/plotting 2025-06-02T00:43:54,091 copying src/concord/plotting/pl_path.py -> build/lib/concord/plotting 2025-06-02T00:43:54,093 copying src/concord/plotting/pl_tda.py -> build/lib/concord/plotting 2025-06-02T00:43:54,096 copying src/concord/plotting/palettes.py -> build/lib/concord/plotting 2025-06-02T00:43:54,098 copying src/concord/plotting/__init__.py -> build/lib/concord/plotting 2025-06-02T00:43:54,100 copying src/concord/plotting/pl_general.py -> build/lib/concord/plotting 2025-06-02T00:43:54,102 copying src/concord/plotting/pl_heatmap.py -> build/lib/concord/plotting 2025-06-02T00:43:54,105 copying src/concord/plotting/pl_enrichment.py -> build/lib/concord/plotting 2025-06-02T00:43:54,107 copying src/concord/plotting/pl_graph.py -> build/lib/concord/plotting 2025-06-02T00:43:54,110 copying src/concord/plotting/pl_geometry.py -> build/lib/concord/plotting 2025-06-02T00:43:54,112 copying src/concord/plotting/pl_benchmark.py -> build/lib/concord/plotting 2025-06-02T00:43:54,115 copying src/concord/plotting/pl_embedding.py -> build/lib/concord/plotting 2025-06-02T00:43:54,119 copying src/concord/plotting/pl_batch.py -> build/lib/concord/plotting 2025-06-02T00:43:54,122 copying src/concord/plotting/pl_model.py -> build/lib/concord/plotting 2025-06-02T00:43:54,124 copying src/concord/plotting/pl_datacoverage.py -> build/lib/concord/plotting 2025-06-02T00:43:54,127 creating build/lib/concord/model 2025-06-02T00:43:54,128 copying src/concord/model/chunkloader.py -> build/lib/concord/model 2025-06-02T00:43:54,131 copying src/concord/model/knn.py -> build/lib/concord/model 2025-06-02T00:43:54,134 copying src/concord/model/build_layer.py -> build/lib/concord/model 2025-06-02T00:43:54,136 copying src/concord/model/__init__.py -> build/lib/concord/model 2025-06-02T00:43:54,138 copying src/concord/model/model.py -> build/lib/concord/model 2025-06-02T00:43:54,142 copying src/concord/model/sampler.py -> build/lib/concord/model 2025-06-02T00:43:54,144 copying src/concord/model/anndataset.py -> build/lib/concord/model 2025-06-02T00:43:54,146 copying src/concord/model/dataloader.py -> build/lib/concord/model 2025-06-02T00:43:54,149 copying src/concord/model/loss.py -> build/lib/concord/model 2025-06-02T00:43:54,150 copying src/concord/model/trainer.py -> build/lib/concord/model 2025-06-02T00:43:54,183 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-02T00:43:54,183 !! 2025-06-02T00:43:54,184 ******************************************************************************** 2025-06-02T00:43:54,185 Please avoid running ``setup.py`` directly. 2025-06-02T00:43:54,185 Instead, use pypa/build, pypa/installer or other 2025-06-02T00:43:54,186 standards-based tools. 2025-06-02T00:43:54,187 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-02T00:43:54,187 or your builds will no longer be supported. 2025-06-02T00:43:54,188 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-02T00:43:54,189 ******************************************************************************** 2025-06-02T00:43:54,190 !! 2025-06-02T00:43:54,191 self.initialize_options() 2025-06-02T00:43:54,214 installing to build/bdist.linux-armv7l/wheel 2025-06-02T00:43:54,215 running install 2025-06-02T00:43:54,238 running install_lib 2025-06-02T00:43:54,265 creating build/bdist.linux-armv7l/wheel 2025-06-02T00:43:54,269 creating build/bdist.linux-armv7l/wheel/concord 2025-06-02T00:43:54,270 copying build/lib/concord/__init__.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T00:43:54,274 creating build/bdist.linux-armv7l/wheel/concord/utils 2025-06-02T00:43:54,275 copying build/lib/concord/utils/evaluator.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,278 copying build/lib/concord/utils/run_integration_methods.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,281 copying build/lib/concord/utils/other_util.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,283 copying build/lib/concord/utils/value_check.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,285 copying build/lib/concord/utils/Hs_Mm_conversion.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,288 copying build/lib/concord/utils/path_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,291 copying build/lib/concord/utils/preprocessor.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,294 copying build/lib/concord/utils/enrichment_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,296 copying build/lib/concord/utils/run_dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,299 copying build/lib/concord/utils/coverage_estimator.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,301 copying build/lib/concord/utils/batch_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,303 copying build/lib/concord/utils/sparsity.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,305 copying build/lib/concord/utils/io.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,307 copying build/lib/concord/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,309 copying build/lib/concord/utils/feature_selector.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,311 copying build/lib/concord/utils/simulation.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,314 copying build/lib/concord/utils/cellxgene.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,316 copying build/lib/concord/utils/timer.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,318 copying build/lib/concord/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,320 copying build/lib/concord/utils/benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,325 copying build/lib/concord/utils/tda.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,327 copying build/lib/concord/utils/cell_cycle.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,328 copying build/lib/concord/utils/visCello.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,331 copying build/lib/concord/utils/doublet_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,333 copying build/lib/concord/utils/estimate_aug_mask_prob.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,334 copying build/lib/concord/utils/importance_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,336 copying build/lib/concord/utils/anndata_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T00:43:54,339 copying build/lib/concord/concord.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T00:43:54,341 copying build/lib/concord/ul.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T00:43:54,344 creating build/bdist.linux-armv7l/wheel/concord/plotting 2025-06-02T00:43:54,345 copying build/lib/concord/plotting/pl_path.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,347 copying build/lib/concord/plotting/pl_tda.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,350 copying build/lib/concord/plotting/palettes.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,353 copying build/lib/concord/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,355 copying build/lib/concord/plotting/pl_general.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,358 copying build/lib/concord/plotting/pl_heatmap.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,361 copying build/lib/concord/plotting/pl_enrichment.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,364 copying build/lib/concord/plotting/pl_graph.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,368 copying build/lib/concord/plotting/pl_geometry.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,371 copying build/lib/concord/plotting/pl_benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,374 copying build/lib/concord/plotting/pl_embedding.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,379 copying build/lib/concord/plotting/pl_batch.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,381 copying build/lib/concord/plotting/pl_model.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,384 copying build/lib/concord/plotting/pl_datacoverage.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T00:43:54,387 copying build/lib/concord/ml.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T00:43:54,389 copying build/lib/concord/pl.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T00:43:54,392 creating build/bdist.linux-armv7l/wheel/concord/model 2025-06-02T00:43:54,393 copying build/lib/concord/model/chunkloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T00:43:54,396 copying build/lib/concord/model/knn.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T00:43:54,398 copying build/lib/concord/model/build_layer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T00:43:54,400 copying build/lib/concord/model/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T00:43:54,402 copying build/lib/concord/model/model.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T00:43:54,404 copying build/lib/concord/model/sampler.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T00:43:54,407 copying build/lib/concord/model/anndataset.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T00:43:54,409 copying build/lib/concord/model/dataloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T00:43:54,411 copying build/lib/concord/model/loss.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T00:43:54,413 copying build/lib/concord/model/trainer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T00:43:54,415 running install_egg_info 2025-06-02T00:43:54,449 running egg_info 2025-06-02T00:43:54,477 writing src/concord_sc.egg-info/PKG-INFO 2025-06-02T00:43:54,483 writing dependency_links to src/concord_sc.egg-info/dependency_links.txt 2025-06-02T00:43:54,486 writing requirements to src/concord_sc.egg-info/requires.txt 2025-06-02T00:43:54,487 writing top-level names to src/concord_sc.egg-info/top_level.txt 2025-06-02T00:43:54,520 reading manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-06-02T00:43:54,525 adding license file 'LICENSE.md' 2025-06-02T00:43:54,529 writing manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-06-02T00:43:54,531 Copying src/concord_sc.egg-info to build/bdist.linux-armv7l/wheel/./concord_sc-0.9.4-py3.11.egg-info 2025-06-02T00:43:54,540 running install_scripts 2025-06-02T00:43:54,551 creating build/bdist.linux-armv7l/wheel/concord_sc-0.9.4.dist-info/WHEEL 2025-06-02T00:43:54,553 creating '/tmp/pip-wheel-s_if8gs5/concord_sc-0.9.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-02T00:43:54,555 adding 'concord/__init__.py' 2025-06-02T00:43:54,560 adding 'concord/concord.py' 2025-06-02T00:43:54,561 adding 'concord/ml.py' 2025-06-02T00:43:54,562 adding 'concord/pl.py' 2025-06-02T00:43:54,563 adding 'concord/ul.py' 2025-06-02T00:43:54,565 adding 'concord/model/__init__.py' 2025-06-02T00:43:54,567 adding 'concord/model/anndataset.py' 2025-06-02T00:43:54,568 adding 'concord/model/build_layer.py' 2025-06-02T00:43:54,570 adding 'concord/model/chunkloader.py' 2025-06-02T00:43:54,572 adding 'concord/model/dataloader.py' 2025-06-02T00:43:54,574 adding 'concord/model/knn.py' 2025-06-02T00:43:54,576 adding 'concord/model/loss.py' 2025-06-02T00:43:54,577 adding 'concord/model/model.py' 2025-06-02T00:43:54,579 adding 'concord/model/sampler.py' 2025-06-02T00:43:54,581 adding 'concord/model/trainer.py' 2025-06-02T00:43:54,583 adding 'concord/plotting/__init__.py' 2025-06-02T00:43:54,585 adding 'concord/plotting/palettes.py' 2025-06-02T00:43:54,586 adding 'concord/plotting/pl_batch.py' 2025-06-02T00:43:54,588 adding 'concord/plotting/pl_benchmark.py' 2025-06-02T00:43:54,589 adding 'concord/plotting/pl_datacoverage.py' 2025-06-02T00:43:54,595 adding 'concord/plotting/pl_embedding.py' 2025-06-02T00:43:54,597 adding 'concord/plotting/pl_enrichment.py' 2025-06-02T00:43:54,598 adding 'concord/plotting/pl_general.py' 2025-06-02T00:43:54,600 adding 'concord/plotting/pl_geometry.py' 2025-06-02T00:43:54,603 adding 'concord/plotting/pl_graph.py' 2025-06-02T00:43:54,605 adding 'concord/plotting/pl_heatmap.py' 2025-06-02T00:43:54,607 adding 'concord/plotting/pl_model.py' 2025-06-02T00:43:54,608 adding 'concord/plotting/pl_path.py' 2025-06-02T00:43:54,610 adding 'concord/plotting/pl_tda.py' 2025-06-02T00:43:54,613 adding 'concord/utils/Hs_Mm_conversion.py' 2025-06-02T00:43:54,614 adding 'concord/utils/__init__.py' 2025-06-02T00:43:54,616 adding 'concord/utils/anndata_utils.py' 2025-06-02T00:43:54,617 adding 'concord/utils/batch_analysis.py' 2025-06-02T00:43:54,621 adding 'concord/utils/benchmark.py' 2025-06-02T00:43:54,622 adding 'concord/utils/cell_cycle.py' 2025-06-02T00:43:54,623 adding 'concord/utils/cellxgene.py' 2025-06-02T00:43:54,625 adding 'concord/utils/coverage_estimator.py' 2025-06-02T00:43:54,626 adding 'concord/utils/doublet_utils.py' 2025-06-02T00:43:54,628 adding 'concord/utils/enrichment_analysis.py' 2025-06-02T00:43:54,629 adding 'concord/utils/estimate_aug_mask_prob.py' 2025-06-02T00:43:54,630 adding 'concord/utils/evaluator.py' 2025-06-02T00:43:54,632 adding 'concord/utils/feature_selector.py' 2025-06-02T00:43:54,634 adding 'concord/utils/geometry.py' 2025-06-02T00:43:54,636 adding 'concord/utils/importance_analysis.py' 2025-06-02T00:43:54,637 adding 'concord/utils/io.py' 2025-06-02T00:43:54,638 adding 'concord/utils/other_util.py' 2025-06-02T00:43:54,640 adding 'concord/utils/path_analysis.py' 2025-06-02T00:43:54,641 adding 'concord/utils/preprocessor.py' 2025-06-02T00:43:54,643 adding 'concord/utils/run_dim_reduction.py' 2025-06-02T00:43:54,645 adding 'concord/utils/run_integration_methods.py' 2025-06-02T00:43:54,650 adding 'concord/utils/simulation.py' 2025-06-02T00:43:54,652 adding 'concord/utils/sparsity.py' 2025-06-02T00:43:54,654 adding 'concord/utils/tda.py' 2025-06-02T00:43:54,655 adding 'concord/utils/timer.py' 2025-06-02T00:43:54,656 adding 'concord/utils/value_check.py' 2025-06-02T00:43:54,658 adding 'concord/utils/visCello.py' 2025-06-02T00:43:54,661 adding 'concord_sc-0.9.4.dist-info/licenses/LICENSE.md' 2025-06-02T00:43:54,662 adding 'concord_sc-0.9.4.dist-info/METADATA' 2025-06-02T00:43:54,663 adding 'concord_sc-0.9.4.dist-info/WHEEL' 2025-06-02T00:43:54,664 adding 'concord_sc-0.9.4.dist-info/top_level.txt' 2025-06-02T00:43:54,666 adding 'concord_sc-0.9.4.dist-info/RECORD' 2025-06-02T00:43:54,670 removing build/bdist.linux-armv7l/wheel 2025-06-02T00:43:54,796 Building wheel for concord-sc (setup.py): finished with status 'done' 2025-06-02T00:43:54,799 Created wheel for concord-sc: filename=concord_sc-0.9.4-py3-none-any.whl size=140954 sha256=f5dfb4611bdc7ccdd08d2dcd716401b469adfbf32e8f43de38aa0e7afe9a6fc5 2025-06-02T00:43:54,801 Stored in directory: /tmp/pip-ephem-wheel-cache-lzm56xe4/wheels/32/f1/a2/6eef1bc7cb999cad03d4bb81b08055220573833be22dfd0d30 2025-06-02T00:43:54,815 Successfully built concord-sc 2025-06-02T00:43:54,821 Removed build tracker: '/tmp/pip-build-tracker-9u66u89g'