2025-06-02T17:35:08,133 Created temporary directory: /tmp/pip-build-tracker-dpncm2fh 2025-06-02T17:35:08,134 Initialized build tracking at /tmp/pip-build-tracker-dpncm2fh 2025-06-02T17:35:08,134 Created build tracker: /tmp/pip-build-tracker-dpncm2fh 2025-06-02T17:35:08,135 Entered build tracker: /tmp/pip-build-tracker-dpncm2fh 2025-06-02T17:35:08,136 Created temporary directory: /tmp/pip-wheel-yykhv6or 2025-06-02T17:35:08,140 Created temporary directory: /tmp/pip-ephem-wheel-cache-2wpfq04w 2025-06-02T17:35:08,188 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-02T17:35:08,191 2 location(s) to search for versions of concord-sc: 2025-06-02T17:35:08,191 * https://pypi.org/simple/concord-sc/ 2025-06-02T17:35:08,191 * https://www.piwheels.org/simple/concord-sc/ 2025-06-02T17:35:08,192 Fetching project page and analyzing links: https://pypi.org/simple/concord-sc/ 2025-06-02T17:35:08,192 Getting page https://pypi.org/simple/concord-sc/ 2025-06-02T17:35:08,194 Found index url https://pypi.org/simple/ 2025-06-02T17:35:08,342 Fetched page https://pypi.org/simple/concord-sc/ as application/vnd.pypi.simple.v1+json 2025-06-02T17:35:08,345 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) 2025-06-02T17:35:08,346 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 2025-06-02T17:35:08,347 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) 2025-06-02T17:35:08,348 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 2025-06-02T17:35:08,349 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) 2025-06-02T17:35:08,349 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 2025-06-02T17:35:08,350 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) 2025-06-02T17:35:08,351 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 2025-06-02T17:35:08,352 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) 2025-06-02T17:35:08,352 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 2025-06-02T17:35:08,353 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) 2025-06-02T17:35:08,354 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 2025-06-02T17:35:08,355 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) 2025-06-02T17:35:08,355 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 2025-06-02T17:35:08,356 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) 2025-06-02T17:35:08,356 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 2025-06-02T17:35:08,357 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) 2025-06-02T17:35:08,357 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 2025-06-02T17:35:08,358 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) 2025-06-02T17:35:08,359 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 2025-06-02T17:35:08,360 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) 2025-06-02T17:35:08,360 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 2025-06-02T17:35:08,361 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) 2025-06-02T17:35:08,362 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 2025-06-02T17:35:08,363 Fetching project page and analyzing links: https://www.piwheels.org/simple/concord-sc/ 2025-06-02T17:35:08,363 Getting page https://www.piwheels.org/simple/concord-sc/ 2025-06-02T17:35:08,365 Found index url https://www.piwheels.org/simple/ 2025-06-02T17:35:08,530 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/ 2025-06-02T17:35:09,192 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/ 2025-06-02T17:35:10,358 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/ 2025-06-02T17:35:12,528 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/ 2025-06-02T17:35:16,703 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/ 2025-06-02T17:35:16,875 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 2025-06-02T17:35:16,876 Skipping link: not a file: https://www.piwheels.org/simple/concord-sc/ 2025-06-02T17:35:16,877 Skipping link: not a file: https://pypi.org/simple/concord-sc/ 2025-06-02T17:35:16,900 Given no hashes to check 1 links for project 'concord-sc': discarding no candidates 2025-06-02T17:35:16,902 Collecting concord-sc==0.9.5 2025-06-02T17:35:16,905 Created temporary directory: /tmp/pip-unpack-kb4gosl4 2025-06-02T17:35:17,332 Downloading concord_sc-0.9.5.tar.gz (123 kB) 2025-06-02T17:35:17,562 Added concord-sc==0.9.5 from https://files.pythonhosted.org/packages/d8/f0/b8974243a19b799f97589ac5853c40426cc2fd261969d4950880df87f562/concord_sc-0.9.5.tar.gz to build tracker '/tmp/pip-build-tracker-dpncm2fh' 2025-06-02T17:35:17,565 Running setup.py (path:/tmp/pip-wheel-yykhv6or/concord-sc_88f75e9e7d024e2e96b146330e8ed5f0/setup.py) egg_info for package concord-sc 2025-06-02T17:35:17,566 Created temporary directory: /tmp/pip-pip-egg-info-3vso4lvg 2025-06-02T17:35:17,567 Preparing metadata (setup.py): started 2025-06-02T17:35:17,568 Running command python setup.py egg_info 2025-06-02T17:35:18,464 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-02T17:35:18,464 !! 2025-06-02T17:35:18,465 ******************************************************************************** 2025-06-02T17:35:18,466 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-02T17:35:18,467 License :: OSI Approved :: MIT License 2025-06-02T17:35:18,468 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-02T17:35:18,469 ******************************************************************************** 2025-06-02T17:35:18,470 !! 2025-06-02T17:35:18,471 self._finalize_license_expression() 2025-06-02T17:35:18,495 running egg_info 2025-06-02T17:35:18,523 creating /tmp/pip-pip-egg-info-3vso4lvg/concord_sc.egg-info 2025-06-02T17:35:18,524 writing /tmp/pip-pip-egg-info-3vso4lvg/concord_sc.egg-info/PKG-INFO 2025-06-02T17:35:18,530 writing dependency_links to /tmp/pip-pip-egg-info-3vso4lvg/concord_sc.egg-info/dependency_links.txt 2025-06-02T17:35:18,534 writing requirements to /tmp/pip-pip-egg-info-3vso4lvg/concord_sc.egg-info/requires.txt 2025-06-02T17:35:18,535 writing top-level names to /tmp/pip-pip-egg-info-3vso4lvg/concord_sc.egg-info/top_level.txt 2025-06-02T17:35:18,537 writing manifest file '/tmp/pip-pip-egg-info-3vso4lvg/concord_sc.egg-info/SOURCES.txt' 2025-06-02T17:35:18,627 reading manifest file '/tmp/pip-pip-egg-info-3vso4lvg/concord_sc.egg-info/SOURCES.txt' 2025-06-02T17:35:18,629 adding license file 'LICENSE.md' 2025-06-02T17:35:18,633 writing manifest file '/tmp/pip-pip-egg-info-3vso4lvg/concord_sc.egg-info/SOURCES.txt' 2025-06-02T17:35:18,739 Preparing metadata (setup.py): finished with status 'done' 2025-06-02T17:35:18,743 Source in /tmp/pip-wheel-yykhv6or/concord-sc_88f75e9e7d024e2e96b146330e8ed5f0 has version 0.9.5, which satisfies requirement concord-sc==0.9.5 from https://files.pythonhosted.org/packages/d8/f0/b8974243a19b799f97589ac5853c40426cc2fd261969d4950880df87f562/concord_sc-0.9.5.tar.gz 2025-06-02T17:35:18,744 Removed concord-sc==0.9.5 from https://files.pythonhosted.org/packages/d8/f0/b8974243a19b799f97589ac5853c40426cc2fd261969d4950880df87f562/concord_sc-0.9.5.tar.gz from build tracker '/tmp/pip-build-tracker-dpncm2fh' 2025-06-02T17:35:18,755 Created temporary directory: /tmp/pip-unpack-srfurnbb 2025-06-02T17:35:18,756 Created temporary directory: /tmp/pip-unpack-sagsazhv 2025-06-02T17:35:18,757 Building wheels for collected packages: concord-sc 2025-06-02T17:35:18,761 Created temporary directory: /tmp/pip-wheel-34450nvj 2025-06-02T17:35:18,762 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 2025-06-02T17:35:18,763 Building wheel for concord-sc (setup.py): started 2025-06-02T17:35:18,764 Destination directory: /tmp/pip-wheel-34450nvj 2025-06-02T17:35:18,765 Running command python setup.py bdist_wheel 2025-06-02T17:35:19,612 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-02T17:35:19,612 !! 2025-06-02T17:35:19,613 ******************************************************************************** 2025-06-02T17:35:19,614 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-02T17:35:19,615 License :: OSI Approved :: MIT License 2025-06-02T17:35:19,617 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-02T17:35:19,617 ******************************************************************************** 2025-06-02T17:35:19,618 !! 2025-06-02T17:35:19,619 self._finalize_license_expression() 2025-06-02T17:35:19,620 running bdist_wheel 2025-06-02T17:35:19,748 running build 2025-06-02T17:35:19,749 running build_py 2025-06-02T17:35:20,004 creating build/lib/concord 2025-06-02T17:35:20,006 copying src/concord/ml.py -> build/lib/concord 2025-06-02T17:35:20,009 copying src/concord/concord.py -> build/lib/concord 2025-06-02T17:35:20,012 copying src/concord/__init__.py -> build/lib/concord 2025-06-02T17:35:20,014 copying src/concord/ul.py -> build/lib/concord 2025-06-02T17:35:20,016 copying src/concord/pl.py -> build/lib/concord 2025-06-02T17:35:20,019 creating build/lib/concord/utils 2025-06-02T17:35:20,020 copying src/concord/utils/estimate_aug_mask_prob.py -> build/lib/concord/utils 2025-06-02T17:35:20,022 copying src/concord/utils/sparsity.py -> build/lib/concord/utils 2025-06-02T17:35:20,024 copying src/concord/utils/other_util.py -> build/lib/concord/utils 2025-06-02T17:35:20,026 copying src/concord/utils/tda.py -> build/lib/concord/utils 2025-06-02T17:35:20,029 copying src/concord/utils/run_integration_methods.py -> build/lib/concord/utils 2025-06-02T17:35:20,032 copying src/concord/utils/importance_analysis.py -> build/lib/concord/utils 2025-06-02T17:35:20,034 copying src/concord/utils/path_analysis.py -> build/lib/concord/utils 2025-06-02T17:35:20,037 copying src/concord/utils/run_dim_reduction.py -> build/lib/concord/utils 2025-06-02T17:35:20,039 copying src/concord/utils/visCello.py -> build/lib/concord/utils 2025-06-02T17:35:20,042 copying src/concord/utils/__init__.py -> build/lib/concord/utils 2025-06-02T17:35:20,044 copying src/concord/utils/coverage_estimator.py -> build/lib/concord/utils 2025-06-02T17:35:20,046 copying src/concord/utils/preprocessor.py -> build/lib/concord/utils 2025-06-02T17:35:20,048 copying src/concord/utils/feature_selector.py -> build/lib/concord/utils 2025-06-02T17:35:20,052 copying src/concord/utils/evaluator.py -> build/lib/concord/utils 2025-06-02T17:35:20,054 copying src/concord/utils/value_check.py -> build/lib/concord/utils 2025-06-02T17:35:20,056 copying src/concord/utils/enrichment_analysis.py -> build/lib/concord/utils 2025-06-02T17:35:20,058 copying src/concord/utils/anndata_utils.py -> build/lib/concord/utils 2025-06-02T17:35:20,060 copying src/concord/utils/benchmark.py -> build/lib/concord/utils 2025-06-02T17:35:20,063 copying src/concord/utils/simulation.py -> build/lib/concord/utils 2025-06-02T17:35:20,067 copying src/concord/utils/timer.py -> build/lib/concord/utils 2025-06-02T17:35:20,069 copying src/concord/utils/io.py -> build/lib/concord/utils 2025-06-02T17:35:20,071 copying src/concord/utils/batch_analysis.py -> build/lib/concord/utils 2025-06-02T17:35:20,073 copying src/concord/utils/cell_cycle.py -> build/lib/concord/utils 2025-06-02T17:35:20,075 copying src/concord/utils/geometry.py -> build/lib/concord/utils 2025-06-02T17:35:20,077 copying src/concord/utils/doublet_utils.py -> build/lib/concord/utils 2025-06-02T17:35:20,080 copying src/concord/utils/Hs_Mm_conversion.py -> build/lib/concord/utils 2025-06-02T17:35:20,082 copying src/concord/utils/cellxgene.py -> build/lib/concord/utils 2025-06-02T17:35:20,085 creating build/lib/concord/model 2025-06-02T17:35:20,086 copying src/concord/model/knn.py -> build/lib/concord/model 2025-06-02T17:35:20,089 copying src/concord/model/model.py -> build/lib/concord/model 2025-06-02T17:35:20,091 copying src/concord/model/dataloader.py -> build/lib/concord/model 2025-06-02T17:35:20,094 copying src/concord/model/sampler.py -> build/lib/concord/model 2025-06-02T17:35:20,096 copying src/concord/model/build_layer.py -> build/lib/concord/model 2025-06-02T17:35:20,099 copying src/concord/model/__init__.py -> build/lib/concord/model 2025-06-02T17:35:20,100 copying src/concord/model/chunkloader.py -> build/lib/concord/model 2025-06-02T17:35:20,103 copying src/concord/model/trainer.py -> build/lib/concord/model 2025-06-02T17:35:20,106 copying src/concord/model/anndataset.py -> build/lib/concord/model 2025-06-02T17:35:20,108 copying src/concord/model/loss.py -> build/lib/concord/model 2025-06-02T17:35:20,111 creating build/lib/concord/plotting 2025-06-02T17:35:20,112 copying src/concord/plotting/pl_tda.py -> build/lib/concord/plotting 2025-06-02T17:35:20,115 copying src/concord/plotting/pl_enrichment.py -> build/lib/concord/plotting 2025-06-02T17:35:20,118 copying src/concord/plotting/pl_datacoverage.py -> build/lib/concord/plotting 2025-06-02T17:35:20,120 copying src/concord/plotting/__init__.py -> build/lib/concord/plotting 2025-06-02T17:35:20,122 copying src/concord/plotting/pl_geometry.py -> build/lib/concord/plotting 2025-06-02T17:35:20,125 copying src/concord/plotting/palettes.py -> build/lib/concord/plotting 2025-06-02T17:35:20,127 copying src/concord/plotting/pl_graph.py -> build/lib/concord/plotting 2025-06-02T17:35:20,130 copying src/concord/plotting/pl_model.py -> build/lib/concord/plotting 2025-06-02T17:35:20,132 copying src/concord/plotting/pl_batch.py -> build/lib/concord/plotting 2025-06-02T17:35:20,134 copying src/concord/plotting/pl_heatmap.py -> build/lib/concord/plotting 2025-06-02T17:35:20,138 copying src/concord/plotting/pl_path.py -> build/lib/concord/plotting 2025-06-02T17:35:20,140 copying src/concord/plotting/pl_embedding.py -> build/lib/concord/plotting 2025-06-02T17:35:20,143 copying src/concord/plotting/pl_benchmark.py -> build/lib/concord/plotting 2025-06-02T17:35:20,146 copying src/concord/plotting/pl_general.py -> build/lib/concord/plotting 2025-06-02T17:35:20,185 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-02T17:35:20,185 !! 2025-06-02T17:35:20,186 ******************************************************************************** 2025-06-02T17:35:20,187 Please avoid running ``setup.py`` directly. 2025-06-02T17:35:20,187 Instead, use pypa/build, pypa/installer or other 2025-06-02T17:35:20,188 standards-based tools. 2025-06-02T17:35:20,189 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-02T17:35:20,189 or your builds will no longer be supported. 2025-06-02T17:35:20,190 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-02T17:35:20,191 ******************************************************************************** 2025-06-02T17:35:20,192 !! 2025-06-02T17:35:20,192 self.initialize_options() 2025-06-02T17:35:20,213 installing to build/bdist.linux-armv7l/wheel 2025-06-02T17:35:20,214 running install 2025-06-02T17:35:20,239 running install_lib 2025-06-02T17:35:20,266 creating build/bdist.linux-armv7l/wheel 2025-06-02T17:35:20,268 creating build/bdist.linux-armv7l/wheel/concord 2025-06-02T17:35:20,269 copying build/lib/concord/ml.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T17:35:20,271 copying build/lib/concord/concord.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T17:35:20,275 creating build/bdist.linux-armv7l/wheel/concord/utils 2025-06-02T17:35:20,276 copying build/lib/concord/utils/estimate_aug_mask_prob.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,279 copying build/lib/concord/utils/sparsity.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,280 copying build/lib/concord/utils/other_util.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,282 copying build/lib/concord/utils/tda.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,285 copying build/lib/concord/utils/run_integration_methods.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,287 copying build/lib/concord/utils/importance_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,289 copying build/lib/concord/utils/path_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,292 copying build/lib/concord/utils/run_dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,294 copying build/lib/concord/utils/visCello.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,297 copying build/lib/concord/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,299 copying build/lib/concord/utils/coverage_estimator.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,301 copying build/lib/concord/utils/preprocessor.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,303 copying build/lib/concord/utils/feature_selector.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,306 copying build/lib/concord/utils/evaluator.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,308 copying build/lib/concord/utils/value_check.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,310 copying build/lib/concord/utils/enrichment_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,313 copying build/lib/concord/utils/anndata_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,316 copying build/lib/concord/utils/benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,319 copying build/lib/concord/utils/simulation.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,322 copying build/lib/concord/utils/timer.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,324 copying build/lib/concord/utils/io.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,326 copying build/lib/concord/utils/batch_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,328 copying build/lib/concord/utils/cell_cycle.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,330 copying build/lib/concord/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,333 copying build/lib/concord/utils/doublet_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,335 copying build/lib/concord/utils/Hs_Mm_conversion.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,337 copying build/lib/concord/utils/cellxgene.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T17:35:20,340 creating build/bdist.linux-armv7l/wheel/concord/model 2025-06-02T17:35:20,341 copying build/lib/concord/model/knn.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T17:35:20,344 copying build/lib/concord/model/model.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T17:35:20,347 copying build/lib/concord/model/dataloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T17:35:20,351 copying build/lib/concord/model/sampler.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T17:35:20,353 copying build/lib/concord/model/build_layer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T17:35:20,355 copying build/lib/concord/model/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T17:35:20,358 copying build/lib/concord/model/chunkloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T17:35:20,362 copying build/lib/concord/model/trainer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T17:35:20,364 copying build/lib/concord/model/anndataset.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T17:35:20,367 copying build/lib/concord/model/loss.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T17:35:20,369 copying build/lib/concord/__init__.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T17:35:20,371 copying build/lib/concord/ul.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T17:35:20,374 creating build/bdist.linux-armv7l/wheel/concord/plotting 2025-06-02T17:35:20,375 copying build/lib/concord/plotting/pl_tda.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,378 copying build/lib/concord/plotting/pl_enrichment.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,381 copying build/lib/concord/plotting/pl_datacoverage.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,383 copying build/lib/concord/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,385 copying build/lib/concord/plotting/pl_geometry.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,388 copying build/lib/concord/plotting/palettes.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,390 copying build/lib/concord/plotting/pl_graph.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,393 copying build/lib/concord/plotting/pl_model.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,396 copying build/lib/concord/plotting/pl_batch.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,398 copying build/lib/concord/plotting/pl_heatmap.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,400 copying build/lib/concord/plotting/pl_path.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,402 copying build/lib/concord/plotting/pl_embedding.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,406 copying build/lib/concord/plotting/pl_benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,409 copying build/lib/concord/plotting/pl_general.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T17:35:20,410 copying build/lib/concord/pl.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T17:35:20,412 running install_egg_info 2025-06-02T17:35:20,450 running egg_info 2025-06-02T17:35:20,479 writing src/concord_sc.egg-info/PKG-INFO 2025-06-02T17:35:20,485 writing dependency_links to src/concord_sc.egg-info/dependency_links.txt 2025-06-02T17:35:20,489 writing requirements to src/concord_sc.egg-info/requires.txt 2025-06-02T17:35:20,490 writing top-level names to src/concord_sc.egg-info/top_level.txt 2025-06-02T17:35:20,526 reading manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-06-02T17:35:20,532 adding license file 'LICENSE.md' 2025-06-02T17:35:20,537 writing manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-06-02T17:35:20,538 Copying src/concord_sc.egg-info to build/bdist.linux-armv7l/wheel/./concord_sc-0.9.5-py3.11.egg-info 2025-06-02T17:35:20,548 running install_scripts 2025-06-02T17:35:20,560 creating build/bdist.linux-armv7l/wheel/concord_sc-0.9.5.dist-info/WHEEL 2025-06-02T17:35:20,563 creating '/tmp/pip-wheel-34450nvj/concord_sc-0.9.5-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-02T17:35:20,566 adding 'concord/__init__.py' 2025-06-02T17:35:20,571 adding 'concord/concord.py' 2025-06-02T17:35:20,573 adding 'concord/ml.py' 2025-06-02T17:35:20,574 adding 'concord/pl.py' 2025-06-02T17:35:20,575 adding 'concord/ul.py' 2025-06-02T17:35:20,578 adding 'concord/model/__init__.py' 2025-06-02T17:35:20,580 adding 'concord/model/anndataset.py' 2025-06-02T17:35:20,581 adding 'concord/model/build_layer.py' 2025-06-02T17:35:20,583 adding 'concord/model/chunkloader.py' 2025-06-02T17:35:20,587 adding 'concord/model/dataloader.py' 2025-06-02T17:35:20,589 adding 'concord/model/knn.py' 2025-06-02T17:35:20,591 adding 'concord/model/loss.py' 2025-06-02T17:35:20,593 adding 'concord/model/model.py' 2025-06-02T17:35:20,594 adding 'concord/model/sampler.py' 2025-06-02T17:35:20,596 adding 'concord/model/trainer.py' 2025-06-02T17:35:20,598 adding 'concord/plotting/__init__.py' 2025-06-02T17:35:20,600 adding 'concord/plotting/palettes.py' 2025-06-02T17:35:20,602 adding 'concord/plotting/pl_batch.py' 2025-06-02T17:35:20,604 adding 'concord/plotting/pl_benchmark.py' 2025-06-02T17:35:20,605 adding 'concord/plotting/pl_datacoverage.py' 2025-06-02T17:35:20,612 adding 'concord/plotting/pl_embedding.py' 2025-06-02T17:35:20,614 adding 'concord/plotting/pl_enrichment.py' 2025-06-02T17:35:20,615 adding 'concord/plotting/pl_general.py' 2025-06-02T17:35:20,617 adding 'concord/plotting/pl_geometry.py' 2025-06-02T17:35:20,620 adding 'concord/plotting/pl_graph.py' 2025-06-02T17:35:20,623 adding 'concord/plotting/pl_heatmap.py' 2025-06-02T17:35:20,625 adding 'concord/plotting/pl_model.py' 2025-06-02T17:35:20,626 adding 'concord/plotting/pl_path.py' 2025-06-02T17:35:20,629 adding 'concord/plotting/pl_tda.py' 2025-06-02T17:35:20,631 adding 'concord/utils/Hs_Mm_conversion.py' 2025-06-02T17:35:20,632 adding 'concord/utils/__init__.py' 2025-06-02T17:35:20,634 adding 'concord/utils/anndata_utils.py' 2025-06-02T17:35:20,636 adding 'concord/utils/batch_analysis.py' 2025-06-02T17:35:20,639 adding 'concord/utils/benchmark.py' 2025-06-02T17:35:20,641 adding 'concord/utils/cell_cycle.py' 2025-06-02T17:35:20,642 adding 'concord/utils/cellxgene.py' 2025-06-02T17:35:20,644 adding 'concord/utils/coverage_estimator.py' 2025-06-02T17:35:20,645 adding 'concord/utils/doublet_utils.py' 2025-06-02T17:35:20,647 adding 'concord/utils/enrichment_analysis.py' 2025-06-02T17:35:20,648 adding 'concord/utils/estimate_aug_mask_prob.py' 2025-06-02T17:35:20,650 adding 'concord/utils/evaluator.py' 2025-06-02T17:35:20,652 adding 'concord/utils/feature_selector.py' 2025-06-02T17:35:20,654 adding 'concord/utils/geometry.py' 2025-06-02T17:35:20,656 adding 'concord/utils/importance_analysis.py' 2025-06-02T17:35:20,658 adding 'concord/utils/io.py' 2025-06-02T17:35:20,659 adding 'concord/utils/other_util.py' 2025-06-02T17:35:20,661 adding 'concord/utils/path_analysis.py' 2025-06-02T17:35:20,662 adding 'concord/utils/preprocessor.py' 2025-06-02T17:35:20,664 adding 'concord/utils/run_dim_reduction.py' 2025-06-02T17:35:20,666 adding 'concord/utils/run_integration_methods.py' 2025-06-02T17:35:20,673 adding 'concord/utils/simulation.py' 2025-06-02T17:35:20,674 adding 'concord/utils/sparsity.py' 2025-06-02T17:35:20,676 adding 'concord/utils/tda.py' 2025-06-02T17:35:20,677 adding 'concord/utils/timer.py' 2025-06-02T17:35:20,679 adding 'concord/utils/value_check.py' 2025-06-02T17:35:20,680 adding 'concord/utils/visCello.py' 2025-06-02T17:35:20,683 adding 'concord_sc-0.9.5.dist-info/licenses/LICENSE.md' 2025-06-02T17:35:20,685 adding 'concord_sc-0.9.5.dist-info/METADATA' 2025-06-02T17:35:20,686 adding 'concord_sc-0.9.5.dist-info/WHEEL' 2025-06-02T17:35:20,686 adding 'concord_sc-0.9.5.dist-info/top_level.txt' 2025-06-02T17:35:20,688 adding 'concord_sc-0.9.5.dist-info/RECORD' 2025-06-02T17:35:20,691 removing build/bdist.linux-armv7l/wheel 2025-06-02T17:35:20,815 Building wheel for concord-sc (setup.py): finished with status 'done' 2025-06-02T17:35:20,820 Created wheel for concord-sc: filename=concord_sc-0.9.5-py3-none-any.whl size=140971 sha256=77d4ddcd59ad8d9cb04d3a6d2ef5a4299f02777d040b794e5aa2aa67e447b116 2025-06-02T17:35:20,821 Stored in directory: /tmp/pip-ephem-wheel-cache-2wpfq04w/wheels/17/1a/e1/8d2566a86e3ac43a48398d903a7e6e4b9e40f2e84f152ee19c 2025-06-02T17:35:20,835 Successfully built concord-sc 2025-06-02T17:35:20,842 Removed build tracker: '/tmp/pip-build-tracker-dpncm2fh'