2025-06-02T11:42:34,174 Created temporary directory: /tmp/pip-build-tracker-1106txnj 2025-06-02T11:42:34,175 Initialized build tracking at /tmp/pip-build-tracker-1106txnj 2025-06-02T11:42:34,175 Created build tracker: /tmp/pip-build-tracker-1106txnj 2025-06-02T11:42:34,176 Entered build tracker: /tmp/pip-build-tracker-1106txnj 2025-06-02T11:42:34,177 Created temporary directory: /tmp/pip-wheel-v5oi09ba 2025-06-02T11:42:34,181 Created temporary directory: /tmp/pip-ephem-wheel-cache-kh65h0og 2025-06-02T11:42:34,227 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-02T11:42:34,230 2 location(s) to search for versions of concord-sc: 2025-06-02T11:42:34,230 * https://pypi.org/simple/concord-sc/ 2025-06-02T11:42:34,230 * https://www.piwheels.org/simple/concord-sc/ 2025-06-02T11:42:34,230 Fetching project page and analyzing links: https://pypi.org/simple/concord-sc/ 2025-06-02T11:42:34,231 Getting page https://pypi.org/simple/concord-sc/ 2025-06-02T11:42:34,233 Found index url https://pypi.org/simple/ 2025-06-02T11:42:34,456 Fetched page https://pypi.org/simple/concord-sc/ as application/vnd.pypi.simple.v1+json 2025-06-02T11:42:34,460 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) 2025-06-02T11:42:34,461 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 2025-06-02T11:42:34,461 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) 2025-06-02T11:42:34,462 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 2025-06-02T11:42:34,463 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) 2025-06-02T11:42:34,463 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 2025-06-02T11:42:34,464 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) 2025-06-02T11:42:34,464 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 2025-06-02T11:42:34,465 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) 2025-06-02T11:42:34,466 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 2025-06-02T11:42:34,466 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) 2025-06-02T11:42:34,467 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 2025-06-02T11:42:34,468 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) 2025-06-02T11:42:34,468 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 2025-06-02T11:42:34,469 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) 2025-06-02T11:42:34,469 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 2025-06-02T11:42:34,470 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) 2025-06-02T11:42:34,470 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 2025-06-02T11:42:34,471 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) 2025-06-02T11:42:34,471 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 2025-06-02T11:42:34,472 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) 2025-06-02T11:42:34,473 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 2025-06-02T11:42:34,473 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) 2025-06-02T11:42:34,474 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 2025-06-02T11:42:34,475 Fetching project page and analyzing links: https://www.piwheels.org/simple/concord-sc/ 2025-06-02T11:42:34,475 Getting page https://www.piwheels.org/simple/concord-sc/ 2025-06-02T11:42:34,477 Found index url https://www.piwheels.org/simple/ 2025-06-02T11:42:34,632 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/ 2025-06-02T11:42:35,281 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/ 2025-06-02T11:42:36,432 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/ 2025-06-02T11:42:38,654 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/ 2025-06-02T11:42:42,871 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/ 2025-06-02T11:42:43,059 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 2025-06-02T11:42:43,061 Skipping link: not a file: https://www.piwheels.org/simple/concord-sc/ 2025-06-02T11:42:43,061 Skipping link: not a file: https://pypi.org/simple/concord-sc/ 2025-06-02T11:42:43,080 Given no hashes to check 1 links for project 'concord-sc': discarding no candidates 2025-06-02T11:42:43,082 Collecting concord-sc==1.0.7 2025-06-02T11:42:43,084 Created temporary directory: /tmp/pip-unpack-uxfd3sf7 2025-06-02T11:42:43,307 Downloading concord_sc-1.0.7.tar.gz (136 kB) 2025-06-02T11:42:43,524 Added concord-sc==1.0.7 from https://files.pythonhosted.org/packages/ab/d0/12581f7b36e31b10b2301f87bde00115c774b47fbf025d25b1e1437993e3/concord_sc-1.0.7.tar.gz to build tracker '/tmp/pip-build-tracker-1106txnj' 2025-06-02T11:42:43,527 Running setup.py (path:/tmp/pip-wheel-v5oi09ba/concord-sc_9dcd12d44ce346b7bd204f0178f67428/setup.py) egg_info for package concord-sc 2025-06-02T11:42:43,528 Created temporary directory: /tmp/pip-pip-egg-info-1m2tsn76 2025-06-02T11:42:43,528 Preparing metadata (setup.py): started 2025-06-02T11:42:43,530 Running command python setup.py egg_info 2025-06-02T11:42:44,382 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-02T11:42:44,383 !! 2025-06-02T11:42:44,384 ******************************************************************************** 2025-06-02T11:42:44,384 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-02T11:42:44,386 License :: OSI Approved :: MIT License 2025-06-02T11:42:44,387 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-02T11:42:44,387 ******************************************************************************** 2025-06-02T11:42:44,389 !! 2025-06-02T11:42:44,389 self._finalize_license_expression() 2025-06-02T11:42:44,412 running egg_info 2025-06-02T11:42:44,438 creating /tmp/pip-pip-egg-info-1m2tsn76/concord_sc.egg-info 2025-06-02T11:42:44,439 writing /tmp/pip-pip-egg-info-1m2tsn76/concord_sc.egg-info/PKG-INFO 2025-06-02T11:42:44,445 writing dependency_links to /tmp/pip-pip-egg-info-1m2tsn76/concord_sc.egg-info/dependency_links.txt 2025-06-02T11:42:44,449 writing requirements to /tmp/pip-pip-egg-info-1m2tsn76/concord_sc.egg-info/requires.txt 2025-06-02T11:42:44,450 writing top-level names to /tmp/pip-pip-egg-info-1m2tsn76/concord_sc.egg-info/top_level.txt 2025-06-02T11:42:44,451 writing manifest file '/tmp/pip-pip-egg-info-1m2tsn76/concord_sc.egg-info/SOURCES.txt' 2025-06-02T11:42:44,542 reading manifest file '/tmp/pip-pip-egg-info-1m2tsn76/concord_sc.egg-info/SOURCES.txt' 2025-06-02T11:42:44,544 adding license file 'LICENSE.md' 2025-06-02T11:42:44,548 writing manifest file '/tmp/pip-pip-egg-info-1m2tsn76/concord_sc.egg-info/SOURCES.txt' 2025-06-02T11:42:44,653 Preparing metadata (setup.py): finished with status 'done' 2025-06-02T11:42:44,657 Source in /tmp/pip-wheel-v5oi09ba/concord-sc_9dcd12d44ce346b7bd204f0178f67428 has version 1.0.7, which satisfies requirement concord-sc==1.0.7 from https://files.pythonhosted.org/packages/ab/d0/12581f7b36e31b10b2301f87bde00115c774b47fbf025d25b1e1437993e3/concord_sc-1.0.7.tar.gz 2025-06-02T11:42:44,658 Removed concord-sc==1.0.7 from https://files.pythonhosted.org/packages/ab/d0/12581f7b36e31b10b2301f87bde00115c774b47fbf025d25b1e1437993e3/concord_sc-1.0.7.tar.gz from build tracker '/tmp/pip-build-tracker-1106txnj' 2025-06-02T11:42:44,669 Created temporary directory: /tmp/pip-unpack-q7dwru5x 2025-06-02T11:42:44,670 Created temporary directory: /tmp/pip-unpack-tcaqgz2r 2025-06-02T11:42:44,671 Building wheels for collected packages: concord-sc 2025-06-02T11:42:44,675 Created temporary directory: /tmp/pip-wheel-0_4beirn 2025-06-02T11:42:44,676 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 2025-06-02T11:42:44,677 Building wheel for concord-sc (setup.py): started 2025-06-02T11:42:44,678 Destination directory: /tmp/pip-wheel-0_4beirn 2025-06-02T11:42:44,678 Running command python setup.py bdist_wheel 2025-06-02T11:42:45,539 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-02T11:42:45,540 !! 2025-06-02T11:42:45,541 ******************************************************************************** 2025-06-02T11:42:45,541 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-02T11:42:45,542 License :: OSI Approved :: MIT License 2025-06-02T11:42:45,543 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-02T11:42:45,544 ******************************************************************************** 2025-06-02T11:42:45,545 !! 2025-06-02T11:42:45,546 self._finalize_license_expression() 2025-06-02T11:42:45,546 running bdist_wheel 2025-06-02T11:42:45,671 running build 2025-06-02T11:42:45,671 running build_py 2025-06-02T11:42:45,701 creating build/lib/concord 2025-06-02T11:42:45,704 copying src/concord/concord.py -> build/lib/concord 2025-06-02T11:42:45,709 copying src/concord/sm.py -> build/lib/concord 2025-06-02T11:42:45,711 copying src/concord/bm.py -> build/lib/concord 2025-06-02T11:42:45,713 copying src/concord/__init__.py -> build/lib/concord 2025-06-02T11:42:45,715 copying src/concord/pl.py -> build/lib/concord 2025-06-02T11:42:45,717 copying src/concord/ul.py -> build/lib/concord 2025-06-02T11:42:45,719 copying src/concord/ml.py -> build/lib/concord 2025-06-02T11:42:45,722 creating build/lib/concord/benchmarking 2025-06-02T11:42:45,723 copying src/concord/benchmarking/time_memory.py -> build/lib/concord/benchmarking 2025-06-02T11:42:45,726 copying src/concord/benchmarking/linear_probe.py -> build/lib/concord/benchmarking 2025-06-02T11:42:45,728 copying src/concord/benchmarking/__init__.py -> build/lib/concord/benchmarking 2025-06-02T11:42:45,730 copying src/concord/benchmarking/pipeline_integration.py -> build/lib/concord/benchmarking 2025-06-02T11:42:45,732 copying src/concord/benchmarking/benchmark.py -> build/lib/concord/benchmarking 2025-06-02T11:42:45,735 copying src/concord/benchmarking/geometry.py -> build/lib/concord/benchmarking 2025-06-02T11:42:45,738 copying src/concord/benchmarking/tda.py -> build/lib/concord/benchmarking 2025-06-02T11:42:45,740 copying src/concord/benchmarking/pipeline_dim_reduction.py -> build/lib/concord/benchmarking 2025-06-02T11:42:45,742 copying src/concord/benchmarking/knn_probe.py -> build/lib/concord/benchmarking 2025-06-02T11:42:45,745 creating build/lib/concord/utils 2025-06-02T11:42:45,746 copying src/concord/utils/integration_methods.py -> build/lib/concord/utils 2025-06-02T11:42:45,749 copying src/concord/utils/path_analysis.py -> build/lib/concord/utils 2025-06-02T11:42:45,751 copying src/concord/utils/dim_reduction.py -> build/lib/concord/utils 2025-06-02T11:42:45,753 copying src/concord/utils/enrichment_analysis.py -> build/lib/concord/utils 2025-06-02T11:42:45,755 copying src/concord/utils/value_check.py -> build/lib/concord/utils 2025-06-02T11:42:45,757 copying src/concord/utils/Hs_Mm_conversion.py -> build/lib/concord/utils 2025-06-02T11:42:45,759 copying src/concord/utils/coverage_estimator.py -> build/lib/concord/utils 2025-06-02T11:42:45,761 copying src/concord/utils/feature_selector.py -> build/lib/concord/utils 2025-06-02T11:42:45,763 copying src/concord/utils/anndata_utils.py -> build/lib/concord/utils 2025-06-02T11:42:45,766 copying src/concord/utils/doublet_utils.py -> build/lib/concord/utils 2025-06-02T11:42:45,768 copying src/concord/utils/estimate_dropout_rate.py -> build/lib/concord/utils 2025-06-02T11:42:45,770 copying src/concord/utils/importance_analysis.py -> build/lib/concord/utils 2025-06-02T11:42:45,772 copying src/concord/utils/other_util.py -> build/lib/concord/utils 2025-06-02T11:42:45,773 copying src/concord/utils/__init__.py -> build/lib/concord/utils 2025-06-02T11:42:45,775 copying src/concord/utils/io.py -> build/lib/concord/utils 2025-06-02T11:42:45,777 copying src/concord/utils/visCello.py -> build/lib/concord/utils 2025-06-02T11:42:45,779 copying src/concord/utils/cell_cycle.py -> build/lib/concord/utils 2025-06-02T11:42:45,781 copying src/concord/utils/batch_analysis.py -> build/lib/concord/utils 2025-06-02T11:42:45,783 creating build/lib/concord/plotting 2025-06-02T11:42:45,785 copying src/concord/plotting/pl_model.py -> build/lib/concord/plotting 2025-06-02T11:42:45,787 copying src/concord/plotting/pl_embedding.py -> build/lib/concord/plotting 2025-06-02T11:42:45,790 copying src/concord/plotting/pl_path.py -> build/lib/concord/plotting 2025-06-02T11:42:45,792 copying src/concord/plotting/pl_enrichment.py -> build/lib/concord/plotting 2025-06-02T11:42:45,794 copying src/concord/plotting/pl_tda.py -> build/lib/concord/plotting 2025-06-02T11:42:45,797 copying src/concord/plotting/pl_general.py -> build/lib/concord/plotting 2025-06-02T11:42:45,799 copying src/concord/plotting/pl_heatmap.py -> build/lib/concord/plotting 2025-06-02T11:42:45,801 copying src/concord/plotting/__init__.py -> build/lib/concord/plotting 2025-06-02T11:42:45,803 copying src/concord/plotting/pl_batch.py -> build/lib/concord/plotting 2025-06-02T11:42:45,805 copying src/concord/plotting/pl_geometry.py -> build/lib/concord/plotting 2025-06-02T11:42:45,807 copying src/concord/plotting/palettes.py -> build/lib/concord/plotting 2025-06-02T11:42:45,809 copying src/concord/plotting/pl_benchmark.py -> build/lib/concord/plotting 2025-06-02T11:42:45,812 copying src/concord/plotting/pl_datacoverage.py -> build/lib/concord/plotting 2025-06-02T11:42:45,813 copying src/concord/plotting/pl_graph.py -> build/lib/concord/plotting 2025-06-02T11:42:45,817 creating build/lib/concord/model 2025-06-02T11:42:45,818 copying src/concord/model/build_layer.py -> build/lib/concord/model 2025-06-02T11:42:45,820 copying src/concord/model/augment.py -> build/lib/concord/model 2025-06-02T11:42:45,822 copying src/concord/model/knn.py -> build/lib/concord/model 2025-06-02T11:42:45,824 copying src/concord/model/model.py -> build/lib/concord/model 2025-06-02T11:42:45,827 copying src/concord/model/loss.py -> build/lib/concord/model 2025-06-02T11:42:45,829 copying src/concord/model/chunkloader.py -> build/lib/concord/model 2025-06-02T11:42:45,831 copying src/concord/model/trainer.py -> build/lib/concord/model 2025-06-02T11:42:45,833 copying src/concord/model/__init__.py -> build/lib/concord/model 2025-06-02T11:42:45,835 copying src/concord/model/anndataset.py -> build/lib/concord/model 2025-06-02T11:42:45,837 copying src/concord/model/sampler.py -> build/lib/concord/model 2025-06-02T11:42:45,839 copying src/concord/model/dataloader.py -> build/lib/concord/model 2025-06-02T11:42:45,842 creating build/lib/concord/simulation 2025-06-02T11:42:45,843 copying src/concord/simulation/__init__.py -> build/lib/concord/simulation 2025-06-02T11:42:45,845 copying src/concord/simulation/simulation.py -> build/lib/concord/simulation 2025-06-02T11:42:45,884 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-02T11:42:45,884 !! 2025-06-02T11:42:45,886 ******************************************************************************** 2025-06-02T11:42:45,886 Please avoid running ``setup.py`` directly. 2025-06-02T11:42:45,887 Instead, use pypa/build, pypa/installer or other 2025-06-02T11:42:45,887 standards-based tools. 2025-06-02T11:42:45,888 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-02T11:42:45,889 or your builds will no longer be supported. 2025-06-02T11:42:45,890 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-02T11:42:45,890 ******************************************************************************** 2025-06-02T11:42:45,891 !! 2025-06-02T11:42:45,892 self.initialize_options() 2025-06-02T11:42:45,912 installing to build/bdist.linux-armv7l/wheel 2025-06-02T11:42:45,912 running install 2025-06-02T11:42:45,936 running install_lib 2025-06-02T11:42:45,963 creating build/bdist.linux-armv7l/wheel 2025-06-02T11:42:45,965 creating build/bdist.linux-armv7l/wheel/concord 2025-06-02T11:42:45,966 copying build/lib/concord/concord.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T11:42:45,970 creating build/bdist.linux-armv7l/wheel/concord/benchmarking 2025-06-02T11:42:45,971 copying build/lib/concord/benchmarking/time_memory.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-06-02T11:42:45,973 copying build/lib/concord/benchmarking/linear_probe.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-06-02T11:42:45,976 copying build/lib/concord/benchmarking/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-06-02T11:42:45,977 copying build/lib/concord/benchmarking/pipeline_integration.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-06-02T11:42:45,980 copying build/lib/concord/benchmarking/benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-06-02T11:42:45,982 copying build/lib/concord/benchmarking/geometry.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-06-02T11:42:45,985 copying build/lib/concord/benchmarking/tda.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-06-02T11:42:45,987 copying build/lib/concord/benchmarking/pipeline_dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-06-02T11:42:45,989 copying build/lib/concord/benchmarking/knn_probe.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-06-02T11:42:45,991 copying build/lib/concord/sm.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T11:42:45,993 copying build/lib/concord/bm.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T11:42:45,995 copying build/lib/concord/__init__.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T11:42:45,997 creating build/bdist.linux-armv7l/wheel/concord/utils 2025-06-02T11:42:45,998 copying build/lib/concord/utils/integration_methods.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,000 copying build/lib/concord/utils/path_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,003 copying build/lib/concord/utils/dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,005 copying build/lib/concord/utils/enrichment_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,007 copying build/lib/concord/utils/value_check.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,008 copying build/lib/concord/utils/Hs_Mm_conversion.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,010 copying build/lib/concord/utils/coverage_estimator.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,012 copying build/lib/concord/utils/feature_selector.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,015 copying build/lib/concord/utils/anndata_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,017 copying build/lib/concord/utils/doublet_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,019 copying build/lib/concord/utils/estimate_dropout_rate.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,021 copying build/lib/concord/utils/importance_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,023 copying build/lib/concord/utils/other_util.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,025 copying build/lib/concord/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,026 copying build/lib/concord/utils/io.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,028 copying build/lib/concord/utils/visCello.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,031 copying build/lib/concord/utils/cell_cycle.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,033 copying build/lib/concord/utils/batch_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-02T11:42:46,035 copying build/lib/concord/pl.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T11:42:46,036 copying build/lib/concord/ul.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T11:42:46,039 creating build/bdist.linux-armv7l/wheel/concord/plotting 2025-06-02T11:42:46,040 copying build/lib/concord/plotting/pl_model.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,042 copying build/lib/concord/plotting/pl_embedding.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,045 copying build/lib/concord/plotting/pl_path.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,047 copying build/lib/concord/plotting/pl_enrichment.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,049 copying build/lib/concord/plotting/pl_tda.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,052 copying build/lib/concord/plotting/pl_general.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,053 copying build/lib/concord/plotting/pl_heatmap.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,056 copying build/lib/concord/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,058 copying build/lib/concord/plotting/pl_batch.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,060 copying build/lib/concord/plotting/pl_geometry.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,062 copying build/lib/concord/plotting/palettes.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,064 copying build/lib/concord/plotting/pl_benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,067 copying build/lib/concord/plotting/pl_datacoverage.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,069 copying build/lib/concord/plotting/pl_graph.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-02T11:42:46,072 creating build/bdist.linux-armv7l/wheel/concord/model 2025-06-02T11:42:46,073 copying build/lib/concord/model/build_layer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T11:42:46,075 copying build/lib/concord/model/augment.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T11:42:46,076 copying build/lib/concord/model/knn.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T11:42:46,079 copying build/lib/concord/model/model.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T11:42:46,081 copying build/lib/concord/model/loss.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T11:42:46,083 copying build/lib/concord/model/chunkloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T11:42:46,085 copying build/lib/concord/model/trainer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T11:42:46,087 copying build/lib/concord/model/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T11:42:46,089 copying build/lib/concord/model/anndataset.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T11:42:46,091 copying build/lib/concord/model/sampler.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T11:42:46,093 copying build/lib/concord/model/dataloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-02T11:42:46,096 copying build/lib/concord/ml.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-02T11:42:46,098 creating build/bdist.linux-armv7l/wheel/concord/simulation 2025-06-02T11:42:46,099 copying build/lib/concord/simulation/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/simulation 2025-06-02T11:42:46,101 copying build/lib/concord/simulation/simulation.py -> build/bdist.linux-armv7l/wheel/./concord/simulation 2025-06-02T11:42:46,104 running install_egg_info 2025-06-02T11:42:46,137 running egg_info 2025-06-02T11:42:46,165 writing src/concord_sc.egg-info/PKG-INFO 2025-06-02T11:42:46,171 writing dependency_links to src/concord_sc.egg-info/dependency_links.txt 2025-06-02T11:42:46,174 writing requirements to src/concord_sc.egg-info/requires.txt 2025-06-02T11:42:46,175 writing top-level names to src/concord_sc.egg-info/top_level.txt 2025-06-02T11:42:46,211 reading manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-06-02T11:42:46,216 adding license file 'LICENSE.md' 2025-06-02T11:42:46,221 writing manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-06-02T11:42:46,222 Copying src/concord_sc.egg-info to build/bdist.linux-armv7l/wheel/./concord_sc-1.0.7-py3.11.egg-info 2025-06-02T11:42:46,232 running install_scripts 2025-06-02T11:42:46,244 creating build/bdist.linux-armv7l/wheel/concord_sc-1.0.7.dist-info/WHEEL 2025-06-02T11:42:46,246 creating '/tmp/pip-wheel-0_4beirn/concord_sc-1.0.7-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-02T11:42:46,249 adding 'concord/__init__.py' 2025-06-02T11:42:46,250 adding 'concord/bm.py' 2025-06-02T11:42:46,255 adding 'concord/concord.py' 2025-06-02T11:42:46,257 adding 'concord/ml.py' 2025-06-02T11:42:46,258 adding 'concord/pl.py' 2025-06-02T11:42:46,259 adding 'concord/sm.py' 2025-06-02T11:42:46,261 adding 'concord/ul.py' 2025-06-02T11:42:46,262 adding 'concord/benchmarking/__init__.py' 2025-06-02T11:42:46,267 adding 'concord/benchmarking/benchmark.py' 2025-06-02T11:42:46,270 adding 'concord/benchmarking/geometry.py' 2025-06-02T11:42:46,271 adding 'concord/benchmarking/knn_probe.py' 2025-06-02T11:42:46,274 adding 'concord/benchmarking/linear_probe.py' 2025-06-02T11:42:46,275 adding 'concord/benchmarking/pipeline_dim_reduction.py' 2025-06-02T11:42:46,277 adding 'concord/benchmarking/pipeline_integration.py' 2025-06-02T11:42:46,279 adding 'concord/benchmarking/tda.py' 2025-06-02T11:42:46,281 adding 'concord/benchmarking/time_memory.py' 2025-06-02T11:42:46,283 adding 'concord/model/__init__.py' 2025-06-02T11:42:46,284 adding 'concord/model/anndataset.py' 2025-06-02T11:42:46,285 adding 'concord/model/augment.py' 2025-06-02T11:42:46,287 adding 'concord/model/build_layer.py' 2025-06-02T11:42:46,288 adding 'concord/model/chunkloader.py' 2025-06-02T11:42:46,290 adding 'concord/model/dataloader.py' 2025-06-02T11:42:46,292 adding 'concord/model/knn.py' 2025-06-02T11:42:46,293 adding 'concord/model/loss.py' 2025-06-02T11:42:46,294 adding 'concord/model/model.py' 2025-06-02T11:42:46,296 adding 'concord/model/sampler.py' 2025-06-02T11:42:46,298 adding 'concord/model/trainer.py' 2025-06-02T11:42:46,300 adding 'concord/plotting/__init__.py' 2025-06-02T11:42:46,302 adding 'concord/plotting/palettes.py' 2025-06-02T11:42:46,303 adding 'concord/plotting/pl_batch.py' 2025-06-02T11:42:46,305 adding 'concord/plotting/pl_benchmark.py' 2025-06-02T11:42:46,306 adding 'concord/plotting/pl_datacoverage.py' 2025-06-02T11:42:46,312 adding 'concord/plotting/pl_embedding.py' 2025-06-02T11:42:46,314 adding 'concord/plotting/pl_enrichment.py' 2025-06-02T11:42:46,315 adding 'concord/plotting/pl_general.py' 2025-06-02T11:42:46,317 adding 'concord/plotting/pl_geometry.py' 2025-06-02T11:42:46,320 adding 'concord/plotting/pl_graph.py' 2025-06-02T11:42:46,322 adding 'concord/plotting/pl_heatmap.py' 2025-06-02T11:42:46,323 adding 'concord/plotting/pl_model.py' 2025-06-02T11:42:46,325 adding 'concord/plotting/pl_path.py' 2025-06-02T11:42:46,327 adding 'concord/plotting/pl_tda.py' 2025-06-02T11:42:46,329 adding 'concord/simulation/__init__.py' 2025-06-02T11:42:46,333 adding 'concord/simulation/simulation.py' 2025-06-02T11:42:46,335 adding 'concord/utils/Hs_Mm_conversion.py' 2025-06-02T11:42:46,336 adding 'concord/utils/__init__.py' 2025-06-02T11:42:46,339 adding 'concord/utils/anndata_utils.py' 2025-06-02T11:42:46,340 adding 'concord/utils/batch_analysis.py' 2025-06-02T11:42:46,341 adding 'concord/utils/cell_cycle.py' 2025-06-02T11:42:46,343 adding 'concord/utils/coverage_estimator.py' 2025-06-02T11:42:46,344 adding 'concord/utils/dim_reduction.py' 2025-06-02T11:42:46,346 adding 'concord/utils/doublet_utils.py' 2025-06-02T11:42:46,347 adding 'concord/utils/enrichment_analysis.py' 2025-06-02T11:42:46,348 adding 'concord/utils/estimate_dropout_rate.py' 2025-06-02T11:42:46,350 adding 'concord/utils/feature_selector.py' 2025-06-02T11:42:46,352 adding 'concord/utils/importance_analysis.py' 2025-06-02T11:42:46,354 adding 'concord/utils/integration_methods.py' 2025-06-02T11:42:46,355 adding 'concord/utils/io.py' 2025-06-02T11:42:46,356 adding 'concord/utils/other_util.py' 2025-06-02T11:42:46,358 adding 'concord/utils/path_analysis.py' 2025-06-02T11:42:46,359 adding 'concord/utils/value_check.py' 2025-06-02T11:42:46,361 adding 'concord/utils/visCello.py' 2025-06-02T11:42:46,364 adding 'concord_sc-1.0.7.dist-info/licenses/LICENSE.md' 2025-06-02T11:42:46,366 adding 'concord_sc-1.0.7.dist-info/METADATA' 2025-06-02T11:42:46,367 adding 'concord_sc-1.0.7.dist-info/WHEEL' 2025-06-02T11:42:46,368 adding 'concord_sc-1.0.7.dist-info/top_level.txt' 2025-06-02T11:42:46,370 adding 'concord_sc-1.0.7.dist-info/RECORD' 2025-06-02T11:42:46,373 removing build/bdist.linux-armv7l/wheel 2025-06-02T11:42:46,497 Building wheel for concord-sc (setup.py): finished with status 'done' 2025-06-02T11:42:46,501 Created wheel for concord-sc: filename=concord_sc-1.0.7-py3-none-any.whl size=155182 sha256=6f9ab22e15d1d7435b46b2d3dca82e607c397231133668c18fc62127ba845533 2025-06-02T11:42:46,502 Stored in directory: /tmp/pip-ephem-wheel-cache-kh65h0og/wheels/1c/5f/4f/3156e9a259bc6a152775a1eb78b58a7661a4d76f164d1cfda7 2025-06-02T11:42:46,516 Successfully built concord-sc 2025-06-02T11:42:46,523 Removed build tracker: '/tmp/pip-build-tracker-1106txnj'