2025-06-05T09:47:31,822 Created temporary directory: /tmp/pip-build-tracker-tbwwvyvz 2025-06-05T09:47:31,823 Initialized build tracking at /tmp/pip-build-tracker-tbwwvyvz 2025-06-05T09:47:31,824 Created build tracker: /tmp/pip-build-tracker-tbwwvyvz 2025-06-05T09:47:31,824 Entered build tracker: /tmp/pip-build-tracker-tbwwvyvz 2025-06-05T09:47:31,825 Created temporary directory: /tmp/pip-wheel-_kcl75xy 2025-06-05T09:47:31,829 Created temporary directory: /tmp/pip-ephem-wheel-cache-9f5buu9q 2025-06-05T09:47:31,877 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-05T09:47:31,879 2 location(s) to search for versions of concord-sc: 2025-06-05T09:47:31,879 * https://pypi.org/simple/concord-sc/ 2025-06-05T09:47:31,879 * https://www.piwheels.org/simple/concord-sc/ 2025-06-05T09:47:31,880 Fetching project page and analyzing links: https://pypi.org/simple/concord-sc/ 2025-06-05T09:47:31,881 Getting page https://pypi.org/simple/concord-sc/ 2025-06-05T09:47:31,882 Found index url https://pypi.org/simple/ 2025-06-05T09:47:32,032 Fetched page https://pypi.org/simple/concord-sc/ as application/vnd.pypi.simple.v1+json 2025-06-05T09:47:32,036 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) 2025-06-05T09:47:32,037 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 2025-06-05T09:47:32,038 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) 2025-06-05T09:47:32,039 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 2025-06-05T09:47:32,039 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) 2025-06-05T09:47:32,040 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 2025-06-05T09:47:32,041 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) 2025-06-05T09:47:32,042 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 2025-06-05T09:47:32,042 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) 2025-06-05T09:47:32,043 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 2025-06-05T09:47:32,044 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) 2025-06-05T09:47:32,044 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 2025-06-05T09:47:32,045 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) 2025-06-05T09:47:32,046 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 2025-06-05T09:47:32,046 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) 2025-06-05T09:47:32,047 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 2025-06-05T09:47:32,047 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) 2025-06-05T09:47:32,048 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 2025-06-05T09:47:32,049 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) 2025-06-05T09:47:32,049 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 2025-06-05T09:47:32,050 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) 2025-06-05T09:47:32,051 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 2025-06-05T09:47:32,052 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) 2025-06-05T09:47:32,052 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 2025-06-05T09:47:32,053 Fetching project page and analyzing links: https://www.piwheels.org/simple/concord-sc/ 2025-06-05T09:47:32,054 Getting page https://www.piwheels.org/simple/concord-sc/ 2025-06-05T09:47:32,055 Found index url https://www.piwheels.org/simple/ 2025-06-05T09:47:32,203 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/ 2025-06-05T09:47:32,858 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/ 2025-06-05T09:47:34,005 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/ 2025-06-05T09:47:36,220 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/ 2025-06-05T09:47:40,438 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/ 2025-06-05T09:47:40,652 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 2025-06-05T09:47:40,654 Skipping link: not a file: https://www.piwheels.org/simple/concord-sc/ 2025-06-05T09:47:40,654 Skipping link: not a file: https://pypi.org/simple/concord-sc/ 2025-06-05T09:47:40,674 Given no hashes to check 1 links for project 'concord-sc': discarding no candidates 2025-06-05T09:47:40,676 Collecting concord-sc==0.9.7 2025-06-05T09:47:40,678 Created temporary directory: /tmp/pip-unpack-3y7bocqq 2025-06-05T09:47:40,897 Downloading concord_sc-0.9.7.tar.gz (123 kB) 2025-06-05T09:47:41,108 Added concord-sc==0.9.7 from https://files.pythonhosted.org/packages/7b/7e/afc7826dc853c736974af065a5092ff6256f1718222a4eb91d403cc4d52c/concord_sc-0.9.7.tar.gz to build tracker '/tmp/pip-build-tracker-tbwwvyvz' 2025-06-05T09:47:41,110 Running setup.py (path:/tmp/pip-wheel-_kcl75xy/concord-sc_b072f0bf9310426b9a7b9f62b2e71b82/setup.py) egg_info for package concord-sc 2025-06-05T09:47:41,111 Created temporary directory: /tmp/pip-pip-egg-info-8jk37kss 2025-06-05T09:47:41,112 Preparing metadata (setup.py): started 2025-06-05T09:47:41,113 Running command python setup.py egg_info 2025-06-05T09:47:42,012 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-05T09:47:42,012 !! 2025-06-05T09:47:42,013 ******************************************************************************** 2025-06-05T09:47:42,014 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-05T09:47:42,015 License :: OSI Approved :: MIT License 2025-06-05T09:47:42,016 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-05T09:47:42,017 ******************************************************************************** 2025-06-05T09:47:42,018 !! 2025-06-05T09:47:42,018 self._finalize_license_expression() 2025-06-05T09:47:42,041 running egg_info 2025-06-05T09:47:42,067 creating /tmp/pip-pip-egg-info-8jk37kss/concord_sc.egg-info 2025-06-05T09:47:42,068 writing /tmp/pip-pip-egg-info-8jk37kss/concord_sc.egg-info/PKG-INFO 2025-06-05T09:47:42,074 writing dependency_links to /tmp/pip-pip-egg-info-8jk37kss/concord_sc.egg-info/dependency_links.txt 2025-06-05T09:47:42,078 writing requirements to /tmp/pip-pip-egg-info-8jk37kss/concord_sc.egg-info/requires.txt 2025-06-05T09:47:42,079 writing top-level names to /tmp/pip-pip-egg-info-8jk37kss/concord_sc.egg-info/top_level.txt 2025-06-05T09:47:42,080 writing manifest file '/tmp/pip-pip-egg-info-8jk37kss/concord_sc.egg-info/SOURCES.txt' 2025-06-05T09:47:42,169 reading manifest file '/tmp/pip-pip-egg-info-8jk37kss/concord_sc.egg-info/SOURCES.txt' 2025-06-05T09:47:42,170 adding license file 'LICENSE.md' 2025-06-05T09:47:42,174 writing manifest file '/tmp/pip-pip-egg-info-8jk37kss/concord_sc.egg-info/SOURCES.txt' 2025-06-05T09:47:42,279 Preparing metadata (setup.py): finished with status 'done' 2025-06-05T09:47:42,283 Source in /tmp/pip-wheel-_kcl75xy/concord-sc_b072f0bf9310426b9a7b9f62b2e71b82 has version 0.9.7, which satisfies requirement concord-sc==0.9.7 from https://files.pythonhosted.org/packages/7b/7e/afc7826dc853c736974af065a5092ff6256f1718222a4eb91d403cc4d52c/concord_sc-0.9.7.tar.gz 2025-06-05T09:47:42,284 Removed concord-sc==0.9.7 from https://files.pythonhosted.org/packages/7b/7e/afc7826dc853c736974af065a5092ff6256f1718222a4eb91d403cc4d52c/concord_sc-0.9.7.tar.gz from build tracker '/tmp/pip-build-tracker-tbwwvyvz' 2025-06-05T09:47:42,296 Created temporary directory: /tmp/pip-unpack-1af_ruih 2025-06-05T09:47:42,297 Created temporary directory: /tmp/pip-unpack-4ph8r9wz 2025-06-05T09:47:42,297 Building wheels for collected packages: concord-sc 2025-06-05T09:47:42,302 Created temporary directory: /tmp/pip-wheel-xoz0adek 2025-06-05T09:47:42,303 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 2025-06-05T09:47:42,304 Building wheel for concord-sc (setup.py): started 2025-06-05T09:47:42,305 Destination directory: /tmp/pip-wheel-xoz0adek 2025-06-05T09:47:42,305 Running command python setup.py bdist_wheel 2025-06-05T09:47:43,127 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-06-05T09:47:43,127 !! 2025-06-05T09:47:43,128 ******************************************************************************** 2025-06-05T09:47:43,129 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-06-05T09:47:43,130 License :: OSI Approved :: MIT License 2025-06-05T09:47:43,132 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-06-05T09:47:43,132 ******************************************************************************** 2025-06-05T09:47:43,133 !! 2025-06-05T09:47:43,134 self._finalize_license_expression() 2025-06-05T09:47:43,135 running bdist_wheel 2025-06-05T09:47:43,258 running build 2025-06-05T09:47:43,259 running build_py 2025-06-05T09:47:43,289 creating build/lib/concord 2025-06-05T09:47:43,291 copying src/concord/ul.py -> build/lib/concord 2025-06-05T09:47:43,294 copying src/concord/__init__.py -> build/lib/concord 2025-06-05T09:47:43,296 copying src/concord/pl.py -> build/lib/concord 2025-06-05T09:47:43,298 copying src/concord/ml.py -> build/lib/concord 2025-06-05T09:47:43,300 copying src/concord/concord.py -> build/lib/concord 2025-06-05T09:47:43,304 creating build/lib/concord/utils 2025-06-05T09:47:43,305 copying src/concord/utils/__init__.py -> build/lib/concord/utils 2025-06-05T09:47:43,307 copying src/concord/utils/run_dim_reduction.py -> build/lib/concord/utils 2025-06-05T09:47:43,309 copying src/concord/utils/doublet_utils.py -> build/lib/concord/utils 2025-06-05T09:47:43,312 copying src/concord/utils/cell_cycle.py -> build/lib/concord/utils 2025-06-05T09:47:43,314 copying src/concord/utils/tda.py -> build/lib/concord/utils 2025-06-05T09:47:43,316 copying src/concord/utils/io.py -> build/lib/concord/utils 2025-06-05T09:47:43,318 copying src/concord/utils/batch_analysis.py -> build/lib/concord/utils 2025-06-05T09:47:43,320 copying src/concord/utils/timer.py -> build/lib/concord/utils 2025-06-05T09:47:43,322 copying src/concord/utils/visCello.py -> build/lib/concord/utils 2025-06-05T09:47:43,325 copying src/concord/utils/feature_selector.py -> build/lib/concord/utils 2025-06-05T09:47:43,327 copying src/concord/utils/simulation.py -> build/lib/concord/utils 2025-06-05T09:47:43,330 copying src/concord/utils/evaluator.py -> build/lib/concord/utils 2025-06-05T09:47:43,333 copying src/concord/utils/benchmark.py -> build/lib/concord/utils 2025-06-05T09:47:43,335 copying src/concord/utils/anndata_utils.py -> build/lib/concord/utils 2025-06-05T09:47:43,338 copying src/concord/utils/value_check.py -> build/lib/concord/utils 2025-06-05T09:47:43,340 copying src/concord/utils/sparsity.py -> build/lib/concord/utils 2025-06-05T09:47:43,342 copying src/concord/utils/other_util.py -> build/lib/concord/utils 2025-06-05T09:47:43,344 copying src/concord/utils/run_integration_methods.py -> build/lib/concord/utils 2025-06-05T09:47:43,346 copying src/concord/utils/enrichment_analysis.py -> build/lib/concord/utils 2025-06-05T09:47:43,348 copying src/concord/utils/estimate_aug_mask_prob.py -> build/lib/concord/utils 2025-06-05T09:47:43,350 copying src/concord/utils/geometry.py -> build/lib/concord/utils 2025-06-05T09:47:43,353 copying src/concord/utils/cellxgene.py -> build/lib/concord/utils 2025-06-05T09:47:43,355 copying src/concord/utils/preprocessor.py -> build/lib/concord/utils 2025-06-05T09:47:43,357 copying src/concord/utils/Hs_Mm_conversion.py -> build/lib/concord/utils 2025-06-05T09:47:43,359 copying src/concord/utils/path_analysis.py -> build/lib/concord/utils 2025-06-05T09:47:43,361 copying src/concord/utils/importance_analysis.py -> build/lib/concord/utils 2025-06-05T09:47:43,364 copying src/concord/utils/coverage_estimator.py -> build/lib/concord/utils 2025-06-05T09:47:43,366 creating build/lib/concord/model 2025-06-05T09:47:43,367 copying src/concord/model/chunkloader.py -> build/lib/concord/model 2025-06-05T09:47:43,370 copying src/concord/model/loss.py -> build/lib/concord/model 2025-06-05T09:47:43,372 copying src/concord/model/__init__.py -> build/lib/concord/model 2025-06-05T09:47:43,374 copying src/concord/model/sampler.py -> build/lib/concord/model 2025-06-05T09:47:43,377 copying src/concord/model/knn.py -> build/lib/concord/model 2025-06-05T09:47:43,379 copying src/concord/model/trainer.py -> build/lib/concord/model 2025-06-05T09:47:43,382 copying src/concord/model/model.py -> build/lib/concord/model 2025-06-05T09:47:43,385 copying src/concord/model/anndataset.py -> build/lib/concord/model 2025-06-05T09:47:43,387 copying src/concord/model/dataloader.py -> build/lib/concord/model 2025-06-05T09:47:43,390 copying src/concord/model/build_layer.py -> build/lib/concord/model 2025-06-05T09:47:43,393 creating build/lib/concord/plotting 2025-06-05T09:47:43,394 copying src/concord/plotting/pl_general.py -> build/lib/concord/plotting 2025-06-05T09:47:43,396 copying src/concord/plotting/pl_graph.py -> build/lib/concord/plotting 2025-06-05T09:47:43,398 copying src/concord/plotting/pl_batch.py -> build/lib/concord/plotting 2025-06-05T09:47:43,401 copying src/concord/plotting/__init__.py -> build/lib/concord/plotting 2025-06-05T09:47:43,402 copying src/concord/plotting/pl_geometry.py -> build/lib/concord/plotting 2025-06-05T09:47:43,405 copying src/concord/plotting/palettes.py -> build/lib/concord/plotting 2025-06-05T09:47:43,408 copying src/concord/plotting/pl_benchmark.py -> build/lib/concord/plotting 2025-06-05T09:47:43,410 copying src/concord/plotting/pl_tda.py -> build/lib/concord/plotting 2025-06-05T09:47:43,413 copying src/concord/plotting/pl_heatmap.py -> build/lib/concord/plotting 2025-06-05T09:47:43,416 copying src/concord/plotting/pl_model.py -> build/lib/concord/plotting 2025-06-05T09:47:43,418 copying src/concord/plotting/pl_path.py -> build/lib/concord/plotting 2025-06-05T09:47:43,420 copying src/concord/plotting/pl_embedding.py -> build/lib/concord/plotting 2025-06-05T09:47:43,424 copying src/concord/plotting/pl_datacoverage.py -> build/lib/concord/plotting 2025-06-05T09:47:43,426 copying src/concord/plotting/pl_enrichment.py -> build/lib/concord/plotting 2025-06-05T09:47:43,459 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-05T09:47:43,459 !! 2025-06-05T09:47:43,460 ******************************************************************************** 2025-06-05T09:47:43,461 Please avoid running ``setup.py`` directly. 2025-06-05T09:47:43,461 Instead, use pypa/build, pypa/installer or other 2025-06-05T09:47:43,462 standards-based tools. 2025-06-05T09:47:43,463 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-05T09:47:43,463 or your builds will no longer be supported. 2025-06-05T09:47:43,464 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-05T09:47:43,465 ******************************************************************************** 2025-06-05T09:47:43,465 !! 2025-06-05T09:47:43,466 self.initialize_options() 2025-06-05T09:47:43,485 installing to build/bdist.linux-armv7l/wheel 2025-06-05T09:47:43,486 running install 2025-06-05T09:47:43,509 running install_lib 2025-06-05T09:47:43,535 creating build/bdist.linux-armv7l/wheel 2025-06-05T09:47:43,537 creating build/bdist.linux-armv7l/wheel/concord 2025-06-05T09:47:43,538 copying build/lib/concord/ul.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-05T09:47:43,540 copying build/lib/concord/__init__.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-05T09:47:43,543 creating build/bdist.linux-armv7l/wheel/concord/utils 2025-06-05T09:47:43,543 copying build/lib/concord/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,545 copying build/lib/concord/utils/run_dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,547 copying build/lib/concord/utils/doublet_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,550 copying build/lib/concord/utils/cell_cycle.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,551 copying build/lib/concord/utils/tda.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,554 copying build/lib/concord/utils/io.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,555 copying build/lib/concord/utils/batch_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,557 copying build/lib/concord/utils/timer.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,559 copying build/lib/concord/utils/visCello.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,561 copying build/lib/concord/utils/feature_selector.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,564 copying build/lib/concord/utils/simulation.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,567 copying build/lib/concord/utils/evaluator.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,569 copying build/lib/concord/utils/benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,571 copying build/lib/concord/utils/anndata_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,574 copying build/lib/concord/utils/value_check.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,575 copying build/lib/concord/utils/sparsity.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,577 copying build/lib/concord/utils/other_util.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,579 copying build/lib/concord/utils/run_integration_methods.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,581 copying build/lib/concord/utils/enrichment_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,583 copying build/lib/concord/utils/estimate_aug_mask_prob.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,585 copying build/lib/concord/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,587 copying build/lib/concord/utils/cellxgene.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,589 copying build/lib/concord/utils/preprocessor.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,591 copying build/lib/concord/utils/Hs_Mm_conversion.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,593 copying build/lib/concord/utils/path_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,595 copying build/lib/concord/utils/importance_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,597 copying build/lib/concord/utils/coverage_estimator.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-06-05T09:47:43,599 copying build/lib/concord/pl.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-05T09:47:43,601 creating build/bdist.linux-armv7l/wheel/concord/model 2025-06-05T09:47:43,602 copying build/lib/concord/model/chunkloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-05T09:47:43,605 copying build/lib/concord/model/loss.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-05T09:47:43,607 copying build/lib/concord/model/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-05T09:47:43,608 copying build/lib/concord/model/sampler.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-05T09:47:43,610 copying build/lib/concord/model/knn.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-05T09:47:43,613 copying build/lib/concord/model/trainer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-05T09:47:43,615 copying build/lib/concord/model/model.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-05T09:47:43,617 copying build/lib/concord/model/anndataset.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-05T09:47:43,620 copying build/lib/concord/model/dataloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-05T09:47:43,622 copying build/lib/concord/model/build_layer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-06-05T09:47:43,624 copying build/lib/concord/ml.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-05T09:47:43,626 copying build/lib/concord/concord.py -> build/bdist.linux-armv7l/wheel/./concord 2025-06-05T09:47:43,629 creating build/bdist.linux-armv7l/wheel/concord/plotting 2025-06-05T09:47:43,630 copying build/lib/concord/plotting/pl_general.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,632 copying build/lib/concord/plotting/pl_graph.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,634 copying build/lib/concord/plotting/pl_batch.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,636 copying build/lib/concord/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,638 copying build/lib/concord/plotting/pl_geometry.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,640 copying build/lib/concord/plotting/palettes.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,643 copying build/lib/concord/plotting/pl_benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,645 copying build/lib/concord/plotting/pl_tda.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,647 copying build/lib/concord/plotting/pl_heatmap.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,650 copying build/lib/concord/plotting/pl_model.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,652 copying build/lib/concord/plotting/pl_path.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,654 copying build/lib/concord/plotting/pl_embedding.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,657 copying build/lib/concord/plotting/pl_datacoverage.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,659 copying build/lib/concord/plotting/pl_enrichment.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-06-05T09:47:43,661 running install_egg_info 2025-06-05T09:47:43,694 running egg_info 2025-06-05T09:47:43,723 writing src/concord_sc.egg-info/PKG-INFO 2025-06-05T09:47:43,729 writing dependency_links to src/concord_sc.egg-info/dependency_links.txt 2025-06-05T09:47:43,732 writing requirements to src/concord_sc.egg-info/requires.txt 2025-06-05T09:47:43,733 writing top-level names to src/concord_sc.egg-info/top_level.txt 2025-06-05T09:47:43,766 reading manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-06-05T09:47:43,772 adding license file 'LICENSE.md' 2025-06-05T09:47:43,776 writing manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-06-05T09:47:43,778 Copying src/concord_sc.egg-info to build/bdist.linux-armv7l/wheel/./concord_sc-0.9.7-py3.11.egg-info 2025-06-05T09:47:43,788 running install_scripts 2025-06-05T09:47:43,799 creating build/bdist.linux-armv7l/wheel/concord_sc-0.9.7.dist-info/WHEEL 2025-06-05T09:47:43,801 creating '/tmp/pip-wheel-xoz0adek/concord_sc-0.9.7-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-05T09:47:43,804 adding 'concord/__init__.py' 2025-06-05T09:47:43,808 adding 'concord/concord.py' 2025-06-05T09:47:43,809 adding 'concord/ml.py' 2025-06-05T09:47:43,811 adding 'concord/pl.py' 2025-06-05T09:47:43,812 adding 'concord/ul.py' 2025-06-05T09:47:43,814 adding 'concord/model/__init__.py' 2025-06-05T09:47:43,815 adding 'concord/model/anndataset.py' 2025-06-05T09:47:43,817 adding 'concord/model/build_layer.py' 2025-06-05T09:47:43,819 adding 'concord/model/chunkloader.py' 2025-06-05T09:47:43,821 adding 'concord/model/dataloader.py' 2025-06-05T09:47:43,823 adding 'concord/model/knn.py' 2025-06-05T09:47:43,824 adding 'concord/model/loss.py' 2025-06-05T09:47:43,826 adding 'concord/model/model.py' 2025-06-05T09:47:43,828 adding 'concord/model/sampler.py' 2025-06-05T09:47:43,830 adding 'concord/model/trainer.py' 2025-06-05T09:47:43,832 adding 'concord/plotting/__init__.py' 2025-06-05T09:47:43,833 adding 'concord/plotting/palettes.py' 2025-06-05T09:47:43,835 adding 'concord/plotting/pl_batch.py' 2025-06-05T09:47:43,836 adding 'concord/plotting/pl_benchmark.py' 2025-06-05T09:47:43,838 adding 'concord/plotting/pl_datacoverage.py' 2025-06-05T09:47:43,844 adding 'concord/plotting/pl_embedding.py' 2025-06-05T09:47:43,846 adding 'concord/plotting/pl_enrichment.py' 2025-06-05T09:47:43,847 adding 'concord/plotting/pl_general.py' 2025-06-05T09:47:43,849 adding 'concord/plotting/pl_geometry.py' 2025-06-05T09:47:43,851 adding 'concord/plotting/pl_graph.py' 2025-06-05T09:47:43,854 adding 'concord/plotting/pl_heatmap.py' 2025-06-05T09:47:43,856 adding 'concord/plotting/pl_model.py' 2025-06-05T09:47:43,857 adding 'concord/plotting/pl_path.py' 2025-06-05T09:47:43,859 adding 'concord/plotting/pl_tda.py' 2025-06-05T09:47:43,862 adding 'concord/utils/Hs_Mm_conversion.py' 2025-06-05T09:47:43,863 adding 'concord/utils/__init__.py' 2025-06-05T09:47:43,865 adding 'concord/utils/anndata_utils.py' 2025-06-05T09:47:43,866 adding 'concord/utils/batch_analysis.py' 2025-06-05T09:47:43,869 adding 'concord/utils/benchmark.py' 2025-06-05T09:47:43,871 adding 'concord/utils/cell_cycle.py' 2025-06-05T09:47:43,872 adding 'concord/utils/cellxgene.py' 2025-06-05T09:47:43,874 adding 'concord/utils/coverage_estimator.py' 2025-06-05T09:47:43,875 adding 'concord/utils/doublet_utils.py' 2025-06-05T09:47:43,877 adding 'concord/utils/enrichment_analysis.py' 2025-06-05T09:47:43,878 adding 'concord/utils/estimate_aug_mask_prob.py' 2025-06-05T09:47:43,879 adding 'concord/utils/evaluator.py' 2025-06-05T09:47:43,881 adding 'concord/utils/feature_selector.py' 2025-06-05T09:47:43,884 adding 'concord/utils/geometry.py' 2025-06-05T09:47:43,885 adding 'concord/utils/importance_analysis.py' 2025-06-05T09:47:43,886 adding 'concord/utils/io.py' 2025-06-05T09:47:43,888 adding 'concord/utils/other_util.py' 2025-06-05T09:47:43,889 adding 'concord/utils/path_analysis.py' 2025-06-05T09:47:43,891 adding 'concord/utils/preprocessor.py' 2025-06-05T09:47:43,892 adding 'concord/utils/run_dim_reduction.py' 2025-06-05T09:47:43,894 adding 'concord/utils/run_integration_methods.py' 2025-06-05T09:47:43,900 adding 'concord/utils/simulation.py' 2025-06-05T09:47:43,901 adding 'concord/utils/sparsity.py' 2025-06-05T09:47:43,903 adding 'concord/utils/tda.py' 2025-06-05T09:47:43,904 adding 'concord/utils/timer.py' 2025-06-05T09:47:43,905 adding 'concord/utils/value_check.py' 2025-06-05T09:47:43,907 adding 'concord/utils/visCello.py' 2025-06-05T09:47:43,910 adding 'concord_sc-0.9.7.dist-info/licenses/LICENSE.md' 2025-06-05T09:47:43,911 adding 'concord_sc-0.9.7.dist-info/METADATA' 2025-06-05T09:47:43,912 adding 'concord_sc-0.9.7.dist-info/WHEEL' 2025-06-05T09:47:43,913 adding 'concord_sc-0.9.7.dist-info/top_level.txt' 2025-06-05T09:47:43,915 adding 'concord_sc-0.9.7.dist-info/RECORD' 2025-06-05T09:47:43,918 removing build/bdist.linux-armv7l/wheel 2025-06-05T09:47:44,039 Building wheel for concord-sc (setup.py): finished with status 'done' 2025-06-05T09:47:44,043 Created wheel for concord-sc: filename=concord_sc-0.9.7-py3-none-any.whl size=140413 sha256=3cef1a7cbb0ad4d86b9a59e18714d7ae5cc36464d93a5cc32c14e77e9b250f2b 2025-06-05T09:47:44,044 Stored in directory: /tmp/pip-ephem-wheel-cache-9f5buu9q/wheels/10/38/80/46bc417c9ab0f2176fb25bfe5ea7a2d84a7908c93140ec53f8 2025-06-05T09:47:44,058 Successfully built concord-sc 2025-06-05T09:47:44,066 Removed build tracker: '/tmp/pip-build-tracker-tbwwvyvz'