2025-05-30T20:58:06,659 Created temporary directory: /tmp/pip-build-tracker-fhz7ykps
2025-05-30T20:58:06,661 Initialized build tracking at /tmp/pip-build-tracker-fhz7ykps
2025-05-30T20:58:06,661 Created build tracker: /tmp/pip-build-tracker-fhz7ykps
2025-05-30T20:58:06,662 Entered build tracker: /tmp/pip-build-tracker-fhz7ykps
2025-05-30T20:58:06,663 Created temporary directory: /tmp/pip-wheel-etz4iuwq
2025-05-30T20:58:06,667 Created temporary directory: /tmp/pip-ephem-wheel-cache-5w2ugc9u
2025-05-30T20:58:06,721 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-05-30T20:58:06,723 2 location(s) to search for versions of concord-sc:
2025-05-30T20:58:06,723 * https://pypi.org/simple/concord-sc/
2025-05-30T20:58:06,723 * https://www.piwheels.org/simple/concord-sc/
2025-05-30T20:58:06,724 Fetching project page and analyzing links: https://pypi.org/simple/concord-sc/
2025-05-30T20:58:06,725 Getting page https://pypi.org/simple/concord-sc/
2025-05-30T20:58:06,727 Found index url https://pypi.org/simple/
2025-05-30T20:58:06,954 Fetched page https://pypi.org/simple/concord-sc/ as application/vnd.pypi.simple.v1+json
2025-05-30T20:58:06,963   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)
2025-05-30T20:58:06,965   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
2025-05-30T20:58:06,966   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)
2025-05-30T20:58:06,967   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
2025-05-30T20:58:06,969   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)
2025-05-30T20:58:06,970   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
2025-05-30T20:58:06,970   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)
2025-05-30T20:58:06,971   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
2025-05-30T20:58:06,972   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)
2025-05-30T20:58:06,973   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
2025-05-30T20:58:06,973   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)
2025-05-30T20:58:06,974   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
2025-05-30T20:58:06,975   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)
2025-05-30T20:58:06,976   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
2025-05-30T20:58:06,976   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)
2025-05-30T20:58:06,977   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
2025-05-30T20:58:06,977   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)
2025-05-30T20:58:06,978   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
2025-05-30T20:58:06,978   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)
2025-05-30T20:58:06,979   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
2025-05-30T20:58:06,980   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)
2025-05-30T20:58:06,981   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
2025-05-30T20:58:06,981   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)
2025-05-30T20:58:06,982   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
2025-05-30T20:58:06,983 Fetching project page and analyzing links: https://www.piwheels.org/simple/concord-sc/
2025-05-30T20:58:06,984 Getting page https://www.piwheels.org/simple/concord-sc/
2025-05-30T20:58:06,985 Found index url https://www.piwheels.org/simple/
2025-05-30T20:58:07,147 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/
2025-05-30T20:58:07,807 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/
2025-05-30T20:58:08,981 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/
2025-05-30T20:58:11,159 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/
2025-05-30T20:58:15,333 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/
2025-05-30T20:58:15,514 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
2025-05-30T20:58:15,516 Skipping link: not a file: https://www.piwheels.org/simple/concord-sc/
2025-05-30T20:58:15,517 Skipping link: not a file: https://pypi.org/simple/concord-sc/
2025-05-30T20:58:15,535 Given no hashes to check 1 links for project 'concord-sc': discarding no candidates
2025-05-30T20:58:15,537 Collecting concord-sc==1.0.0
2025-05-30T20:58:15,540   Created temporary directory: /tmp/pip-unpack-j39vb6sl
2025-05-30T20:58:15,767   Downloading concord_sc-1.0.0.tar.gz (126 kB)
2025-05-30T20:58:16,009   Added concord-sc==1.0.0 from https://files.pythonhosted.org/packages/63/85/ee633bc44868c73f1a70b7d84c23b359c820e1b2f2fd9d9d39269788ad49/concord_sc-1.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-fhz7ykps'
2025-05-30T20:58:16,011   Running setup.py (path:/tmp/pip-wheel-etz4iuwq/concord-sc_1e787d3fa9ea474788399b2922b9934d/setup.py) egg_info for package concord-sc
2025-05-30T20:58:16,012   Created temporary directory: /tmp/pip-pip-egg-info-kdja2hcz
2025-05-30T20:58:16,013   Preparing metadata (setup.py): started
2025-05-30T20:58:16,014   Running command python setup.py egg_info
2025-05-30T20:58:16,879   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-05-30T20:58:16,879   !!

2025-05-30T20:58:16,880           ********************************************************************************
2025-05-30T20:58:16,881           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-05-30T20:58:16,882           License :: OSI Approved :: MIT License

2025-05-30T20:58:16,883           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-05-30T20:58:16,883           ********************************************************************************

2025-05-30T20:58:16,885   !!
2025-05-30T20:58:16,885     self._finalize_license_expression()
2025-05-30T20:58:16,909   running egg_info
2025-05-30T20:58:16,937   creating /tmp/pip-pip-egg-info-kdja2hcz/concord_sc.egg-info
2025-05-30T20:58:16,938   writing /tmp/pip-pip-egg-info-kdja2hcz/concord_sc.egg-info/PKG-INFO
2025-05-30T20:58:16,945   writing dependency_links to /tmp/pip-pip-egg-info-kdja2hcz/concord_sc.egg-info/dependency_links.txt
2025-05-30T20:58:16,948   writing requirements to /tmp/pip-pip-egg-info-kdja2hcz/concord_sc.egg-info/requires.txt
2025-05-30T20:58:16,949   writing top-level names to /tmp/pip-pip-egg-info-kdja2hcz/concord_sc.egg-info/top_level.txt
2025-05-30T20:58:16,951   writing manifest file '/tmp/pip-pip-egg-info-kdja2hcz/concord_sc.egg-info/SOURCES.txt'
2025-05-30T20:58:17,048   reading manifest file '/tmp/pip-pip-egg-info-kdja2hcz/concord_sc.egg-info/SOURCES.txt'
2025-05-30T20:58:17,050   adding license file 'LICENSE.md'
2025-05-30T20:58:17,054   writing manifest file '/tmp/pip-pip-egg-info-kdja2hcz/concord_sc.egg-info/SOURCES.txt'
2025-05-30T20:58:17,164   Preparing metadata (setup.py): finished with status 'done'
2025-05-30T20:58:17,168   Source in /tmp/pip-wheel-etz4iuwq/concord-sc_1e787d3fa9ea474788399b2922b9934d has version 1.0.0, which satisfies requirement concord-sc==1.0.0 from https://files.pythonhosted.org/packages/63/85/ee633bc44868c73f1a70b7d84c23b359c820e1b2f2fd9d9d39269788ad49/concord_sc-1.0.0.tar.gz
2025-05-30T20:58:17,169   Removed concord-sc==1.0.0 from https://files.pythonhosted.org/packages/63/85/ee633bc44868c73f1a70b7d84c23b359c820e1b2f2fd9d9d39269788ad49/concord_sc-1.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-fhz7ykps'
2025-05-30T20:58:17,180 Created temporary directory: /tmp/pip-unpack-l20ride6
2025-05-30T20:58:17,181 Created temporary directory: /tmp/pip-unpack-7vc6j625
2025-05-30T20:58:17,182 Building wheels for collected packages: concord-sc
2025-05-30T20:58:17,186   Created temporary directory: /tmp/pip-wheel-v39msx1r
2025-05-30T20:58:17,186   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
2025-05-30T20:58:17,188   Building wheel for concord-sc (setup.py): started
2025-05-30T20:58:17,189   Destination directory: /tmp/pip-wheel-v39msx1r
2025-05-30T20:58:17,189   Running command python setup.py bdist_wheel
2025-05-30T20:58:18,015   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-05-30T20:58:18,015   !!

2025-05-30T20:58:18,016           ********************************************************************************
2025-05-30T20:58:18,017           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-05-30T20:58:18,018           License :: OSI Approved :: MIT License

2025-05-30T20:58:18,019           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-05-30T20:58:18,020           ********************************************************************************

2025-05-30T20:58:18,021   !!
2025-05-30T20:58:18,021     self._finalize_license_expression()
2025-05-30T20:58:18,022   running bdist_wheel
2025-05-30T20:58:18,157   running build
2025-05-30T20:58:18,158   running build_py
2025-05-30T20:58:18,190   creating build/lib/concord
2025-05-30T20:58:18,193   copying src/concord/__init__.py -> build/lib/concord
2025-05-30T20:58:18,195   copying src/concord/concord.py -> build/lib/concord
2025-05-30T20:58:18,198   copying src/concord/bm.py -> build/lib/concord
2025-05-30T20:58:18,201   copying src/concord/ul.py -> build/lib/concord
2025-05-30T20:58:18,203   copying src/concord/ml.py -> build/lib/concord
2025-05-30T20:58:18,205   copying src/concord/sm.py -> build/lib/concord
2025-05-30T20:58:18,207   copying src/concord/pl.py -> build/lib/concord
2025-05-30T20:58:18,210   creating build/lib/concord/utils
2025-05-30T20:58:18,211   copying src/concord/utils/other_util.py -> build/lib/concord/utils
2025-05-30T20:58:18,214   copying src/concord/utils/value_check.py -> build/lib/concord/utils
2025-05-30T20:58:18,216   copying src/concord/utils/Hs_Mm_conversion.py -> build/lib/concord/utils
2025-05-30T20:58:18,218   copying src/concord/utils/path_analysis.py -> build/lib/concord/utils
2025-05-30T20:58:18,221   copying src/concord/utils/enrichment_analysis.py -> build/lib/concord/utils
2025-05-30T20:58:18,223   copying src/concord/utils/coverage_estimator.py -> build/lib/concord/utils
2025-05-30T20:58:18,225   copying src/concord/utils/batch_analysis.py -> build/lib/concord/utils
2025-05-30T20:58:18,227   copying src/concord/utils/io.py -> build/lib/concord/utils
2025-05-30T20:58:18,229   copying src/concord/utils/__init__.py -> build/lib/concord/utils
2025-05-30T20:58:18,231   copying src/concord/utils/feature_selector.py -> build/lib/concord/utils
2025-05-30T20:58:18,234   copying src/concord/utils/estimate_dropout_rate.py -> build/lib/concord/utils
2025-05-30T20:58:18,236   copying src/concord/utils/integration_methods.py -> build/lib/concord/utils
2025-05-30T20:58:18,238   copying src/concord/utils/cell_cycle.py -> build/lib/concord/utils
2025-05-30T20:58:18,240   copying src/concord/utils/dim_reduction.py -> build/lib/concord/utils
2025-05-30T20:58:18,243   copying src/concord/utils/visCello.py -> build/lib/concord/utils
2025-05-30T20:58:18,246   copying src/concord/utils/doublet_utils.py -> build/lib/concord/utils
2025-05-30T20:58:18,248   copying src/concord/utils/importance_analysis.py -> build/lib/concord/utils
2025-05-30T20:58:18,250   copying src/concord/utils/anndata_utils.py -> build/lib/concord/utils
2025-05-30T20:58:18,254   creating build/lib/concord/plotting
2025-05-30T20:58:18,255   copying src/concord/plotting/pl_path.py -> build/lib/concord/plotting
2025-05-30T20:58:18,257   copying src/concord/plotting/pl_tda.py -> build/lib/concord/plotting
2025-05-30T20:58:18,260   copying src/concord/plotting/palettes.py -> build/lib/concord/plotting
2025-05-30T20:58:18,263   copying src/concord/plotting/__init__.py -> build/lib/concord/plotting
2025-05-30T20:58:18,265   copying src/concord/plotting/pl_general.py -> build/lib/concord/plotting
2025-05-30T20:58:18,267   copying src/concord/plotting/pl_heatmap.py -> build/lib/concord/plotting
2025-05-30T20:58:18,270   copying src/concord/plotting/pl_enrichment.py -> build/lib/concord/plotting
2025-05-30T20:58:18,272   copying src/concord/plotting/pl_graph.py -> build/lib/concord/plotting
2025-05-30T20:58:18,275   copying src/concord/plotting/pl_geometry.py -> build/lib/concord/plotting
2025-05-30T20:58:18,277   copying src/concord/plotting/pl_benchmark.py -> build/lib/concord/plotting
2025-05-30T20:58:18,280   copying src/concord/plotting/pl_embedding.py -> build/lib/concord/plotting
2025-05-30T20:58:18,284   copying src/concord/plotting/pl_batch.py -> build/lib/concord/plotting
2025-05-30T20:58:18,286   copying src/concord/plotting/pl_model.py -> build/lib/concord/plotting
2025-05-30T20:58:18,288   copying src/concord/plotting/pl_datacoverage.py -> build/lib/concord/plotting
2025-05-30T20:58:18,292   creating build/lib/concord/simulation
2025-05-30T20:58:18,294   copying src/concord/simulation/__init__.py -> build/lib/concord/simulation
2025-05-30T20:58:18,299   copying src/concord/simulation/simulation.py -> build/lib/concord/simulation
2025-05-30T20:58:18,308   creating build/lib/concord/model
2025-05-30T20:58:18,312   copying src/concord/model/chunkloader.py -> build/lib/concord/model
2025-05-30T20:58:18,319   copying src/concord/model/knn.py -> build/lib/concord/model
2025-05-30T20:58:18,327   copying src/concord/model/build_layer.py -> build/lib/concord/model
2025-05-30T20:58:18,334   copying src/concord/model/__init__.py -> build/lib/concord/model
2025-05-30T20:58:18,338   copying src/concord/model/model.py -> build/lib/concord/model
2025-05-30T20:58:18,342   copying src/concord/model/sampler.py -> build/lib/concord/model
2025-05-30T20:58:18,345   copying src/concord/model/anndataset.py -> build/lib/concord/model
2025-05-30T20:58:18,349   copying src/concord/model/dataloader.py -> build/lib/concord/model
2025-05-30T20:58:18,353   copying src/concord/model/loss.py -> build/lib/concord/model
2025-05-30T20:58:18,356   copying src/concord/model/trainer.py -> build/lib/concord/model
2025-05-30T20:58:18,360   creating build/lib/concord/benchmarking
2025-05-30T20:58:18,362   copying src/concord/benchmarking/time_memory.py -> build/lib/concord/benchmarking
2025-05-30T20:58:18,364   copying src/concord/benchmarking/__init__.py -> build/lib/concord/benchmarking
2025-05-30T20:58:18,367   copying src/concord/benchmarking/pipeline_integration.py -> build/lib/concord/benchmarking
2025-05-30T20:58:18,370   copying src/concord/benchmarking/knn_probe.py -> build/lib/concord/benchmarking
2025-05-30T20:58:18,372   copying src/concord/benchmarking/geometry.py -> build/lib/concord/benchmarking
2025-05-30T20:58:18,375   copying src/concord/benchmarking/benchmark.py -> build/lib/concord/benchmarking
2025-05-30T20:58:18,378   copying src/concord/benchmarking/tda.py -> build/lib/concord/benchmarking
2025-05-30T20:58:18,381   copying src/concord/benchmarking/pipeline_dim_reduction.py -> build/lib/concord/benchmarking
2025-05-30T20:58:18,383   copying src/concord/benchmarking/linear_probe.py -> build/lib/concord/benchmarking
2025-05-30T20:58:18,426   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-05-30T20:58:18,427   !!

2025-05-30T20:58:18,428           ********************************************************************************
2025-05-30T20:58:18,428           Please avoid running ``setup.py`` directly.
2025-05-30T20:58:18,429           Instead, use pypa/build, pypa/installer or other
2025-05-30T20:58:18,429           standards-based tools.

2025-05-30T20:58:18,430           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-05-30T20:58:18,431           or your builds will no longer be supported.

2025-05-30T20:58:18,432           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-05-30T20:58:18,432           ********************************************************************************

2025-05-30T20:58:18,433   !!
2025-05-30T20:58:18,434     self.initialize_options()
2025-05-30T20:58:18,456   installing to build/bdist.linux-armv7l/wheel
2025-05-30T20:58:18,456   running install
2025-05-30T20:58:18,482   running install_lib
2025-05-30T20:58:18,509   creating build/bdist.linux-armv7l/wheel
2025-05-30T20:58:18,511   creating build/bdist.linux-armv7l/wheel/concord
2025-05-30T20:58:18,512   copying build/lib/concord/__init__.py -> build/bdist.linux-armv7l/wheel/./concord
2025-05-30T20:58:18,515   creating build/bdist.linux-armv7l/wheel/concord/utils
2025-05-30T20:58:18,516   copying build/lib/concord/utils/other_util.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,518   copying build/lib/concord/utils/value_check.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,520   copying build/lib/concord/utils/Hs_Mm_conversion.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,522   copying build/lib/concord/utils/path_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,524   copying build/lib/concord/utils/enrichment_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,526   copying build/lib/concord/utils/coverage_estimator.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,528   copying build/lib/concord/utils/batch_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,530   copying build/lib/concord/utils/io.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,532   copying build/lib/concord/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,534   copying build/lib/concord/utils/feature_selector.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,537   copying build/lib/concord/utils/estimate_dropout_rate.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,539   copying build/lib/concord/utils/integration_methods.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,542   copying build/lib/concord/utils/cell_cycle.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,544   copying build/lib/concord/utils/dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,547   copying build/lib/concord/utils/visCello.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,549   copying build/lib/concord/utils/doublet_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,552   copying build/lib/concord/utils/importance_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,554   copying build/lib/concord/utils/anndata_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-05-30T20:58:18,557   copying build/lib/concord/concord.py -> build/bdist.linux-armv7l/wheel/./concord
2025-05-30T20:58:18,560   copying build/lib/concord/bm.py -> build/bdist.linux-armv7l/wheel/./concord
2025-05-30T20:58:18,562   copying build/lib/concord/ul.py -> build/bdist.linux-armv7l/wheel/./concord
2025-05-30T20:58:18,565   creating build/bdist.linux-armv7l/wheel/concord/plotting
2025-05-30T20:58:18,566   copying build/lib/concord/plotting/pl_path.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,569   copying build/lib/concord/plotting/pl_tda.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,572   copying build/lib/concord/plotting/palettes.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,574   copying build/lib/concord/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,576   copying build/lib/concord/plotting/pl_general.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,578   copying build/lib/concord/plotting/pl_heatmap.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,581   copying build/lib/concord/plotting/pl_enrichment.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,583   copying build/lib/concord/plotting/pl_graph.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,586   copying build/lib/concord/plotting/pl_geometry.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,588   copying build/lib/concord/plotting/pl_benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,591   copying build/lib/concord/plotting/pl_embedding.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,594   copying build/lib/concord/plotting/pl_batch.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,596   copying build/lib/concord/plotting/pl_model.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,599   copying build/lib/concord/plotting/pl_datacoverage.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-05-30T20:58:18,601   copying build/lib/concord/ml.py -> build/bdist.linux-armv7l/wheel/./concord
2025-05-30T20:58:18,603   copying build/lib/concord/sm.py -> build/bdist.linux-armv7l/wheel/./concord
2025-05-30T20:58:18,606   creating build/bdist.linux-armv7l/wheel/concord/simulation
2025-05-30T20:58:18,607   copying build/lib/concord/simulation/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/simulation
2025-05-30T20:58:18,610   copying build/lib/concord/simulation/simulation.py -> build/bdist.linux-armv7l/wheel/./concord/simulation
2025-05-30T20:58:18,613   copying build/lib/concord/pl.py -> build/bdist.linux-armv7l/wheel/./concord
2025-05-30T20:58:18,616   creating build/bdist.linux-armv7l/wheel/concord/model
2025-05-30T20:58:18,618   copying build/lib/concord/model/chunkloader.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-05-30T20:58:18,620   copying build/lib/concord/model/knn.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-05-30T20:58:18,622   copying build/lib/concord/model/build_layer.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-05-30T20:58:18,625   copying build/lib/concord/model/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-05-30T20:58:18,626   copying build/lib/concord/model/model.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-05-30T20:58:18,629   copying build/lib/concord/model/sampler.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-05-30T20:58:18,632   copying build/lib/concord/model/anndataset.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-05-30T20:58:18,634   copying build/lib/concord/model/dataloader.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-05-30T20:58:18,637   copying build/lib/concord/model/loss.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-05-30T20:58:18,639   copying build/lib/concord/model/trainer.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-05-30T20:58:18,642   creating build/bdist.linux-armv7l/wheel/concord/benchmarking
2025-05-30T20:58:18,643   copying build/lib/concord/benchmarking/time_memory.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-05-30T20:58:18,645   copying build/lib/concord/benchmarking/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-05-30T20:58:18,647   copying build/lib/concord/benchmarking/pipeline_integration.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-05-30T20:58:18,650   copying build/lib/concord/benchmarking/knn_probe.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-05-30T20:58:18,653   copying build/lib/concord/benchmarking/geometry.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-05-30T20:58:18,656   copying build/lib/concord/benchmarking/benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-05-30T20:58:18,659   copying build/lib/concord/benchmarking/tda.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-05-30T20:58:18,661   copying build/lib/concord/benchmarking/pipeline_dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-05-30T20:58:18,664   copying build/lib/concord/benchmarking/linear_probe.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-05-30T20:58:18,666   running install_egg_info
2025-05-30T20:58:18,705   running egg_info
2025-05-30T20:58:18,735   writing src/concord_sc.egg-info/PKG-INFO
2025-05-30T20:58:18,741   writing dependency_links to src/concord_sc.egg-info/dependency_links.txt
2025-05-30T20:58:18,745   writing requirements to src/concord_sc.egg-info/requires.txt
2025-05-30T20:58:18,746   writing top-level names to src/concord_sc.egg-info/top_level.txt
2025-05-30T20:58:18,785   reading manifest file 'src/concord_sc.egg-info/SOURCES.txt'
2025-05-30T20:58:18,790   adding license file 'LICENSE.md'
2025-05-30T20:58:18,795   writing manifest file 'src/concord_sc.egg-info/SOURCES.txt'
2025-05-30T20:58:18,797   Copying src/concord_sc.egg-info to build/bdist.linux-armv7l/wheel/./concord_sc-1.0.0-py3.11.egg-info
2025-05-30T20:58:18,807   running install_scripts
2025-05-30T20:58:18,819   creating build/bdist.linux-armv7l/wheel/concord_sc-1.0.0.dist-info/WHEEL
2025-05-30T20:58:18,823   creating '/tmp/pip-wheel-v39msx1r/concord_sc-1.0.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-05-30T20:58:18,826   adding 'concord/__init__.py'
2025-05-30T20:58:18,828   adding 'concord/bm.py'
2025-05-30T20:58:18,835   adding 'concord/concord.py'
2025-05-30T20:58:18,837   adding 'concord/ml.py'
2025-05-30T20:58:18,838   adding 'concord/pl.py'
2025-05-30T20:58:18,839   adding 'concord/sm.py'
2025-05-30T20:58:18,841   adding 'concord/ul.py'
2025-05-30T20:58:18,843   adding 'concord/benchmarking/__init__.py'
2025-05-30T20:58:18,847   adding 'concord/benchmarking/benchmark.py'
2025-05-30T20:58:18,849   adding 'concord/benchmarking/geometry.py'
2025-05-30T20:58:18,851   adding 'concord/benchmarking/knn_probe.py'
2025-05-30T20:58:18,854   adding 'concord/benchmarking/linear_probe.py'
2025-05-30T20:58:18,856   adding 'concord/benchmarking/pipeline_dim_reduction.py'
2025-05-30T20:58:18,857   adding 'concord/benchmarking/pipeline_integration.py'
2025-05-30T20:58:18,859   adding 'concord/benchmarking/tda.py'
2025-05-30T20:58:18,861   adding 'concord/benchmarking/time_memory.py'
2025-05-30T20:58:18,863   adding 'concord/model/__init__.py'
2025-05-30T20:58:18,864   adding 'concord/model/anndataset.py'
2025-05-30T20:58:18,866   adding 'concord/model/build_layer.py'
2025-05-30T20:58:18,867   adding 'concord/model/chunkloader.py'
2025-05-30T20:58:18,869   adding 'concord/model/dataloader.py'
2025-05-30T20:58:18,871   adding 'concord/model/knn.py'
2025-05-30T20:58:18,872   adding 'concord/model/loss.py'
2025-05-30T20:58:18,874   adding 'concord/model/model.py'
2025-05-30T20:58:18,876   adding 'concord/model/sampler.py'
2025-05-30T20:58:18,878   adding 'concord/model/trainer.py'
2025-05-30T20:58:18,880   adding 'concord/plotting/__init__.py'
2025-05-30T20:58:18,882   adding 'concord/plotting/palettes.py'
2025-05-30T20:58:18,883   adding 'concord/plotting/pl_batch.py'
2025-05-30T20:58:18,885   adding 'concord/plotting/pl_benchmark.py'
2025-05-30T20:58:18,886   adding 'concord/plotting/pl_datacoverage.py'
2025-05-30T20:58:18,893   adding 'concord/plotting/pl_embedding.py'
2025-05-30T20:58:18,895   adding 'concord/plotting/pl_enrichment.py'
2025-05-30T20:58:18,896   adding 'concord/plotting/pl_general.py'
2025-05-30T20:58:18,898   adding 'concord/plotting/pl_geometry.py'
2025-05-30T20:58:18,900   adding 'concord/plotting/pl_graph.py'
2025-05-30T20:58:18,903   adding 'concord/plotting/pl_heatmap.py'
2025-05-30T20:58:18,905   adding 'concord/plotting/pl_model.py'
2025-05-30T20:58:18,906   adding 'concord/plotting/pl_path.py'
2025-05-30T20:58:18,908   adding 'concord/plotting/pl_tda.py'
2025-05-30T20:58:18,910   adding 'concord/simulation/__init__.py'
2025-05-30T20:58:18,915   adding 'concord/simulation/simulation.py'
2025-05-30T20:58:18,917   adding 'concord/utils/Hs_Mm_conversion.py'
2025-05-30T20:58:18,918   adding 'concord/utils/__init__.py'
2025-05-30T20:58:18,921   adding 'concord/utils/anndata_utils.py'
2025-05-30T20:58:18,922   adding 'concord/utils/batch_analysis.py'
2025-05-30T20:58:18,923   adding 'concord/utils/cell_cycle.py'
2025-05-30T20:58:18,925   adding 'concord/utils/coverage_estimator.py'
2025-05-30T20:58:18,926   adding 'concord/utils/dim_reduction.py'
2025-05-30T20:58:18,928   adding 'concord/utils/doublet_utils.py'
2025-05-30T20:58:18,929   adding 'concord/utils/enrichment_analysis.py'
2025-05-30T20:58:18,931   adding 'concord/utils/estimate_dropout_rate.py'
2025-05-30T20:58:18,933   adding 'concord/utils/feature_selector.py'
2025-05-30T20:58:18,934   adding 'concord/utils/importance_analysis.py'
2025-05-30T20:58:18,936   adding 'concord/utils/integration_methods.py'
2025-05-30T20:58:18,938   adding 'concord/utils/io.py'
2025-05-30T20:58:18,939   adding 'concord/utils/other_util.py'
2025-05-30T20:58:18,941   adding 'concord/utils/path_analysis.py'
2025-05-30T20:58:18,942   adding 'concord/utils/value_check.py'
2025-05-30T20:58:18,944   adding 'concord/utils/visCello.py'
2025-05-30T20:58:18,947   adding 'concord_sc-1.0.0.dist-info/licenses/LICENSE.md'
2025-05-30T20:58:18,949   adding 'concord_sc-1.0.0.dist-info/METADATA'
2025-05-30T20:58:18,950   adding 'concord_sc-1.0.0.dist-info/WHEEL'
2025-05-30T20:58:18,951   adding 'concord_sc-1.0.0.dist-info/top_level.txt'
2025-05-30T20:58:18,952   adding 'concord_sc-1.0.0.dist-info/RECORD'
2025-05-30T20:58:18,956   removing build/bdist.linux-armv7l/wheel
2025-05-30T20:58:19,086   Building wheel for concord-sc (setup.py): finished with status 'done'
2025-05-30T20:58:19,090   Created wheel for concord-sc: filename=concord_sc-1.0.0-py3-none-any.whl size=144244 sha256=5f63b8a066b73cd4b7e4bf385d296d3498413f733fd294a7926d13a7de439652
2025-05-30T20:58:19,092   Stored in directory: /tmp/pip-ephem-wheel-cache-5w2ugc9u/wheels/e1/14/e8/96403e07477489c519808019768c168cb316f8b759ae102f19
2025-05-30T20:58:19,108 Successfully built concord-sc
2025-05-30T20:58:19,117 Removed build tracker: '/tmp/pip-build-tracker-fhz7ykps'