2025-06-02T01:04:04,508 Created temporary directory: /tmp/pip-build-tracker-iprve6nv
2025-06-02T01:04:04,509 Initialized build tracking at /tmp/pip-build-tracker-iprve6nv
2025-06-02T01:04:04,510 Created build tracker: /tmp/pip-build-tracker-iprve6nv
2025-06-02T01:04:04,510 Entered build tracker: /tmp/pip-build-tracker-iprve6nv
2025-06-02T01:04:04,511 Created temporary directory: /tmp/pip-wheel-128481ru
2025-06-02T01:04:04,515 Created temporary directory: /tmp/pip-ephem-wheel-cache-gezrfrsm
2025-06-02T01:04:04,565 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-02T01:04:04,567 2 location(s) to search for versions of concord-sc:
2025-06-02T01:04:04,567 * https://pypi.org/simple/concord-sc/
2025-06-02T01:04:04,567 * https://www.piwheels.org/simple/concord-sc/
2025-06-02T01:04:04,568 Fetching project page and analyzing links: https://pypi.org/simple/concord-sc/
2025-06-02T01:04:04,569 Getting page https://pypi.org/simple/concord-sc/
2025-06-02T01:04:04,571 Found index url https://pypi.org/simple/
2025-06-02T01:04:04,796 Fetched page https://pypi.org/simple/concord-sc/ as application/vnd.pypi.simple.v1+json
2025-06-02T01:04:04,804   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)
2025-06-02T01:04:04,806   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
2025-06-02T01:04:04,808   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)
2025-06-02T01:04:04,809   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
2025-06-02T01:04:04,810   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)
2025-06-02T01:04:04,811   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
2025-06-02T01:04:04,812   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)
2025-06-02T01:04:04,813   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
2025-06-02T01:04:04,814   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)
2025-06-02T01:04:04,815   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
2025-06-02T01:04:04,816   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)
2025-06-02T01:04:04,816   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
2025-06-02T01:04:04,817   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)
2025-06-02T01:04:04,818   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
2025-06-02T01:04:04,818   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)
2025-06-02T01:04:04,819   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
2025-06-02T01:04:04,819   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)
2025-06-02T01:04:04,820   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
2025-06-02T01:04:04,821   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)
2025-06-02T01:04:04,821   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
2025-06-02T01:04:04,822   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)
2025-06-02T01:04:04,823   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
2025-06-02T01:04:04,823   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)
2025-06-02T01:04:04,824   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
2025-06-02T01:04:04,825 Fetching project page and analyzing links: https://www.piwheels.org/simple/concord-sc/
2025-06-02T01:04:04,825 Getting page https://www.piwheels.org/simple/concord-sc/
2025-06-02T01:04:04,827 Found index url https://www.piwheels.org/simple/
2025-06-02T01:04:04,986 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/
2025-06-02T01:04:05,642 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/
2025-06-02T01:04:06,822 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/
2025-06-02T01:04:08,993 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/
2025-06-02T01:04:13,162 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/
2025-06-02T01:04:13,335 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
2025-06-02T01:04:13,337 Skipping link: not a file: https://www.piwheels.org/simple/concord-sc/
2025-06-02T01:04:13,338 Skipping link: not a file: https://pypi.org/simple/concord-sc/
2025-06-02T01:04:13,361 Given no hashes to check 1 links for project 'concord-sc': discarding no candidates
2025-06-02T01:04:13,363 Collecting concord-sc==1.0.6
2025-06-02T01:04:13,366   Created temporary directory: /tmp/pip-unpack-w04itrfp
2025-06-02T01:04:13,590   Downloading concord_sc-1.0.6.tar.gz (136 kB)
2025-06-02T01:04:13,852   Added concord-sc==1.0.6 from https://files.pythonhosted.org/packages/33/e9/77bcf0dcd825519e077b67e53a201dd2d1ad87e1ec55d0207adcd960d37c/concord_sc-1.0.6.tar.gz to build tracker '/tmp/pip-build-tracker-iprve6nv'
2025-06-02T01:04:13,855   Running setup.py (path:/tmp/pip-wheel-128481ru/concord-sc_f3806242003044a8b8c49f38f25bc472/setup.py) egg_info for package concord-sc
2025-06-02T01:04:13,856   Created temporary directory: /tmp/pip-pip-egg-info-xw2iuuuk
2025-06-02T01:04:13,857   Preparing metadata (setup.py): started
2025-06-02T01:04:13,858   Running command python setup.py egg_info
2025-06-02T01:04:14,786   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-02T01:04:14,786   !!

2025-06-02T01:04:14,787           ********************************************************************************
2025-06-02T01:04:14,788           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-02T01:04:14,790           License :: OSI Approved :: MIT License

2025-06-02T01:04:14,791           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-02T01:04:14,792           ********************************************************************************

2025-06-02T01:04:14,793   !!
2025-06-02T01:04:14,794     self._finalize_license_expression()
2025-06-02T01:04:14,818   running egg_info
2025-06-02T01:04:14,846   creating /tmp/pip-pip-egg-info-xw2iuuuk/concord_sc.egg-info
2025-06-02T01:04:14,847   writing /tmp/pip-pip-egg-info-xw2iuuuk/concord_sc.egg-info/PKG-INFO
2025-06-02T01:04:14,854   writing dependency_links to /tmp/pip-pip-egg-info-xw2iuuuk/concord_sc.egg-info/dependency_links.txt
2025-06-02T01:04:14,858   writing requirements to /tmp/pip-pip-egg-info-xw2iuuuk/concord_sc.egg-info/requires.txt
2025-06-02T01:04:14,860   writing top-level names to /tmp/pip-pip-egg-info-xw2iuuuk/concord_sc.egg-info/top_level.txt
2025-06-02T01:04:14,861   writing manifest file '/tmp/pip-pip-egg-info-xw2iuuuk/concord_sc.egg-info/SOURCES.txt'
2025-06-02T01:04:14,963   reading manifest file '/tmp/pip-pip-egg-info-xw2iuuuk/concord_sc.egg-info/SOURCES.txt'
2025-06-02T01:04:14,965   adding license file 'LICENSE.md'
2025-06-02T01:04:14,970   writing manifest file '/tmp/pip-pip-egg-info-xw2iuuuk/concord_sc.egg-info/SOURCES.txt'
2025-06-02T01:04:15,076   Preparing metadata (setup.py): finished with status 'done'
2025-06-02T01:04:15,081   Source in /tmp/pip-wheel-128481ru/concord-sc_f3806242003044a8b8c49f38f25bc472 has version 1.0.6, which satisfies requirement concord-sc==1.0.6 from https://files.pythonhosted.org/packages/33/e9/77bcf0dcd825519e077b67e53a201dd2d1ad87e1ec55d0207adcd960d37c/concord_sc-1.0.6.tar.gz
2025-06-02T01:04:15,081   Removed concord-sc==1.0.6 from https://files.pythonhosted.org/packages/33/e9/77bcf0dcd825519e077b67e53a201dd2d1ad87e1ec55d0207adcd960d37c/concord_sc-1.0.6.tar.gz from build tracker '/tmp/pip-build-tracker-iprve6nv'
2025-06-02T01:04:15,094 Created temporary directory: /tmp/pip-unpack-4srl2v0m
2025-06-02T01:04:15,095 Created temporary directory: /tmp/pip-unpack-yfi1qoy5
2025-06-02T01:04:15,095 Building wheels for collected packages: concord-sc
2025-06-02T01:04:15,100   Created temporary directory: /tmp/pip-wheel-z886podn
2025-06-02T01:04:15,101   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
2025-06-02T01:04:15,102   Building wheel for concord-sc (setup.py): started
2025-06-02T01:04:15,104   Destination directory: /tmp/pip-wheel-z886podn
2025-06-02T01:04:15,104   Running command python setup.py bdist_wheel
2025-06-02T01:04:15,972   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-02T01:04:15,973   !!

2025-06-02T01:04:15,974           ********************************************************************************
2025-06-02T01:04:15,974           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-02T01:04:15,976           License :: OSI Approved :: MIT License

2025-06-02T01:04:15,977           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-02T01:04:15,978           ********************************************************************************

2025-06-02T01:04:15,979   !!
2025-06-02T01:04:15,980     self._finalize_license_expression()
2025-06-02T01:04:15,981   running bdist_wheel
2025-06-02T01:04:16,115   running build
2025-06-02T01:04:16,116   running build_py
2025-06-02T01:04:16,151   creating build/lib/concord
2025-06-02T01:04:16,153   copying src/concord/sm.py -> build/lib/concord
2025-06-02T01:04:16,155   copying src/concord/__init__.py -> build/lib/concord
2025-06-02T01:04:16,158   copying src/concord/bm.py -> build/lib/concord
2025-06-02T01:04:16,160   copying src/concord/ul.py -> build/lib/concord
2025-06-02T01:04:16,162   copying src/concord/pl.py -> build/lib/concord
2025-06-02T01:04:16,164   copying src/concord/ml.py -> build/lib/concord
2025-06-02T01:04:16,165   copying src/concord/concord.py -> build/lib/concord
2025-06-02T01:04:16,170   creating build/lib/concord/plotting
2025-06-02T01:04:16,171   copying src/concord/plotting/pl_datacoverage.py -> build/lib/concord/plotting
2025-06-02T01:04:16,173   copying src/concord/plotting/pl_general.py -> build/lib/concord/plotting
2025-06-02T01:04:16,176   copying src/concord/plotting/__init__.py -> build/lib/concord/plotting
2025-06-02T01:04:16,178   copying src/concord/plotting/pl_heatmap.py -> build/lib/concord/plotting
2025-06-02T01:04:16,183   copying src/concord/plotting/pl_tda.py -> build/lib/concord/plotting
2025-06-02T01:04:16,189   copying src/concord/plotting/pl_benchmark.py -> build/lib/concord/plotting
2025-06-02T01:04:16,193   copying src/concord/plotting/pl_model.py -> build/lib/concord/plotting
2025-06-02T01:04:16,195   copying src/concord/plotting/pl_graph.py -> build/lib/concord/plotting
2025-06-02T01:04:16,199   copying src/concord/plotting/pl_geometry.py -> build/lib/concord/plotting
2025-06-02T01:04:16,202   copying src/concord/plotting/pl_embedding.py -> build/lib/concord/plotting
2025-06-02T01:04:16,206   copying src/concord/plotting/pl_path.py -> build/lib/concord/plotting
2025-06-02T01:04:16,208   copying src/concord/plotting/pl_enrichment.py -> build/lib/concord/plotting
2025-06-02T01:04:16,211   copying src/concord/plotting/pl_batch.py -> build/lib/concord/plotting
2025-06-02T01:04:16,214   copying src/concord/plotting/palettes.py -> build/lib/concord/plotting
2025-06-02T01:04:16,217   creating build/lib/concord/simulation
2025-06-02T01:04:16,218   copying src/concord/simulation/__init__.py -> build/lib/concord/simulation
2025-06-02T01:04:16,221   copying src/concord/simulation/simulation.py -> build/lib/concord/simulation
2025-06-02T01:04:16,225   creating build/lib/concord/benchmarking
2025-06-02T01:04:16,226   copying src/concord/benchmarking/__init__.py -> build/lib/concord/benchmarking
2025-06-02T01:04:16,229   copying src/concord/benchmarking/geometry.py -> build/lib/concord/benchmarking
2025-06-02T01:04:16,232   copying src/concord/benchmarking/integration_methods.py -> build/lib/concord/benchmarking
2025-06-02T01:04:16,235   copying src/concord/benchmarking/benchmark.py -> build/lib/concord/benchmarking
2025-06-02T01:04:16,240   copying src/concord/benchmarking/pipeline_integration.py -> build/lib/concord/benchmarking
2025-06-02T01:04:16,244   copying src/concord/benchmarking/pipeline_dim_reduction.py -> build/lib/concord/benchmarking
2025-06-02T01:04:16,247   copying src/concord/benchmarking/tda.py -> build/lib/concord/benchmarking
2025-06-02T01:04:16,250   copying src/concord/benchmarking/knn_probe.py -> build/lib/concord/benchmarking
2025-06-02T01:04:16,252   copying src/concord/benchmarking/linear_probe.py -> build/lib/concord/benchmarking
2025-06-02T01:04:16,256   copying src/concord/benchmarking/time_memory.py -> build/lib/concord/benchmarking
2025-06-02T01:04:16,259   creating build/lib/concord/model
2025-06-02T01:04:16,260   copying src/concord/model/knn.py -> build/lib/concord/model
2025-06-02T01:04:16,264   copying src/concord/model/__init__.py -> build/lib/concord/model
2025-06-02T01:04:16,266   copying src/concord/model/model.py -> build/lib/concord/model
2025-06-02T01:04:16,269   copying src/concord/model/build_layer.py -> build/lib/concord/model
2025-06-02T01:04:16,272   copying src/concord/model/loss.py -> build/lib/concord/model
2025-06-02T01:04:16,274   copying src/concord/model/chunkloader.py -> build/lib/concord/model
2025-06-02T01:04:16,277   copying src/concord/model/anndataset.py -> build/lib/concord/model
2025-06-02T01:04:16,280   copying src/concord/model/dataloader.py -> build/lib/concord/model
2025-06-02T01:04:16,283   copying src/concord/model/augment.py -> build/lib/concord/model
2025-06-02T01:04:16,285   copying src/concord/model/trainer.py -> build/lib/concord/model
2025-06-02T01:04:16,288   copying src/concord/model/sampler.py -> build/lib/concord/model
2025-06-02T01:04:16,293   creating build/lib/concord/utils
2025-06-02T01:04:16,294   copying src/concord/utils/cell_cycle.py -> build/lib/concord/utils
2025-06-02T01:04:16,296   copying src/concord/utils/doublet_utils.py -> build/lib/concord/utils
2025-06-02T01:04:16,299   copying src/concord/utils/__init__.py -> build/lib/concord/utils
2025-06-02T01:04:16,301   copying src/concord/utils/path_analysis.py -> build/lib/concord/utils
2025-06-02T01:04:16,304   copying src/concord/utils/visCello.py -> build/lib/concord/utils
2025-06-02T01:04:16,307   copying src/concord/utils/other_util.py -> build/lib/concord/utils
2025-06-02T01:04:16,309   copying src/concord/utils/io.py -> build/lib/concord/utils
2025-06-02T01:04:16,312   copying src/concord/utils/estimate_dropout_rate.py -> build/lib/concord/utils
2025-06-02T01:04:16,314   copying src/concord/utils/coverage_estimator.py -> build/lib/concord/utils
2025-06-02T01:04:16,316   copying src/concord/utils/anndata_utils.py -> build/lib/concord/utils
2025-06-02T01:04:16,319   copying src/concord/utils/feature_selector.py -> build/lib/concord/utils
2025-06-02T01:04:16,322   copying src/concord/utils/batch_analysis.py -> build/lib/concord/utils
2025-06-02T01:04:16,325   copying src/concord/utils/enrichment_analysis.py -> build/lib/concord/utils
2025-06-02T01:04:16,328   copying src/concord/utils/dim_reduction.py -> build/lib/concord/utils
2025-06-02T01:04:16,330   copying src/concord/utils/Hs_Mm_conversion.py -> build/lib/concord/utils
2025-06-02T01:04:16,333   copying src/concord/utils/value_check.py -> build/lib/concord/utils
2025-06-02T01:04:16,335   copying src/concord/utils/importance_analysis.py -> build/lib/concord/utils
2025-06-02T01:04:16,375   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-02T01:04:16,375   !!

2025-06-02T01:04:16,377           ********************************************************************************
2025-06-02T01:04:16,377           Please avoid running ``setup.py`` directly.
2025-06-02T01:04:16,377           Instead, use pypa/build, pypa/installer or other
2025-06-02T01:04:16,378           standards-based tools.

2025-06-02T01:04:16,379           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-02T01:04:16,380           or your builds will no longer be supported.

2025-06-02T01:04:16,381           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-02T01:04:16,381           ********************************************************************************

2025-06-02T01:04:16,383   !!
2025-06-02T01:04:16,384     self.initialize_options()
2025-06-02T01:04:16,403   installing to build/bdist.linux-armv7l/wheel
2025-06-02T01:04:16,404   running install
2025-06-02T01:04:16,429   running install_lib
2025-06-02T01:04:16,456   creating build/bdist.linux-armv7l/wheel
2025-06-02T01:04:16,459   creating build/bdist.linux-armv7l/wheel/concord
2025-06-02T01:04:16,460   copying build/lib/concord/sm.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-02T01:04:16,462   copying build/lib/concord/__init__.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-02T01:04:16,464   copying build/lib/concord/bm.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-02T01:04:16,466   creating build/bdist.linux-armv7l/wheel/concord/plotting
2025-06-02T01:04:16,467   copying build/lib/concord/plotting/pl_datacoverage.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,469   copying build/lib/concord/plotting/pl_general.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,471   copying build/lib/concord/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,473   copying build/lib/concord/plotting/pl_heatmap.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,476   copying build/lib/concord/plotting/pl_tda.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,479   copying build/lib/concord/plotting/pl_benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,482   copying build/lib/concord/plotting/pl_model.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,484   copying build/lib/concord/plotting/pl_graph.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,487   copying build/lib/concord/plotting/pl_geometry.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,490   copying build/lib/concord/plotting/pl_embedding.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,494   copying build/lib/concord/plotting/pl_path.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,496   copying build/lib/concord/plotting/pl_enrichment.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,499   copying build/lib/concord/plotting/pl_batch.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,501   copying build/lib/concord/plotting/palettes.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-02T01:04:16,504   copying build/lib/concord/ul.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-02T01:04:16,506   copying build/lib/concord/pl.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-02T01:04:16,508   copying build/lib/concord/ml.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-02T01:04:16,510   creating build/bdist.linux-armv7l/wheel/concord/simulation
2025-06-02T01:04:16,512   copying build/lib/concord/simulation/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/simulation
2025-06-02T01:04:16,514   copying build/lib/concord/simulation/simulation.py -> build/bdist.linux-armv7l/wheel/./concord/simulation
2025-06-02T01:04:16,517   copying build/lib/concord/concord.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-02T01:04:16,521   creating build/bdist.linux-armv7l/wheel/concord/benchmarking
2025-06-02T01:04:16,523   copying build/lib/concord/benchmarking/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-02T01:04:16,525   copying build/lib/concord/benchmarking/geometry.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-02T01:04:16,528   copying build/lib/concord/benchmarking/integration_methods.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-02T01:04:16,531   copying build/lib/concord/benchmarking/benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-02T01:04:16,535   copying build/lib/concord/benchmarking/pipeline_integration.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-02T01:04:16,538   copying build/lib/concord/benchmarking/pipeline_dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-02T01:04:16,541   copying build/lib/concord/benchmarking/tda.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-02T01:04:16,544   copying build/lib/concord/benchmarking/knn_probe.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-02T01:04:16,546   copying build/lib/concord/benchmarking/linear_probe.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-02T01:04:16,549   copying build/lib/concord/benchmarking/time_memory.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-02T01:04:16,553   creating build/bdist.linux-armv7l/wheel/concord/model
2025-06-02T01:04:16,554   copying build/lib/concord/model/knn.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-02T01:04:16,557   copying build/lib/concord/model/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-02T01:04:16,560   copying build/lib/concord/model/model.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-02T01:04:16,563   copying build/lib/concord/model/build_layer.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-02T01:04:16,565   copying build/lib/concord/model/loss.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-02T01:04:16,568   copying build/lib/concord/model/chunkloader.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-02T01:04:16,570   copying build/lib/concord/model/anndataset.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-02T01:04:16,573   copying build/lib/concord/model/dataloader.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-02T01:04:16,576   copying build/lib/concord/model/augment.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-02T01:04:16,579   copying build/lib/concord/model/trainer.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-02T01:04:16,582   copying build/lib/concord/model/sampler.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-02T01:04:16,586   creating build/bdist.linux-armv7l/wheel/concord/utils
2025-06-02T01:04:16,587   copying build/lib/concord/utils/cell_cycle.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,589   copying build/lib/concord/utils/doublet_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,592   copying build/lib/concord/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,594   copying build/lib/concord/utils/path_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,597   copying build/lib/concord/utils/visCello.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,600   copying build/lib/concord/utils/other_util.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,602   copying build/lib/concord/utils/io.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,604   copying build/lib/concord/utils/estimate_dropout_rate.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,607   copying build/lib/concord/utils/coverage_estimator.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,609   copying build/lib/concord/utils/anndata_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,612   copying build/lib/concord/utils/feature_selector.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,615   copying build/lib/concord/utils/batch_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,617   copying build/lib/concord/utils/enrichment_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,620   copying build/lib/concord/utils/dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,623   copying build/lib/concord/utils/Hs_Mm_conversion.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,625   copying build/lib/concord/utils/value_check.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,627   copying build/lib/concord/utils/importance_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-02T01:04:16,629   running install_egg_info
2025-06-02T01:04:16,668   running egg_info
2025-06-02T01:04:16,700   writing src/concord_sc.egg-info/PKG-INFO
2025-06-02T01:04:16,706   writing dependency_links to src/concord_sc.egg-info/dependency_links.txt
2025-06-02T01:04:16,710   writing requirements to src/concord_sc.egg-info/requires.txt
2025-06-02T01:04:16,711   writing top-level names to src/concord_sc.egg-info/top_level.txt
2025-06-02T01:04:16,749   reading manifest file 'src/concord_sc.egg-info/SOURCES.txt'
2025-06-02T01:04:16,755   adding license file 'LICENSE.md'
2025-06-02T01:04:16,760   writing manifest file 'src/concord_sc.egg-info/SOURCES.txt'
2025-06-02T01:04:16,762   Copying src/concord_sc.egg-info to build/bdist.linux-armv7l/wheel/./concord_sc-1.0.6-py3.11.egg-info
2025-06-02T01:04:16,772   running install_scripts
2025-06-02T01:04:16,785   creating build/bdist.linux-armv7l/wheel/concord_sc-1.0.6.dist-info/WHEEL
2025-06-02T01:04:16,788   creating '/tmp/pip-wheel-z886podn/concord_sc-1.0.6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-02T01:04:16,791   adding 'concord/__init__.py'
2025-06-02T01:04:16,793   adding 'concord/bm.py'
2025-06-02T01:04:16,800   adding 'concord/concord.py'
2025-06-02T01:04:16,802   adding 'concord/ml.py'
2025-06-02T01:04:16,804   adding 'concord/pl.py'
2025-06-02T01:04:16,805   adding 'concord/sm.py'
2025-06-02T01:04:16,807   adding 'concord/ul.py'
2025-06-02T01:04:16,809   adding 'concord/benchmarking/__init__.py'
2025-06-02T01:04:16,814   adding 'concord/benchmarking/benchmark.py'
2025-06-02T01:04:16,818   adding 'concord/benchmarking/geometry.py'
2025-06-02T01:04:16,821   adding 'concord/benchmarking/integration_methods.py'
2025-06-02T01:04:16,823   adding 'concord/benchmarking/knn_probe.py'
2025-06-02T01:04:16,826   adding 'concord/benchmarking/linear_probe.py'
2025-06-02T01:04:16,828   adding 'concord/benchmarking/pipeline_dim_reduction.py'
2025-06-02T01:04:16,832   adding 'concord/benchmarking/pipeline_integration.py'
2025-06-02T01:04:16,836   adding 'concord/benchmarking/tda.py'
2025-06-02T01:04:16,839   adding 'concord/benchmarking/time_memory.py'
2025-06-02T01:04:16,841   adding 'concord/model/__init__.py'
2025-06-02T01:04:16,843   adding 'concord/model/anndataset.py'
2025-06-02T01:04:16,845   adding 'concord/model/augment.py'
2025-06-02T01:04:16,846   adding 'concord/model/build_layer.py'
2025-06-02T01:04:16,848   adding 'concord/model/chunkloader.py'
2025-06-02T01:04:16,850   adding 'concord/model/dataloader.py'
2025-06-02T01:04:16,853   adding 'concord/model/knn.py'
2025-06-02T01:04:16,855   adding 'concord/model/loss.py'
2025-06-02T01:04:16,857   adding 'concord/model/model.py'
2025-06-02T01:04:16,860   adding 'concord/model/sampler.py'
2025-06-02T01:04:16,863   adding 'concord/model/trainer.py'
2025-06-02T01:04:16,865   adding 'concord/plotting/__init__.py'
2025-06-02T01:04:16,867   adding 'concord/plotting/palettes.py'
2025-06-02T01:04:16,868   adding 'concord/plotting/pl_batch.py'
2025-06-02T01:04:16,870   adding 'concord/plotting/pl_benchmark.py'
2025-06-02T01:04:16,872   adding 'concord/plotting/pl_datacoverage.py'
2025-06-02T01:04:16,878   adding 'concord/plotting/pl_embedding.py'
2025-06-02T01:04:16,880   adding 'concord/plotting/pl_enrichment.py'
2025-06-02T01:04:16,882   adding 'concord/plotting/pl_general.py'
2025-06-02T01:04:16,884   adding 'concord/plotting/pl_geometry.py'
2025-06-02T01:04:16,887   adding 'concord/plotting/pl_graph.py'
2025-06-02T01:04:16,889   adding 'concord/plotting/pl_heatmap.py'
2025-06-02T01:04:16,891   adding 'concord/plotting/pl_model.py'
2025-06-02T01:04:16,893   adding 'concord/plotting/pl_path.py'
2025-06-02T01:04:16,895   adding 'concord/plotting/pl_tda.py'
2025-06-02T01:04:16,897   adding 'concord/simulation/__init__.py'
2025-06-02T01:04:16,902   adding 'concord/simulation/simulation.py'
2025-06-02T01:04:16,904   adding 'concord/utils/Hs_Mm_conversion.py'
2025-06-02T01:04:16,905   adding 'concord/utils/__init__.py'
2025-06-02T01:04:16,908   adding 'concord/utils/anndata_utils.py'
2025-06-02T01:04:16,910   adding 'concord/utils/batch_analysis.py'
2025-06-02T01:04:16,911   adding 'concord/utils/cell_cycle.py'
2025-06-02T01:04:16,913   adding 'concord/utils/coverage_estimator.py'
2025-06-02T01:04:16,914   adding 'concord/utils/dim_reduction.py'
2025-06-02T01:04:16,916   adding 'concord/utils/doublet_utils.py'
2025-06-02T01:04:16,917   adding 'concord/utils/enrichment_analysis.py'
2025-06-02T01:04:16,919   adding 'concord/utils/estimate_dropout_rate.py'
2025-06-02T01:04:16,921   adding 'concord/utils/feature_selector.py'
2025-06-02T01:04:16,922   adding 'concord/utils/importance_analysis.py'
2025-06-02T01:04:16,924   adding 'concord/utils/io.py'
2025-06-02T01:04:16,925   adding 'concord/utils/other_util.py'
2025-06-02T01:04:16,927   adding 'concord/utils/path_analysis.py'
2025-06-02T01:04:16,929   adding 'concord/utils/value_check.py'
2025-06-02T01:04:16,931   adding 'concord/utils/visCello.py'
2025-06-02T01:04:16,933   adding 'concord_sc-1.0.6.dist-info/licenses/LICENSE.md'
2025-06-02T01:04:16,935   adding 'concord_sc-1.0.6.dist-info/METADATA'
2025-06-02T01:04:16,937   adding 'concord_sc-1.0.6.dist-info/WHEEL'
2025-06-02T01:04:16,938   adding 'concord_sc-1.0.6.dist-info/top_level.txt'
2025-06-02T01:04:16,939   adding 'concord_sc-1.0.6.dist-info/RECORD'
2025-06-02T01:04:16,943   removing build/bdist.linux-armv7l/wheel
2025-06-02T01:04:17,070   Building wheel for concord-sc (setup.py): finished with status 'done'
2025-06-02T01:04:17,074   Created wheel for concord-sc: filename=concord_sc-1.0.6-py3-none-any.whl size=154328 sha256=ac94c5b70d82511fc03bbc94cc5717a4375f2b7550eb56cb0a665ed879cbbe4b
2025-06-02T01:04:17,075   Stored in directory: /tmp/pip-ephem-wheel-cache-gezrfrsm/wheels/27/54/c6/be5f0212b485bb3d6b5de3c24ced8b7af0df7d3b2b94442505
2025-06-02T01:04:17,090 Successfully built concord-sc
2025-06-02T01:04:17,099 Removed build tracker: '/tmp/pip-build-tracker-iprve6nv'