2025-06-01T02:25:03,959 Created temporary directory: /tmp/pip-build-tracker-fmg1h8a7
2025-06-01T02:25:03,961 Initialized build tracking at /tmp/pip-build-tracker-fmg1h8a7
2025-06-01T02:25:03,961 Created build tracker: /tmp/pip-build-tracker-fmg1h8a7
2025-06-01T02:25:03,962 Entered build tracker: /tmp/pip-build-tracker-fmg1h8a7
2025-06-01T02:25:03,962 Created temporary directory: /tmp/pip-wheel-lc3e0zdd
2025-06-01T02:25:03,966 Created temporary directory: /tmp/pip-ephem-wheel-cache-ww1f57ss
2025-06-01T02:25:04,020 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-01T02:25:04,023 2 location(s) to search for versions of concord-sc:
2025-06-01T02:25:04,023 * https://pypi.org/simple/concord-sc/
2025-06-01T02:25:04,023 * https://www.piwheels.org/simple/concord-sc/
2025-06-01T02:25:04,023 Fetching project page and analyzing links: https://pypi.org/simple/concord-sc/
2025-06-01T02:25:04,024 Getting page https://pypi.org/simple/concord-sc/
2025-06-01T02:25:04,026 Found index url https://pypi.org/simple/
2025-06-01T02:25:04,253 Fetched page https://pypi.org/simple/concord-sc/ as application/vnd.pypi.simple.v1+json
2025-06-01T02:25:04,261   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)
2025-06-01T02:25:04,263   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
2025-06-01T02:25:04,264   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)
2025-06-01T02:25:04,266   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
2025-06-01T02:25:04,267   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)
2025-06-01T02:25:04,268   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
2025-06-01T02:25:04,269   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)
2025-06-01T02:25:04,270   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
2025-06-01T02:25:04,271   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)
2025-06-01T02:25:04,272   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
2025-06-01T02:25:04,273   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)
2025-06-01T02:25:04,274   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
2025-06-01T02:25:04,275   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)
2025-06-01T02:25:04,275   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
2025-06-01T02:25:04,276   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)
2025-06-01T02:25:04,276   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
2025-06-01T02:25:04,277   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)
2025-06-01T02:25:04,277   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
2025-06-01T02:25:04,278   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)
2025-06-01T02:25:04,279   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
2025-06-01T02:25:04,279   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)
2025-06-01T02:25:04,280   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
2025-06-01T02:25:04,281   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)
2025-06-01T02:25:04,282   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
2025-06-01T02:25:04,283 Fetching project page and analyzing links: https://www.piwheels.org/simple/concord-sc/
2025-06-01T02:25:04,283 Getting page https://www.piwheels.org/simple/concord-sc/
2025-06-01T02:25:04,285 Found index url https://www.piwheels.org/simple/
2025-06-01T02:25:04,443 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/
2025-06-01T02:25:05,104 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/
2025-06-01T02:25:06,273 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/
2025-06-01T02:25:08,448 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/
2025-06-01T02:25:12,628 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/
2025-06-01T02:25:12,827 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
2025-06-01T02:25:12,829 Skipping link: not a file: https://www.piwheels.org/simple/concord-sc/
2025-06-01T02:25:12,829 Skipping link: not a file: https://pypi.org/simple/concord-sc/
2025-06-01T02:25:12,849 Given no hashes to check 1 links for project 'concord-sc': discarding no candidates
2025-06-01T02:25:12,851 Collecting concord-sc==1.0.4
2025-06-01T02:25:12,854   Created temporary directory: /tmp/pip-unpack-3m3vk28x
2025-06-01T02:25:13,080   Downloading concord_sc-1.0.4.tar.gz (133 kB)
2025-06-01T02:25:13,332   Added concord-sc==1.0.4 from https://files.pythonhosted.org/packages/99/e1/07eba0da0f26e2cd1dfd7ebb52a0b39dd22bbdf6be5a9056e1a84b42cbc2/concord_sc-1.0.4.tar.gz to build tracker '/tmp/pip-build-tracker-fmg1h8a7'
2025-06-01T02:25:13,334   Running setup.py (path:/tmp/pip-wheel-lc3e0zdd/concord-sc_aa62df008c364384ab4dc2c80e282814/setup.py) egg_info for package concord-sc
2025-06-01T02:25:13,335   Created temporary directory: /tmp/pip-pip-egg-info-fce7pd8w
2025-06-01T02:25:13,336   Preparing metadata (setup.py): started
2025-06-01T02:25:13,337   Running command python setup.py egg_info
2025-06-01T02:25:14,253   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-01T02:25:14,254   !!

2025-06-01T02:25:14,255           ********************************************************************************
2025-06-01T02:25:14,256           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-01T02:25:14,257           License :: OSI Approved :: MIT License

2025-06-01T02:25:14,258           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-01T02:25:14,259           ********************************************************************************

2025-06-01T02:25:14,260   !!
2025-06-01T02:25:14,260     self._finalize_license_expression()
2025-06-01T02:25:14,285   running egg_info
2025-06-01T02:25:14,312   creating /tmp/pip-pip-egg-info-fce7pd8w/concord_sc.egg-info
2025-06-01T02:25:14,314   writing /tmp/pip-pip-egg-info-fce7pd8w/concord_sc.egg-info/PKG-INFO
2025-06-01T02:25:14,320   writing dependency_links to /tmp/pip-pip-egg-info-fce7pd8w/concord_sc.egg-info/dependency_links.txt
2025-06-01T02:25:14,324   writing requirements to /tmp/pip-pip-egg-info-fce7pd8w/concord_sc.egg-info/requires.txt
2025-06-01T02:25:14,325   writing top-level names to /tmp/pip-pip-egg-info-fce7pd8w/concord_sc.egg-info/top_level.txt
2025-06-01T02:25:14,326   writing manifest file '/tmp/pip-pip-egg-info-fce7pd8w/concord_sc.egg-info/SOURCES.txt'
2025-06-01T02:25:14,427   reading manifest file '/tmp/pip-pip-egg-info-fce7pd8w/concord_sc.egg-info/SOURCES.txt'
2025-06-01T02:25:14,429   adding license file 'LICENSE.md'
2025-06-01T02:25:14,433   writing manifest file '/tmp/pip-pip-egg-info-fce7pd8w/concord_sc.egg-info/SOURCES.txt'
2025-06-01T02:25:14,539   Preparing metadata (setup.py): finished with status 'done'
2025-06-01T02:25:14,543   Source in /tmp/pip-wheel-lc3e0zdd/concord-sc_aa62df008c364384ab4dc2c80e282814 has version 1.0.4, which satisfies requirement concord-sc==1.0.4 from https://files.pythonhosted.org/packages/99/e1/07eba0da0f26e2cd1dfd7ebb52a0b39dd22bbdf6be5a9056e1a84b42cbc2/concord_sc-1.0.4.tar.gz
2025-06-01T02:25:14,544   Removed concord-sc==1.0.4 from https://files.pythonhosted.org/packages/99/e1/07eba0da0f26e2cd1dfd7ebb52a0b39dd22bbdf6be5a9056e1a84b42cbc2/concord_sc-1.0.4.tar.gz from build tracker '/tmp/pip-build-tracker-fmg1h8a7'
2025-06-01T02:25:14,557 Created temporary directory: /tmp/pip-unpack-kevc0eee
2025-06-01T02:25:14,558 Created temporary directory: /tmp/pip-unpack-29igu7gb
2025-06-01T02:25:14,558 Building wheels for collected packages: concord-sc
2025-06-01T02:25:14,563   Created temporary directory: /tmp/pip-wheel-5elhur3x
2025-06-01T02:25:14,564   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
2025-06-01T02:25:14,565   Building wheel for concord-sc (setup.py): started
2025-06-01T02:25:14,566   Destination directory: /tmp/pip-wheel-5elhur3x
2025-06-01T02:25:14,567   Running command python setup.py bdist_wheel
2025-06-01T02:25:15,421   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-01T02:25:15,422   !!

2025-06-01T02:25:15,423           ********************************************************************************
2025-06-01T02:25:15,423           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-01T02:25:15,425           License :: OSI Approved :: MIT License

2025-06-01T02:25:15,426           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-01T02:25:15,426           ********************************************************************************

2025-06-01T02:25:15,428   !!
2025-06-01T02:25:15,428     self._finalize_license_expression()
2025-06-01T02:25:15,429   running bdist_wheel
2025-06-01T02:25:15,562   running build
2025-06-01T02:25:15,563   running build_py
2025-06-01T02:25:15,594   creating build/lib/concord
2025-06-01T02:25:15,596   copying src/concord/concord.py -> build/lib/concord
2025-06-01T02:25:15,599   copying src/concord/pl.py -> build/lib/concord
2025-06-01T02:25:15,601   copying src/concord/__init__.py -> build/lib/concord
2025-06-01T02:25:15,603   copying src/concord/ul.py -> build/lib/concord
2025-06-01T02:25:15,605   copying src/concord/sm.py -> build/lib/concord
2025-06-01T02:25:15,607   copying src/concord/bm.py -> build/lib/concord
2025-06-01T02:25:15,609   copying src/concord/ml.py -> build/lib/concord
2025-06-01T02:25:15,612   creating build/lib/concord/utils
2025-06-01T02:25:15,613   copying src/concord/utils/anndata_utils.py -> build/lib/concord/utils
2025-06-01T02:25:15,616   copying src/concord/utils/cell_cycle.py -> build/lib/concord/utils
2025-06-01T02:25:15,618   copying src/concord/utils/__init__.py -> build/lib/concord/utils
2025-06-01T02:25:15,619   copying src/concord/utils/dim_reduction.py -> build/lib/concord/utils
2025-06-01T02:25:15,622   copying src/concord/utils/batch_analysis.py -> build/lib/concord/utils
2025-06-01T02:25:15,624   copying src/concord/utils/visCello.py -> build/lib/concord/utils
2025-06-01T02:25:15,627   copying src/concord/utils/other_util.py -> build/lib/concord/utils
2025-06-01T02:25:15,629   copying src/concord/utils/doublet_utils.py -> build/lib/concord/utils
2025-06-01T02:25:15,631   copying src/concord/utils/path_analysis.py -> build/lib/concord/utils
2025-06-01T02:25:15,634   copying src/concord/utils/enrichment_analysis.py -> build/lib/concord/utils
2025-06-01T02:25:15,636   copying src/concord/utils/estimate_dropout_rate.py -> build/lib/concord/utils
2025-06-01T02:25:15,638   copying src/concord/utils/Hs_Mm_conversion.py -> build/lib/concord/utils
2025-06-01T02:25:15,641   copying src/concord/utils/value_check.py -> build/lib/concord/utils
2025-06-01T02:25:15,643   copying src/concord/utils/io.py -> build/lib/concord/utils
2025-06-01T02:25:15,645   copying src/concord/utils/coverage_estimator.py -> build/lib/concord/utils
2025-06-01T02:25:15,647   copying src/concord/utils/importance_analysis.py -> build/lib/concord/utils
2025-06-01T02:25:15,649   copying src/concord/utils/feature_selector.py -> build/lib/concord/utils
2025-06-01T02:25:15,652   creating build/lib/concord/simulation
2025-06-01T02:25:15,653   copying src/concord/simulation/__init__.py -> build/lib/concord/simulation
2025-06-01T02:25:15,655   copying src/concord/simulation/simulation.py -> build/lib/concord/simulation
2025-06-01T02:25:15,659   creating build/lib/concord/plotting
2025-06-01T02:25:15,660   copying src/concord/plotting/palettes.py -> build/lib/concord/plotting
2025-06-01T02:25:15,663   copying src/concord/plotting/__init__.py -> build/lib/concord/plotting
2025-06-01T02:25:15,665   copying src/concord/plotting/pl_tda.py -> build/lib/concord/plotting
2025-06-01T02:25:15,668   copying src/concord/plotting/pl_heatmap.py -> build/lib/concord/plotting
2025-06-01T02:25:15,670   copying src/concord/plotting/pl_model.py -> build/lib/concord/plotting
2025-06-01T02:25:15,673   copying src/concord/plotting/pl_graph.py -> build/lib/concord/plotting
2025-06-01T02:25:15,676   copying src/concord/plotting/pl_enrichment.py -> build/lib/concord/plotting
2025-06-01T02:25:15,678   copying src/concord/plotting/pl_geometry.py -> build/lib/concord/plotting
2025-06-01T02:25:15,681   copying src/concord/plotting/pl_batch.py -> build/lib/concord/plotting
2025-06-01T02:25:15,683   copying src/concord/plotting/pl_benchmark.py -> build/lib/concord/plotting
2025-06-01T02:25:15,686   copying src/concord/plotting/pl_datacoverage.py -> build/lib/concord/plotting
2025-06-01T02:25:15,688   copying src/concord/plotting/pl_general.py -> build/lib/concord/plotting
2025-06-01T02:25:15,690   copying src/concord/plotting/pl_embedding.py -> build/lib/concord/plotting
2025-06-01T02:25:15,695   copying src/concord/plotting/pl_path.py -> build/lib/concord/plotting
2025-06-01T02:25:15,698   creating build/lib/concord/benchmarking
2025-06-01T02:25:15,699   copying src/concord/benchmarking/geometry.py -> build/lib/concord/benchmarking
2025-06-01T02:25:15,702   copying src/concord/benchmarking/time_memory.py -> build/lib/concord/benchmarking
2025-06-01T02:25:15,705   copying src/concord/benchmarking/__init__.py -> build/lib/concord/benchmarking
2025-06-01T02:25:15,707   copying src/concord/benchmarking/linear_probe.py -> build/lib/concord/benchmarking
2025-06-01T02:25:15,710   copying src/concord/benchmarking/benchmark.py -> build/lib/concord/benchmarking
2025-06-01T02:25:15,713   copying src/concord/benchmarking/pipeline_dim_reduction.py -> build/lib/concord/benchmarking
2025-06-01T02:25:15,716   copying src/concord/benchmarking/tda.py -> build/lib/concord/benchmarking
2025-06-01T02:25:15,718   copying src/concord/benchmarking/pipeline_integration.py -> build/lib/concord/benchmarking
2025-06-01T02:25:15,721   copying src/concord/benchmarking/integration_methods.py -> build/lib/concord/benchmarking
2025-06-01T02:25:15,724   copying src/concord/benchmarking/knn_probe.py -> build/lib/concord/benchmarking
2025-06-01T02:25:15,727   creating build/lib/concord/model
2025-06-01T02:25:15,729   copying src/concord/model/anndataset.py -> build/lib/concord/model
2025-06-01T02:25:15,731   copying src/concord/model/__init__.py -> build/lib/concord/model
2025-06-01T02:25:15,733   copying src/concord/model/sampler.py -> build/lib/concord/model
2025-06-01T02:25:15,736   copying src/concord/model/dataloader.py -> build/lib/concord/model
2025-06-01T02:25:15,739   copying src/concord/model/chunkloader.py -> build/lib/concord/model
2025-06-01T02:25:15,741   copying src/concord/model/trainer.py -> build/lib/concord/model
2025-06-01T02:25:15,743   copying src/concord/model/loss.py -> build/lib/concord/model
2025-06-01T02:25:15,746   copying src/concord/model/knn.py -> build/lib/concord/model
2025-06-01T02:25:15,748   copying src/concord/model/model.py -> build/lib/concord/model
2025-06-01T02:25:15,751   copying src/concord/model/build_layer.py -> build/lib/concord/model
2025-06-01T02:25:15,790   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-01T02:25:15,791   !!

2025-06-01T02:25:15,792           ********************************************************************************
2025-06-01T02:25:15,792           Please avoid running ``setup.py`` directly.
2025-06-01T02:25:15,793           Instead, use pypa/build, pypa/installer or other
2025-06-01T02:25:15,793           standards-based tools.

2025-06-01T02:25:15,795           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-01T02:25:15,795           or your builds will no longer be supported.

2025-06-01T02:25:15,796           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-01T02:25:15,797           ********************************************************************************

2025-06-01T02:25:15,798   !!
2025-06-01T02:25:15,798     self.initialize_options()
2025-06-01T02:25:15,820   installing to build/bdist.linux-armv7l/wheel
2025-06-01T02:25:15,820   running install
2025-06-01T02:25:15,845   running install_lib
2025-06-01T02:25:15,872   creating build/bdist.linux-armv7l/wheel
2025-06-01T02:25:15,874   creating build/bdist.linux-armv7l/wheel/concord
2025-06-01T02:25:15,875   copying build/lib/concord/concord.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-01T02:25:15,879   creating build/bdist.linux-armv7l/wheel/concord/utils
2025-06-01T02:25:15,881   copying build/lib/concord/utils/anndata_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,884   copying build/lib/concord/utils/cell_cycle.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,885   copying build/lib/concord/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,887   copying build/lib/concord/utils/dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,890   copying build/lib/concord/utils/batch_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,892   copying build/lib/concord/utils/visCello.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,894   copying build/lib/concord/utils/other_util.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,897   copying build/lib/concord/utils/doublet_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,899   copying build/lib/concord/utils/path_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,902   copying build/lib/concord/utils/enrichment_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,904   copying build/lib/concord/utils/estimate_dropout_rate.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,907   copying build/lib/concord/utils/Hs_Mm_conversion.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,910   copying build/lib/concord/utils/value_check.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,912   copying build/lib/concord/utils/io.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,914   copying build/lib/concord/utils/coverage_estimator.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,916   copying build/lib/concord/utils/importance_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,918   copying build/lib/concord/utils/feature_selector.py -> build/bdist.linux-armv7l/wheel/./concord/utils
2025-06-01T02:25:15,921   copying build/lib/concord/pl.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-01T02:25:15,924   creating build/bdist.linux-armv7l/wheel/concord/simulation
2025-06-01T02:25:15,925   copying build/lib/concord/simulation/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/simulation
2025-06-01T02:25:15,927   copying build/lib/concord/simulation/simulation.py -> build/bdist.linux-armv7l/wheel/./concord/simulation
2025-06-01T02:25:15,931   creating build/bdist.linux-armv7l/wheel/concord/plotting
2025-06-01T02:25:15,933   copying build/lib/concord/plotting/palettes.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,935   copying build/lib/concord/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,937   copying build/lib/concord/plotting/pl_tda.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,940   copying build/lib/concord/plotting/pl_heatmap.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,943   copying build/lib/concord/plotting/pl_model.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,946   copying build/lib/concord/plotting/pl_graph.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,948   copying build/lib/concord/plotting/pl_enrichment.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,951   copying build/lib/concord/plotting/pl_geometry.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,953   copying build/lib/concord/plotting/pl_batch.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,955   copying build/lib/concord/plotting/pl_benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,958   copying build/lib/concord/plotting/pl_datacoverage.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,960   copying build/lib/concord/plotting/pl_general.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,963   copying build/lib/concord/plotting/pl_embedding.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,966   copying build/lib/concord/plotting/pl_path.py -> build/bdist.linux-armv7l/wheel/./concord/plotting
2025-06-01T02:25:15,969   copying build/lib/concord/__init__.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-01T02:25:15,972   creating build/bdist.linux-armv7l/wheel/concord/benchmarking
2025-06-01T02:25:15,973   copying build/lib/concord/benchmarking/geometry.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-01T02:25:15,976   copying build/lib/concord/benchmarking/time_memory.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-01T02:25:15,979   copying build/lib/concord/benchmarking/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-01T02:25:15,981   copying build/lib/concord/benchmarking/linear_probe.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-01T02:25:15,984   copying build/lib/concord/benchmarking/benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-01T02:25:15,988   copying build/lib/concord/benchmarking/pipeline_dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-01T02:25:15,991   copying build/lib/concord/benchmarking/tda.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-01T02:25:15,993   copying build/lib/concord/benchmarking/pipeline_integration.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-01T02:25:15,996   copying build/lib/concord/benchmarking/integration_methods.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-01T02:25:15,999   copying build/lib/concord/benchmarking/knn_probe.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking
2025-06-01T02:25:16,002   copying build/lib/concord/ul.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-01T02:25:16,004   copying build/lib/concord/sm.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-01T02:25:16,007   creating build/bdist.linux-armv7l/wheel/concord/model
2025-06-01T02:25:16,009   copying build/lib/concord/model/anndataset.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-01T02:25:16,012   copying build/lib/concord/model/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-01T02:25:16,014   copying build/lib/concord/model/sampler.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-01T02:25:16,017   copying build/lib/concord/model/dataloader.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-01T02:25:16,020   copying build/lib/concord/model/chunkloader.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-01T02:25:16,022   copying build/lib/concord/model/trainer.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-01T02:25:16,026   copying build/lib/concord/model/loss.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-01T02:25:16,028   copying build/lib/concord/model/knn.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-01T02:25:16,031   copying build/lib/concord/model/model.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-01T02:25:16,034   copying build/lib/concord/model/build_layer.py -> build/bdist.linux-armv7l/wheel/./concord/model
2025-06-01T02:25:16,037   copying build/lib/concord/bm.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-01T02:25:16,039   copying build/lib/concord/ml.py -> build/bdist.linux-armv7l/wheel/./concord
2025-06-01T02:25:16,041   running install_egg_info
2025-06-01T02:25:16,080   running egg_info
2025-06-01T02:25:16,111   writing src/concord_sc.egg-info/PKG-INFO
2025-06-01T02:25:16,118   writing dependency_links to src/concord_sc.egg-info/dependency_links.txt
2025-06-01T02:25:16,122   writing requirements to src/concord_sc.egg-info/requires.txt
2025-06-01T02:25:16,123   writing top-level names to src/concord_sc.egg-info/top_level.txt
2025-06-01T02:25:16,163   reading manifest file 'src/concord_sc.egg-info/SOURCES.txt'
2025-06-01T02:25:16,169   adding license file 'LICENSE.md'
2025-06-01T02:25:16,174   writing manifest file 'src/concord_sc.egg-info/SOURCES.txt'
2025-06-01T02:25:16,176   Copying src/concord_sc.egg-info to build/bdist.linux-armv7l/wheel/./concord_sc-1.0.4-py3.11.egg-info
2025-06-01T02:25:16,188   running install_scripts
2025-06-01T02:25:16,200   creating build/bdist.linux-armv7l/wheel/concord_sc-1.0.4.dist-info/WHEEL
2025-06-01T02:25:16,203   creating '/tmp/pip-wheel-5elhur3x/concord_sc-1.0.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-01T02:25:16,207   adding 'concord/__init__.py'
2025-06-01T02:25:16,209   adding 'concord/bm.py'
2025-06-01T02:25:16,216   adding 'concord/concord.py'
2025-06-01T02:25:16,219   adding 'concord/ml.py'
2025-06-01T02:25:16,221   adding 'concord/pl.py'
2025-06-01T02:25:16,222   adding 'concord/sm.py'
2025-06-01T02:25:16,224   adding 'concord/ul.py'
2025-06-01T02:25:16,226   adding 'concord/benchmarking/__init__.py'
2025-06-01T02:25:16,233   adding 'concord/benchmarking/benchmark.py'
2025-06-01T02:25:16,235   adding 'concord/benchmarking/geometry.py'
2025-06-01T02:25:16,238   adding 'concord/benchmarking/integration_methods.py'
2025-06-01T02:25:16,240   adding 'concord/benchmarking/knn_probe.py'
2025-06-01T02:25:16,243   adding 'concord/benchmarking/linear_probe.py'
2025-06-01T02:25:16,245   adding 'concord/benchmarking/pipeline_dim_reduction.py'
2025-06-01T02:25:16,247   adding 'concord/benchmarking/pipeline_integration.py'
2025-06-01T02:25:16,250   adding 'concord/benchmarking/tda.py'
2025-06-01T02:25:16,251   adding 'concord/benchmarking/time_memory.py'
2025-06-01T02:25:16,253   adding 'concord/model/__init__.py'
2025-06-01T02:25:16,255   adding 'concord/model/anndataset.py'
2025-06-01T02:25:16,256   adding 'concord/model/build_layer.py'
2025-06-01T02:25:16,257   adding 'concord/model/chunkloader.py'
2025-06-01T02:25:16,259   adding 'concord/model/dataloader.py'
2025-06-01T02:25:16,261   adding 'concord/model/knn.py'
2025-06-01T02:25:16,263   adding 'concord/model/loss.py'
2025-06-01T02:25:16,265   adding 'concord/model/model.py'
2025-06-01T02:25:16,267   adding 'concord/model/sampler.py'
2025-06-01T02:25:16,269   adding 'concord/model/trainer.py'
2025-06-01T02:25:16,271   adding 'concord/plotting/__init__.py'
2025-06-01T02:25:16,273   adding 'concord/plotting/palettes.py'
2025-06-01T02:25:16,275   adding 'concord/plotting/pl_batch.py'
2025-06-01T02:25:16,277   adding 'concord/plotting/pl_benchmark.py'
2025-06-01T02:25:16,279   adding 'concord/plotting/pl_datacoverage.py'
2025-06-01T02:25:16,285   adding 'concord/plotting/pl_embedding.py'
2025-06-01T02:25:16,288   adding 'concord/plotting/pl_enrichment.py'
2025-06-01T02:25:16,289   adding 'concord/plotting/pl_general.py'
2025-06-01T02:25:16,291   adding 'concord/plotting/pl_geometry.py'
2025-06-01T02:25:16,294   adding 'concord/plotting/pl_graph.py'
2025-06-01T02:25:16,296   adding 'concord/plotting/pl_heatmap.py'
2025-06-01T02:25:16,298   adding 'concord/plotting/pl_model.py'
2025-06-01T02:25:16,299   adding 'concord/plotting/pl_path.py'
2025-06-01T02:25:16,301   adding 'concord/plotting/pl_tda.py'
2025-06-01T02:25:16,303   adding 'concord/simulation/__init__.py'
2025-06-01T02:25:16,308   adding 'concord/simulation/simulation.py'
2025-06-01T02:25:16,310   adding 'concord/utils/Hs_Mm_conversion.py'
2025-06-01T02:25:16,311   adding 'concord/utils/__init__.py'
2025-06-01T02:25:16,314   adding 'concord/utils/anndata_utils.py'
2025-06-01T02:25:16,315   adding 'concord/utils/batch_analysis.py'
2025-06-01T02:25:16,316   adding 'concord/utils/cell_cycle.py'
2025-06-01T02:25:16,318   adding 'concord/utils/coverage_estimator.py'
2025-06-01T02:25:16,319   adding 'concord/utils/dim_reduction.py'
2025-06-01T02:25:16,321   adding 'concord/utils/doublet_utils.py'
2025-06-01T02:25:16,323   adding 'concord/utils/enrichment_analysis.py'
2025-06-01T02:25:16,324   adding 'concord/utils/estimate_dropout_rate.py'
2025-06-01T02:25:16,326   adding 'concord/utils/feature_selector.py'
2025-06-01T02:25:16,328   adding 'concord/utils/importance_analysis.py'
2025-06-01T02:25:16,329   adding 'concord/utils/io.py'
2025-06-01T02:25:16,331   adding 'concord/utils/other_util.py'
2025-06-01T02:25:16,333   adding 'concord/utils/path_analysis.py'
2025-06-01T02:25:16,334   adding 'concord/utils/value_check.py'
2025-06-01T02:25:16,336   adding 'concord/utils/visCello.py'
2025-06-01T02:25:16,339   adding 'concord_sc-1.0.4.dist-info/licenses/LICENSE.md'
2025-06-01T02:25:16,341   adding 'concord_sc-1.0.4.dist-info/METADATA'
2025-06-01T02:25:16,342   adding 'concord_sc-1.0.4.dist-info/WHEEL'
2025-06-01T02:25:16,343   adding 'concord_sc-1.0.4.dist-info/top_level.txt'
2025-06-01T02:25:16,345   adding 'concord_sc-1.0.4.dist-info/RECORD'
2025-06-01T02:25:16,349   removing build/bdist.linux-armv7l/wheel
2025-06-01T02:25:16,476   Building wheel for concord-sc (setup.py): finished with status 'done'
2025-06-01T02:25:16,480   Created wheel for concord-sc: filename=concord_sc-1.0.4-py3-none-any.whl size=151743 sha256=37e5176cae853d570c2c912c757161b3361f579480efd9bdb7be6cd6c792da7c
2025-06-01T02:25:16,481   Stored in directory: /tmp/pip-ephem-wheel-cache-ww1f57ss/wheels/17/a7/70/2959e4a719a39e3eaad99f36c1bf08d96bc3f16dfacbb4140d
2025-06-01T02:25:16,495 Successfully built concord-sc
2025-06-01T02:25:16,506 Removed build tracker: '/tmp/pip-build-tracker-fmg1h8a7'