2025-09-16T19:52:13,183 Created temporary directory: /tmp/pip-build-tracker-5ej6oxpo 2025-09-16T19:52:13,184 Initialized build tracking at /tmp/pip-build-tracker-5ej6oxpo 2025-09-16T19:52:13,185 Created build tracker: /tmp/pip-build-tracker-5ej6oxpo 2025-09-16T19:52:13,185 Entered build tracker: /tmp/pip-build-tracker-5ej6oxpo 2025-09-16T19:52:13,186 Created temporary directory: /tmp/pip-wheel-hovctz7h 2025-09-16T19:52:13,190 Created temporary directory: /tmp/pip-ephem-wheel-cache-13o7106t 2025-09-16T19:52:13,238 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-16T19:52:13,241 2 location(s) to search for versions of concord-sc: 2025-09-16T19:52:13,241 * https://pypi.org/simple/concord-sc/ 2025-09-16T19:52:13,241 * https://www.piwheels.org/simple/concord-sc/ 2025-09-16T19:52:13,242 Fetching project page and analyzing links: https://pypi.org/simple/concord-sc/ 2025-09-16T19:52:13,242 Getting page https://pypi.org/simple/concord-sc/ 2025-09-16T19:52:13,244 Found index url https://pypi.org/simple/ 2025-09-16T19:52:13,473 Fetched page https://pypi.org/simple/concord-sc/ as application/vnd.pypi.simple.v1+json 2025-09-16T19:52:13,477 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) 2025-09-16T19:52:13,478 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 2025-09-16T19:52:13,479 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) 2025-09-16T19:52:13,479 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 2025-09-16T19:52:13,480 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) 2025-09-16T19:52:13,481 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 2025-09-16T19:52:13,481 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) 2025-09-16T19:52:13,482 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 2025-09-16T19:52:13,482 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) 2025-09-16T19:52:13,483 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 2025-09-16T19:52:13,483 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) 2025-09-16T19:52:13,484 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 2025-09-16T19:52:13,485 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) 2025-09-16T19:52:13,485 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 2025-09-16T19:52:13,486 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) 2025-09-16T19:52:13,486 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 2025-09-16T19:52:13,487 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) 2025-09-16T19:52:13,487 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 2025-09-16T19:52:13,488 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) 2025-09-16T19:52:13,488 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 2025-09-16T19:52:13,489 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) 2025-09-16T19:52:13,489 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 2025-09-16T19:52:13,490 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) 2025-09-16T19:52:13,491 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 2025-09-16T19:52:13,491 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/c0/d0/cf82523f3d6b9efca8e7e6f1565e24621dcfc6ccb1e8e07b94ae5f149b1f/concord_sc-1.0.8-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,492 Found link https://files.pythonhosted.org/packages/12/b8/b36c4e4e0d26a0926f5ffea28db97e4fb94f16d3260320fe23c7275f0281/concord_sc-1.0.8.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 1.0.8 2025-09-16T19:52:13,492 Skipping link: No binaries permitted for concord-sc: https://files.pythonhosted.org/packages/09/83/28cd1289a0de2d6ad4b6ecc98aebf1ceea73d9d2a5b72a1685c28396cbb3/concord_sc-1.0.9-py3-none-any.whl (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,493 Found link https://files.pythonhosted.org/packages/28/53/f5585b031a9af89f66ae0b437116ce7b80f00b041cd73c4544db75e8b0b0/concord_sc-1.0.9.tar.gz (from https://pypi.org/simple/concord-sc/) (requires-python:>=3.7), version: 1.0.9 2025-09-16T19:52:13,494 Fetching project page and analyzing links: https://www.piwheels.org/simple/concord-sc/ 2025-09-16T19:52:13,494 Getting page https://www.piwheels.org/simple/concord-sc/ 2025-09-16T19:52:13,496 Found index url https://www.piwheels.org/simple/ 2025-09-16T19:52:13,668 Fetched page https://www.piwheels.org/simple/concord-sc/ as text/html 2025-09-16T19:52:13,672 Skipping link: No binaries permitted for concord-sc: https://www.piwheels.org/simple/concord-sc/concord_sc-1.0.8-py3-none-any.whl#sha256=391cca75481163cf433645f1514aa26cb5b389b1b777765338d3634d9366b910 (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,673 Skipping link: No binaries permitted for concord-sc: https://archive1.piwheels.org/simple/concord-sc/concord_sc-1.0.7-py3-none-any.whl#sha256=6f9ab22e15d1d7435b46b2d3dca82e607c397231133668c18fc62127ba845533 (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,673 Skipping link: No binaries permitted for concord-sc: https://archive1.piwheels.org/simple/concord-sc/concord_sc-1.0.6-py3-none-any.whl#sha256=ac94c5b70d82511fc03bbc94cc5717a4375f2b7550eb56cb0a665ed879cbbe4b (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,674 Skipping link: No binaries permitted for concord-sc: https://archive1.piwheels.org/simple/concord-sc/concord_sc-1.0.4-py3-none-any.whl#sha256=37e5176cae853d570c2c912c757161b3361f579480efd9bdb7be6cd6c792da7c (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,674 Skipping link: No binaries permitted for concord-sc: https://archive1.piwheels.org/simple/concord-sc/concord_sc-1.0.0-py3-none-any.whl#sha256=5f63b8a066b73cd4b7e4bf385d296d3498413f733fd294a7926d13a7de439652 (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,675 Skipping link: No binaries permitted for concord-sc: https://archive1.piwheels.org/simple/concord-sc/concord_sc-0.9.7-py3-none-any.whl#sha256=3cef1a7cbb0ad4d86b9a59e18714d7ae5cc36464d93a5cc32c14e77e9b250f2b (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,675 Skipping link: No binaries permitted for concord-sc: https://archive1.piwheels.org/simple/concord-sc/concord_sc-0.9.6-py3-none-any.whl#sha256=f1901b2404d6ddebb76cb5b640d0adc977b292f605f2fc39befac054a91dfc6d (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,676 Skipping link: No binaries permitted for concord-sc: https://archive1.piwheels.org/simple/concord-sc/concord_sc-0.9.5-py3-none-any.whl#sha256=77d4ddcd59ad8d9cb04d3a6d2ef5a4299f02777d040b794e5aa2aa67e447b116 (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,676 Skipping link: No binaries permitted for concord-sc: https://archive1.piwheels.org/simple/concord-sc/concord_sc-0.9.4-py3-none-any.whl#sha256=f5dfb4611bdc7ccdd08d2dcd716401b469adfbf32e8f43de38aa0e7afe9a6fc5 (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,677 Skipping link: No binaries permitted for concord-sc: https://archive1.piwheels.org/simple/concord-sc/concord_sc-0.9.3-py3-none-any.whl#sha256=be9cb0040eec5c281a717a4281bd3770b4a7c8213a85987a756d851eebf9cc9e (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,677 Skipping link: No binaries permitted for concord-sc: https://archive1.piwheels.org/simple/concord-sc/concord_sc-0.9.2-py3-none-any.whl#sha256=2263638f4ef6f3e6df29d54592c25736b9a14216e330e882a6388719764b7cc9 (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,678 Skipping link: No binaries permitted for concord-sc: https://archive1.piwheels.org/simple/concord-sc/concord_sc-0.9.1-py3-none-any.whl#sha256=3c3bb2a442ae740b18ca16a7516ab62e95c70d1f9d72ff7aa73af475afd0a252 (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,679 Skipping link: No binaries permitted for concord-sc: https://archive1.piwheels.org/simple/concord-sc/concord_sc-0.9.0-py3-none-any.whl#sha256=ef419331e55fc96cb1955de0be8fc00d13975ddc65b2ac9381510e06ff4412d8 (from https://www.piwheels.org/simple/concord-sc/) (requires-python:>=3.7) 2025-09-16T19:52:13,679 Skipping link: not a file: https://www.piwheels.org/simple/concord-sc/ 2025-09-16T19:52:13,679 Skipping link: not a file: https://pypi.org/simple/concord-sc/ 2025-09-16T19:52:13,698 Given no hashes to check 1 links for project 'concord-sc': discarding no candidates 2025-09-16T19:52:13,700 Collecting concord-sc==1.0.9 2025-09-16T19:52:13,702 Created temporary directory: /tmp/pip-unpack-kat83_y8 2025-09-16T19:52:13,925 Downloading concord_sc-1.0.9.tar.gz (143 kB) 2025-09-16T19:52:14,191 Added concord-sc==1.0.9 from https://files.pythonhosted.org/packages/28/53/f5585b031a9af89f66ae0b437116ce7b80f00b041cd73c4544db75e8b0b0/concord_sc-1.0.9.tar.gz to build tracker '/tmp/pip-build-tracker-5ej6oxpo' 2025-09-16T19:52:14,193 Running setup.py (path:/tmp/pip-wheel-hovctz7h/concord-sc_8e136ab45f4c48fda9770cb1e3de016b/setup.py) egg_info for package concord-sc 2025-09-16T19:52:14,194 Created temporary directory: /tmp/pip-pip-egg-info-6g7vtbeh 2025-09-16T19:52:14,195 Preparing metadata (setup.py): started 2025-09-16T19:52:14,196 Running command python setup.py egg_info 2025-09-16T19:52:15,037 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-16T19:52:15,038 !! 2025-09-16T19:52:15,039 ******************************************************************************** 2025-09-16T19:52:15,039 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-16T19:52:15,040 License :: OSI Approved :: MIT License 2025-09-16T19:52:15,041 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-16T19:52:15,042 ******************************************************************************** 2025-09-16T19:52:15,043 !! 2025-09-16T19:52:15,043 self._finalize_license_expression() 2025-09-16T19:52:15,066 running egg_info 2025-09-16T19:52:15,092 creating /tmp/pip-pip-egg-info-6g7vtbeh/concord_sc.egg-info 2025-09-16T19:52:15,093 writing /tmp/pip-pip-egg-info-6g7vtbeh/concord_sc.egg-info/PKG-INFO 2025-09-16T19:52:15,099 writing dependency_links to /tmp/pip-pip-egg-info-6g7vtbeh/concord_sc.egg-info/dependency_links.txt 2025-09-16T19:52:15,102 writing requirements to /tmp/pip-pip-egg-info-6g7vtbeh/concord_sc.egg-info/requires.txt 2025-09-16T19:52:15,103 writing top-level names to /tmp/pip-pip-egg-info-6g7vtbeh/concord_sc.egg-info/top_level.txt 2025-09-16T19:52:15,105 writing manifest file '/tmp/pip-pip-egg-info-6g7vtbeh/concord_sc.egg-info/SOURCES.txt' 2025-09-16T19:52:15,194 reading manifest file '/tmp/pip-pip-egg-info-6g7vtbeh/concord_sc.egg-info/SOURCES.txt' 2025-09-16T19:52:15,196 adding license file 'LICENSE.md' 2025-09-16T19:52:15,200 writing manifest file '/tmp/pip-pip-egg-info-6g7vtbeh/concord_sc.egg-info/SOURCES.txt' 2025-09-16T19:52:15,305 Preparing metadata (setup.py): finished with status 'done' 2025-09-16T19:52:15,309 Source in /tmp/pip-wheel-hovctz7h/concord-sc_8e136ab45f4c48fda9770cb1e3de016b has version 1.0.9, which satisfies requirement concord-sc==1.0.9 from https://files.pythonhosted.org/packages/28/53/f5585b031a9af89f66ae0b437116ce7b80f00b041cd73c4544db75e8b0b0/concord_sc-1.0.9.tar.gz 2025-09-16T19:52:15,310 Removed concord-sc==1.0.9 from https://files.pythonhosted.org/packages/28/53/f5585b031a9af89f66ae0b437116ce7b80f00b041cd73c4544db75e8b0b0/concord_sc-1.0.9.tar.gz from build tracker '/tmp/pip-build-tracker-5ej6oxpo' 2025-09-16T19:52:15,321 Created temporary directory: /tmp/pip-unpack-2n7rfzj6 2025-09-16T19:52:15,322 Created temporary directory: /tmp/pip-unpack-d1hrd9ka 2025-09-16T19:52:15,323 Building wheels for collected packages: concord-sc 2025-09-16T19:52:15,327 Created temporary directory: /tmp/pip-wheel-mzfn1hrj 2025-09-16T19:52:15,327 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 2025-09-16T19:52:15,329 Building wheel for concord-sc (setup.py): started 2025-09-16T19:52:15,330 Destination directory: /tmp/pip-wheel-mzfn1hrj 2025-09-16T19:52:15,330 Running command python setup.py bdist_wheel 2025-09-16T19:52:16,140 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-16T19:52:16,140 !! 2025-09-16T19:52:16,141 ******************************************************************************** 2025-09-16T19:52:16,142 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-16T19:52:16,143 License :: OSI Approved :: MIT License 2025-09-16T19:52:16,143 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-16T19:52:16,144 ******************************************************************************** 2025-09-16T19:52:16,145 !! 2025-09-16T19:52:16,145 self._finalize_license_expression() 2025-09-16T19:52:16,146 running bdist_wheel 2025-09-16T19:52:16,267 running build 2025-09-16T19:52:16,267 running build_py 2025-09-16T19:52:16,296 creating build/lib/concord 2025-09-16T19:52:16,298 copying src/concord/ul.py -> build/lib/concord 2025-09-16T19:52:16,300 copying src/concord/__init__.py -> build/lib/concord 2025-09-16T19:52:16,302 copying src/concord/bm.py -> build/lib/concord 2025-09-16T19:52:16,304 copying src/concord/pl.py -> build/lib/concord 2025-09-16T19:52:16,305 copying src/concord/ml.py -> build/lib/concord 2025-09-16T19:52:16,307 copying src/concord/sm.py -> build/lib/concord 2025-09-16T19:52:16,309 copying src/concord/concord.py -> build/lib/concord 2025-09-16T19:52:16,313 creating build/lib/concord/utils 2025-09-16T19:52:16,314 copying src/concord/utils/__init__.py -> build/lib/concord/utils 2025-09-16T19:52:16,316 copying src/concord/utils/doublet_utils.py -> build/lib/concord/utils 2025-09-16T19:52:16,318 copying src/concord/utils/cell_cycle.py -> build/lib/concord/utils 2025-09-16T19:52:16,320 copying src/concord/utils/io.py -> build/lib/concord/utils 2025-09-16T19:52:16,322 copying src/concord/utils/batch_analysis.py -> build/lib/concord/utils 2025-09-16T19:52:16,323 copying src/concord/utils/integration_methods.py -> build/lib/concord/utils 2025-09-16T19:52:16,326 copying src/concord/utils/visCello.py -> build/lib/concord/utils 2025-09-16T19:52:16,328 copying src/concord/utils/feature_selector.py -> build/lib/concord/utils 2025-09-16T19:52:16,330 copying src/concord/utils/dim_reduction.py -> build/lib/concord/utils 2025-09-16T19:52:16,332 copying src/concord/utils/anndata_utils.py -> build/lib/concord/utils 2025-09-16T19:52:16,335 copying src/concord/utils/value_check.py -> build/lib/concord/utils 2025-09-16T19:52:16,337 copying src/concord/utils/estimate_dropout_rate.py -> build/lib/concord/utils 2025-09-16T19:52:16,338 copying src/concord/utils/other_util.py -> build/lib/concord/utils 2025-09-16T19:52:16,340 copying src/concord/utils/enrichment_analysis.py -> build/lib/concord/utils 2025-09-16T19:52:16,342 copying src/concord/utils/Hs_Mm_conversion.py -> build/lib/concord/utils 2025-09-16T19:52:16,344 copying src/concord/utils/path_analysis.py -> build/lib/concord/utils 2025-09-16T19:52:16,346 copying src/concord/utils/importance_analysis.py -> build/lib/concord/utils 2025-09-16T19:52:16,348 copying src/concord/utils/coverage_estimator.py -> build/lib/concord/utils 2025-09-16T19:52:16,351 creating build/lib/concord/model 2025-09-16T19:52:16,352 copying src/concord/model/augment.py -> build/lib/concord/model 2025-09-16T19:52:16,354 copying src/concord/model/chunkloader.py -> build/lib/concord/model 2025-09-16T19:52:16,355 copying src/concord/model/loss.py -> build/lib/concord/model 2025-09-16T19:52:16,357 copying src/concord/model/__init__.py -> build/lib/concord/model 2025-09-16T19:52:16,359 copying src/concord/model/sampler.py -> build/lib/concord/model 2025-09-16T19:52:16,361 copying src/concord/model/knn.py -> build/lib/concord/model 2025-09-16T19:52:16,363 copying src/concord/model/trainer.py -> build/lib/concord/model 2025-09-16T19:52:16,366 copying src/concord/model/model.py -> build/lib/concord/model 2025-09-16T19:52:16,368 copying src/concord/model/anndataset.py -> build/lib/concord/model 2025-09-16T19:52:16,370 copying src/concord/model/dataloader.py -> build/lib/concord/model 2025-09-16T19:52:16,372 copying src/concord/model/build_layer.py -> build/lib/concord/model 2025-09-16T19:52:16,374 creating build/lib/concord/benchmarking 2025-09-16T19:52:16,375 copying src/concord/benchmarking/__init__.py -> build/lib/concord/benchmarking 2025-09-16T19:52:16,378 copying src/concord/benchmarking/pipeline_dim_reduction.py -> build/lib/concord/benchmarking 2025-09-16T19:52:16,380 copying src/concord/benchmarking/tda.py -> build/lib/concord/benchmarking 2025-09-16T19:52:16,382 copying src/concord/benchmarking/knn_probe.py -> build/lib/concord/benchmarking 2025-09-16T19:52:16,385 copying src/concord/benchmarking/linear_probe.py -> build/lib/concord/benchmarking 2025-09-16T19:52:16,387 copying src/concord/benchmarking/benchmark.py -> build/lib/concord/benchmarking 2025-09-16T19:52:16,390 copying src/concord/benchmarking/geometry.py -> build/lib/concord/benchmarking 2025-09-16T19:52:16,392 copying src/concord/benchmarking/pipeline_integration.py -> build/lib/concord/benchmarking 2025-09-16T19:52:16,395 copying src/concord/benchmarking/time_memory.py -> build/lib/concord/benchmarking 2025-09-16T19:52:16,397 creating build/lib/concord/simulation 2025-09-16T19:52:16,398 copying src/concord/simulation/__init__.py -> build/lib/concord/simulation 2025-09-16T19:52:16,400 copying src/concord/simulation/simulation.py -> build/lib/concord/simulation 2025-09-16T19:52:16,403 copying src/concord/simulation/advanced_helper.py -> build/lib/concord/simulation 2025-09-16T19:52:16,406 creating build/lib/concord/plotting 2025-09-16T19:52:16,407 copying src/concord/plotting/pl_general.py -> build/lib/concord/plotting 2025-09-16T19:52:16,409 copying src/concord/plotting/pl_graph.py -> build/lib/concord/plotting 2025-09-16T19:52:16,412 copying src/concord/plotting/pl_batch.py -> build/lib/concord/plotting 2025-09-16T19:52:16,413 copying src/concord/plotting/__init__.py -> build/lib/concord/plotting 2025-09-16T19:52:16,415 copying src/concord/plotting/pl_geometry.py -> build/lib/concord/plotting 2025-09-16T19:52:16,418 copying src/concord/plotting/palettes.py -> build/lib/concord/plotting 2025-09-16T19:52:16,420 copying src/concord/plotting/pl_benchmark.py -> build/lib/concord/plotting 2025-09-16T19:52:16,422 copying src/concord/plotting/pl_tda.py -> build/lib/concord/plotting 2025-09-16T19:52:16,425 copying src/concord/plotting/pl_heatmap.py -> build/lib/concord/plotting 2025-09-16T19:52:16,427 copying src/concord/plotting/pl_model.py -> build/lib/concord/plotting 2025-09-16T19:52:16,429 copying src/concord/plotting/pl_path.py -> build/lib/concord/plotting 2025-09-16T19:52:16,431 copying src/concord/plotting/pl_embedding.py -> build/lib/concord/plotting 2025-09-16T19:52:16,434 copying src/concord/plotting/pl_datacoverage.py -> build/lib/concord/plotting 2025-09-16T19:52:16,436 copying src/concord/plotting/pl_enrichment.py -> build/lib/concord/plotting 2025-09-16T19:52:16,470 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-16T19:52:16,471 !! 2025-09-16T19:52:16,472 ******************************************************************************** 2025-09-16T19:52:16,472 Please avoid running ``setup.py`` directly. 2025-09-16T19:52:16,473 Instead, use pypa/build, pypa/installer or other 2025-09-16T19:52:16,473 standards-based tools. 2025-09-16T19:52:16,474 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-16T19:52:16,475 or your builds will no longer be supported. 2025-09-16T19:52:16,476 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-16T19:52:16,476 ******************************************************************************** 2025-09-16T19:52:16,477 !! 2025-09-16T19:52:16,478 self.initialize_options() 2025-09-16T19:52:16,498 installing to build/bdist.linux-armv7l/wheel 2025-09-16T19:52:16,498 running install 2025-09-16T19:52:16,522 running install_lib 2025-09-16T19:52:16,549 creating build/bdist.linux-armv7l/wheel 2025-09-16T19:52:16,551 creating build/bdist.linux-armv7l/wheel/concord 2025-09-16T19:52:16,552 copying build/lib/concord/ul.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-16T19:52:16,554 copying build/lib/concord/__init__.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-16T19:52:16,556 creating build/bdist.linux-armv7l/wheel/concord/utils 2025-09-16T19:52:16,557 copying build/lib/concord/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,559 copying build/lib/concord/utils/doublet_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,561 copying build/lib/concord/utils/cell_cycle.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,563 copying build/lib/concord/utils/io.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,565 copying build/lib/concord/utils/batch_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,566 copying build/lib/concord/utils/integration_methods.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,569 copying build/lib/concord/utils/visCello.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,571 copying build/lib/concord/utils/feature_selector.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,573 copying build/lib/concord/utils/dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,576 copying build/lib/concord/utils/anndata_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,578 copying build/lib/concord/utils/value_check.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,580 copying build/lib/concord/utils/estimate_dropout_rate.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,582 copying build/lib/concord/utils/other_util.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,583 copying build/lib/concord/utils/enrichment_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,585 copying build/lib/concord/utils/Hs_Mm_conversion.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,587 copying build/lib/concord/utils/path_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,590 copying build/lib/concord/utils/importance_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,591 copying build/lib/concord/utils/coverage_estimator.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-16T19:52:16,593 copying build/lib/concord/bm.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-16T19:52:16,595 copying build/lib/concord/pl.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-16T19:52:16,597 creating build/bdist.linux-armv7l/wheel/concord/model 2025-09-16T19:52:16,598 copying build/lib/concord/model/augment.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-16T19:52:16,600 copying build/lib/concord/model/chunkloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-16T19:52:16,602 copying build/lib/concord/model/loss.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-16T19:52:16,604 copying build/lib/concord/model/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-16T19:52:16,606 copying build/lib/concord/model/sampler.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-16T19:52:16,608 copying build/lib/concord/model/knn.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-16T19:52:16,610 copying build/lib/concord/model/trainer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-16T19:52:16,612 copying build/lib/concord/model/model.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-16T19:52:16,615 copying build/lib/concord/model/anndataset.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-16T19:52:16,617 copying build/lib/concord/model/dataloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-16T19:52:16,619 copying build/lib/concord/model/build_layer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-16T19:52:16,621 copying build/lib/concord/ml.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-16T19:52:16,622 copying build/lib/concord/sm.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-16T19:52:16,625 creating build/bdist.linux-armv7l/wheel/concord/benchmarking 2025-09-16T19:52:16,626 copying build/lib/concord/benchmarking/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-16T19:52:16,627 copying build/lib/concord/benchmarking/pipeline_dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-16T19:52:16,630 copying build/lib/concord/benchmarking/tda.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-16T19:52:16,632 copying build/lib/concord/benchmarking/knn_probe.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-16T19:52:16,634 copying build/lib/concord/benchmarking/linear_probe.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-16T19:52:16,636 copying build/lib/concord/benchmarking/benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-16T19:52:16,639 copying build/lib/concord/benchmarking/geometry.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-16T19:52:16,641 copying build/lib/concord/benchmarking/pipeline_integration.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-16T19:52:16,643 copying build/lib/concord/benchmarking/time_memory.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-16T19:52:16,646 copying build/lib/concord/concord.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-16T19:52:16,649 creating build/bdist.linux-armv7l/wheel/concord/simulation 2025-09-16T19:52:16,650 copying build/lib/concord/simulation/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/simulation 2025-09-16T19:52:16,652 copying build/lib/concord/simulation/simulation.py -> build/bdist.linux-armv7l/wheel/./concord/simulation 2025-09-16T19:52:16,655 copying build/lib/concord/simulation/advanced_helper.py -> build/bdist.linux-armv7l/wheel/./concord/simulation 2025-09-16T19:52:16,658 creating build/bdist.linux-armv7l/wheel/concord/plotting 2025-09-16T19:52:16,659 copying build/lib/concord/plotting/pl_general.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,661 copying build/lib/concord/plotting/pl_graph.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,663 copying build/lib/concord/plotting/pl_batch.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,665 copying build/lib/concord/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,667 copying build/lib/concord/plotting/pl_geometry.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,669 copying build/lib/concord/plotting/palettes.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,671 copying build/lib/concord/plotting/pl_benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,673 copying build/lib/concord/plotting/pl_tda.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,676 copying build/lib/concord/plotting/pl_heatmap.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,678 copying build/lib/concord/plotting/pl_model.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,680 copying build/lib/concord/plotting/pl_path.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,682 copying build/lib/concord/plotting/pl_embedding.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,685 copying build/lib/concord/plotting/pl_datacoverage.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,687 copying build/lib/concord/plotting/pl_enrichment.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-16T19:52:16,689 running install_egg_info 2025-09-16T19:52:16,721 running egg_info 2025-09-16T19:52:16,750 writing src/concord_sc.egg-info/PKG-INFO 2025-09-16T19:52:16,756 writing dependency_links to src/concord_sc.egg-info/dependency_links.txt 2025-09-16T19:52:16,759 writing requirements to src/concord_sc.egg-info/requires.txt 2025-09-16T19:52:16,761 writing top-level names to src/concord_sc.egg-info/top_level.txt 2025-09-16T19:52:16,796 reading manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-09-16T19:52:16,801 adding license file 'LICENSE.md' 2025-09-16T19:52:16,807 writing manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-09-16T19:52:16,808 Copying src/concord_sc.egg-info to build/bdist.linux-armv7l/wheel/./concord_sc-1.0.9-py3.11.egg-info 2025-09-16T19:52:16,818 running install_scripts 2025-09-16T19:52:16,830 creating build/bdist.linux-armv7l/wheel/concord_sc-1.0.9.dist-info/WHEEL 2025-09-16T19:52:16,833 creating '/tmp/pip-wheel-mzfn1hrj/concord_sc-1.0.9-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-16T19:52:16,835 adding 'concord/__init__.py' 2025-09-16T19:52:16,836 adding 'concord/bm.py' 2025-09-16T19:52:16,842 adding 'concord/concord.py' 2025-09-16T19:52:16,844 adding 'concord/ml.py' 2025-09-16T19:52:16,845 adding 'concord/pl.py' 2025-09-16T19:52:16,846 adding 'concord/sm.py' 2025-09-16T19:52:16,847 adding 'concord/ul.py' 2025-09-16T19:52:16,849 adding 'concord/benchmarking/__init__.py' 2025-09-16T19:52:16,855 adding 'concord/benchmarking/benchmark.py' 2025-09-16T19:52:16,857 adding 'concord/benchmarking/geometry.py' 2025-09-16T19:52:16,859 adding 'concord/benchmarking/knn_probe.py' 2025-09-16T19:52:16,861 adding 'concord/benchmarking/linear_probe.py' 2025-09-16T19:52:16,863 adding 'concord/benchmarking/pipeline_dim_reduction.py' 2025-09-16T19:52:16,865 adding 'concord/benchmarking/pipeline_integration.py' 2025-09-16T19:52:16,867 adding 'concord/benchmarking/tda.py' 2025-09-16T19:52:16,869 adding 'concord/benchmarking/time_memory.py' 2025-09-16T19:52:16,870 adding 'concord/model/__init__.py' 2025-09-16T19:52:16,872 adding 'concord/model/anndataset.py' 2025-09-16T19:52:16,873 adding 'concord/model/augment.py' 2025-09-16T19:52:16,875 adding 'concord/model/build_layer.py' 2025-09-16T19:52:16,876 adding 'concord/model/chunkloader.py' 2025-09-16T19:52:16,878 adding 'concord/model/dataloader.py' 2025-09-16T19:52:16,880 adding 'concord/model/knn.py' 2025-09-16T19:52:16,882 adding 'concord/model/loss.py' 2025-09-16T19:52:16,883 adding 'concord/model/model.py' 2025-09-16T19:52:16,886 adding 'concord/model/sampler.py' 2025-09-16T19:52:16,888 adding 'concord/model/trainer.py' 2025-09-16T19:52:16,889 adding 'concord/plotting/__init__.py' 2025-09-16T19:52:16,891 adding 'concord/plotting/palettes.py' 2025-09-16T19:52:16,892 adding 'concord/plotting/pl_batch.py' 2025-09-16T19:52:16,894 adding 'concord/plotting/pl_benchmark.py' 2025-09-16T19:52:16,895 adding 'concord/plotting/pl_datacoverage.py' 2025-09-16T19:52:16,902 adding 'concord/plotting/pl_embedding.py' 2025-09-16T19:52:16,904 adding 'concord/plotting/pl_enrichment.py' 2025-09-16T19:52:16,905 adding 'concord/plotting/pl_general.py' 2025-09-16T19:52:16,907 adding 'concord/plotting/pl_geometry.py' 2025-09-16T19:52:16,909 adding 'concord/plotting/pl_graph.py' 2025-09-16T19:52:16,911 adding 'concord/plotting/pl_heatmap.py' 2025-09-16T19:52:16,913 adding 'concord/plotting/pl_model.py' 2025-09-16T19:52:16,914 adding 'concord/plotting/pl_path.py' 2025-09-16T19:52:16,917 adding 'concord/plotting/pl_tda.py' 2025-09-16T19:52:16,918 adding 'concord/simulation/__init__.py' 2025-09-16T19:52:16,920 adding 'concord/simulation/advanced_helper.py' 2025-09-16T19:52:16,925 adding 'concord/simulation/simulation.py' 2025-09-16T19:52:16,927 adding 'concord/utils/Hs_Mm_conversion.py' 2025-09-16T19:52:16,928 adding 'concord/utils/__init__.py' 2025-09-16T19:52:16,930 adding 'concord/utils/anndata_utils.py' 2025-09-16T19:52:16,932 adding 'concord/utils/batch_analysis.py' 2025-09-16T19:52:16,933 adding 'concord/utils/cell_cycle.py' 2025-09-16T19:52:16,934 adding 'concord/utils/coverage_estimator.py' 2025-09-16T19:52:16,936 adding 'concord/utils/dim_reduction.py' 2025-09-16T19:52:16,937 adding 'concord/utils/doublet_utils.py' 2025-09-16T19:52:16,938 adding 'concord/utils/enrichment_analysis.py' 2025-09-16T19:52:16,940 adding 'concord/utils/estimate_dropout_rate.py' 2025-09-16T19:52:16,942 adding 'concord/utils/feature_selector.py' 2025-09-16T19:52:16,943 adding 'concord/utils/importance_analysis.py' 2025-09-16T19:52:16,945 adding 'concord/utils/integration_methods.py' 2025-09-16T19:52:16,946 adding 'concord/utils/io.py' 2025-09-16T19:52:16,948 adding 'concord/utils/other_util.py' 2025-09-16T19:52:16,949 adding 'concord/utils/path_analysis.py' 2025-09-16T19:52:16,950 adding 'concord/utils/value_check.py' 2025-09-16T19:52:16,952 adding 'concord/utils/visCello.py' 2025-09-16T19:52:16,955 adding 'concord_sc-1.0.9.dist-info/licenses/LICENSE.md' 2025-09-16T19:52:16,956 adding 'concord_sc-1.0.9.dist-info/METADATA' 2025-09-16T19:52:16,957 adding 'concord_sc-1.0.9.dist-info/WHEEL' 2025-09-16T19:52:16,958 adding 'concord_sc-1.0.9.dist-info/top_level.txt' 2025-09-16T19:52:16,960 adding 'concord_sc-1.0.9.dist-info/RECORD' 2025-09-16T19:52:16,963 removing build/bdist.linux-armv7l/wheel 2025-09-16T19:52:17,087 Building wheel for concord-sc (setup.py): finished with status 'done' 2025-09-16T19:52:17,091 Created wheel for concord-sc: filename=concord_sc-1.0.9-py3-none-any.whl size=162105 sha256=03316bf3866fcd066cae6b1090a741fc88a0694ec546497672ee9fcb487d4793 2025-09-16T19:52:17,093 Stored in directory: /tmp/pip-ephem-wheel-cache-13o7106t/wheels/23/3c/b3/c9e644154569232e2a1ef52c19cfda13e19ee80fa149128420 2025-09-16T19:52:17,107 Successfully built concord-sc 2025-09-16T19:52:17,114 Removed build tracker: '/tmp/pip-build-tracker-5ej6oxpo'