2025-09-02T15:35:05,342 Created temporary directory: /tmp/pip-build-tracker-4_ibm748 2025-09-02T15:35:05,346 Initialized build tracking at /tmp/pip-build-tracker-4_ibm748 2025-09-02T15:35:05,347 Created build tracker: /tmp/pip-build-tracker-4_ibm748 2025-09-02T15:35:05,348 Entered build tracker: /tmp/pip-build-tracker-4_ibm748 2025-09-02T15:35:05,351 Created temporary directory: /tmp/pip-wheel-d89xyg0b 2025-09-02T15:35:05,356 Created temporary directory: /tmp/pip-ephem-wheel-cache-vukl_hw6 2025-09-02T15:35:05,410 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-02T15:35:05,413 2 location(s) to search for versions of concord-sc: 2025-09-02T15:35:05,413 * https://pypi.org/simple/concord-sc/ 2025-09-02T15:35:05,413 * https://www.piwheels.org/simple/concord-sc/ 2025-09-02T15:35:05,415 Fetching project page and analyzing links: https://pypi.org/simple/concord-sc/ 2025-09-02T15:35:05,416 Getting page https://pypi.org/simple/concord-sc/ 2025-09-02T15:35:05,419 Found index url https://pypi.org/simple/ 2025-09-02T15:35:05,651 Fetched page https://pypi.org/simple/concord-sc/ as application/vnd.pypi.simple.v1+json 2025-09-02T15:35:05,660 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) 2025-09-02T15:35:05,662 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 2025-09-02T15:35:05,663 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) 2025-09-02T15:35:05,664 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 2025-09-02T15:35:05,665 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) 2025-09-02T15:35:05,667 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 2025-09-02T15:35:05,668 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) 2025-09-02T15:35:05,669 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 2025-09-02T15:35:05,670 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) 2025-09-02T15:35:05,670 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 2025-09-02T15:35:05,671 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) 2025-09-02T15:35:05,672 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 2025-09-02T15:35:05,673 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) 2025-09-02T15:35:05,673 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 2025-09-02T15:35:05,674 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) 2025-09-02T15:35:05,674 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 2025-09-02T15:35:05,675 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) 2025-09-02T15:35:05,675 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 2025-09-02T15:35:05,676 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) 2025-09-02T15:35:05,676 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 2025-09-02T15:35:05,677 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) 2025-09-02T15:35:05,678 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 2025-09-02T15:35:05,678 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) 2025-09-02T15:35:05,679 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 2025-09-02T15:35:05,680 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) 2025-09-02T15:35:05,680 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 2025-09-02T15:35:05,681 Fetching project page and analyzing links: https://www.piwheels.org/simple/concord-sc/ 2025-09-02T15:35:05,682 Getting page https://www.piwheels.org/simple/concord-sc/ 2025-09-02T15:35:05,683 Found index url https://www.piwheels.org/simple/ 2025-09-02T15:35:05,875 Fetched page https://www.piwheels.org/simple/concord-sc/ as text/html 2025-09-02T15:35:05,879 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) 2025-09-02T15:35:05,879 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) 2025-09-02T15:35:05,880 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) 2025-09-02T15:35:05,880 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) 2025-09-02T15:35:05,881 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) 2025-09-02T15:35:05,881 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) 2025-09-02T15:35:05,882 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) 2025-09-02T15:35:05,882 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) 2025-09-02T15:35:05,883 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) 2025-09-02T15:35:05,884 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) 2025-09-02T15:35:05,885 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) 2025-09-02T15:35:05,886 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) 2025-09-02T15:35:05,887 Skipping link: not a file: https://www.piwheels.org/simple/concord-sc/ 2025-09-02T15:35:05,888 Skipping link: not a file: https://pypi.org/simple/concord-sc/ 2025-09-02T15:35:05,915 Given no hashes to check 1 links for project 'concord-sc': discarding no candidates 2025-09-02T15:35:05,917 Collecting concord-sc==1.0.8 2025-09-02T15:35:05,919 Created temporary directory: /tmp/pip-unpack-stlru9ta 2025-09-02T15:35:06,172 Downloading concord_sc-1.0.8.tar.gz (142 kB) 2025-09-02T15:35:06,412 Added concord-sc==1.0.8 from https://files.pythonhosted.org/packages/12/b8/b36c4e4e0d26a0926f5ffea28db97e4fb94f16d3260320fe23c7275f0281/concord_sc-1.0.8.tar.gz to build tracker '/tmp/pip-build-tracker-4_ibm748' 2025-09-02T15:35:06,415 Running setup.py (path:/tmp/pip-wheel-d89xyg0b/concord-sc_bdb3ba9d705d4d7b8d3ade53d48c1ca5/setup.py) egg_info for package concord-sc 2025-09-02T15:35:06,416 Created temporary directory: /tmp/pip-pip-egg-info-b3nzx8at 2025-09-02T15:35:06,416 Preparing metadata (setup.py): started 2025-09-02T15:35:06,418 Running command python setup.py egg_info 2025-09-02T15:35:07,291 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-02T15:35:07,291 !! 2025-09-02T15:35:07,292 ******************************************************************************** 2025-09-02T15:35:07,293 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-02T15:35:07,293 License :: OSI Approved :: MIT License 2025-09-02T15:35:07,294 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-02T15:35:07,295 ******************************************************************************** 2025-09-02T15:35:07,296 !! 2025-09-02T15:35:07,297 self._finalize_license_expression() 2025-09-02T15:35:07,319 running egg_info 2025-09-02T15:35:07,347 creating /tmp/pip-pip-egg-info-b3nzx8at/concord_sc.egg-info 2025-09-02T15:35:07,348 writing /tmp/pip-pip-egg-info-b3nzx8at/concord_sc.egg-info/PKG-INFO 2025-09-02T15:35:07,354 writing dependency_links to /tmp/pip-pip-egg-info-b3nzx8at/concord_sc.egg-info/dependency_links.txt 2025-09-02T15:35:07,357 writing requirements to /tmp/pip-pip-egg-info-b3nzx8at/concord_sc.egg-info/requires.txt 2025-09-02T15:35:07,358 writing top-level names to /tmp/pip-pip-egg-info-b3nzx8at/concord_sc.egg-info/top_level.txt 2025-09-02T15:35:07,360 writing manifest file '/tmp/pip-pip-egg-info-b3nzx8at/concord_sc.egg-info/SOURCES.txt' 2025-09-02T15:35:07,455 reading manifest file '/tmp/pip-pip-egg-info-b3nzx8at/concord_sc.egg-info/SOURCES.txt' 2025-09-02T15:35:07,456 adding license file 'LICENSE.md' 2025-09-02T15:35:07,461 writing manifest file '/tmp/pip-pip-egg-info-b3nzx8at/concord_sc.egg-info/SOURCES.txt' 2025-09-02T15:35:07,566 Preparing metadata (setup.py): finished with status 'done' 2025-09-02T15:35:07,570 Source in /tmp/pip-wheel-d89xyg0b/concord-sc_bdb3ba9d705d4d7b8d3ade53d48c1ca5 has version 1.0.8, which satisfies requirement concord-sc==1.0.8 from https://files.pythonhosted.org/packages/12/b8/b36c4e4e0d26a0926f5ffea28db97e4fb94f16d3260320fe23c7275f0281/concord_sc-1.0.8.tar.gz 2025-09-02T15:35:07,571 Removed concord-sc==1.0.8 from https://files.pythonhosted.org/packages/12/b8/b36c4e4e0d26a0926f5ffea28db97e4fb94f16d3260320fe23c7275f0281/concord_sc-1.0.8.tar.gz from build tracker '/tmp/pip-build-tracker-4_ibm748' 2025-09-02T15:35:07,584 Created temporary directory: /tmp/pip-unpack-u_2krfam 2025-09-02T15:35:07,585 Created temporary directory: /tmp/pip-unpack-a825eqk4 2025-09-02T15:35:07,586 Building wheels for collected packages: concord-sc 2025-09-02T15:35:07,590 Created temporary directory: /tmp/pip-wheel-hos08351 2025-09-02T15:35:07,591 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 2025-09-02T15:35:07,593 Building wheel for concord-sc (setup.py): started 2025-09-02T15:35:07,594 Destination directory: /tmp/pip-wheel-hos08351 2025-09-02T15:35:07,594 Running command python setup.py bdist_wheel 2025-09-02T15:35:08,435 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-02T15:35:08,435 !! 2025-09-02T15:35:08,436 ******************************************************************************** 2025-09-02T15:35:08,437 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-02T15:35:08,438 License :: OSI Approved :: MIT License 2025-09-02T15:35:08,439 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-02T15:35:08,439 ******************************************************************************** 2025-09-02T15:35:08,440 !! 2025-09-02T15:35:08,440 self._finalize_license_expression() 2025-09-02T15:35:08,441 running bdist_wheel 2025-09-02T15:35:08,573 running build 2025-09-02T15:35:08,574 running build_py 2025-09-02T15:35:08,606 creating build/lib/concord 2025-09-02T15:35:08,609 copying src/concord/concord.py -> build/lib/concord 2025-09-02T15:35:08,615 copying src/concord/pl.py -> build/lib/concord 2025-09-02T15:35:08,620 copying src/concord/__init__.py -> build/lib/concord 2025-09-02T15:35:08,624 copying src/concord/ul.py -> build/lib/concord 2025-09-02T15:35:08,626 copying src/concord/sm.py -> build/lib/concord 2025-09-02T15:35:08,628 copying src/concord/bm.py -> build/lib/concord 2025-09-02T15:35:08,630 copying src/concord/ml.py -> build/lib/concord 2025-09-02T15:35:08,633 creating build/lib/concord/utils 2025-09-02T15:35:08,635 copying src/concord/utils/anndata_utils.py -> build/lib/concord/utils 2025-09-02T15:35:08,638 copying src/concord/utils/cell_cycle.py -> build/lib/concord/utils 2025-09-02T15:35:08,641 copying src/concord/utils/__init__.py -> build/lib/concord/utils 2025-09-02T15:35:08,643 copying src/concord/utils/dim_reduction.py -> build/lib/concord/utils 2025-09-02T15:35:08,646 copying src/concord/utils/batch_analysis.py -> build/lib/concord/utils 2025-09-02T15:35:08,649 copying src/concord/utils/visCello.py -> build/lib/concord/utils 2025-09-02T15:35:08,651 copying src/concord/utils/other_util.py -> build/lib/concord/utils 2025-09-02T15:35:08,653 copying src/concord/utils/doublet_utils.py -> build/lib/concord/utils 2025-09-02T15:35:08,656 copying src/concord/utils/path_analysis.py -> build/lib/concord/utils 2025-09-02T15:35:08,658 copying src/concord/utils/enrichment_analysis.py -> build/lib/concord/utils 2025-09-02T15:35:08,661 copying src/concord/utils/estimate_dropout_rate.py -> build/lib/concord/utils 2025-09-02T15:35:08,663 copying src/concord/utils/Hs_Mm_conversion.py -> build/lib/concord/utils 2025-09-02T15:35:08,665 copying src/concord/utils/value_check.py -> build/lib/concord/utils 2025-09-02T15:35:08,667 copying src/concord/utils/io.py -> build/lib/concord/utils 2025-09-02T15:35:08,669 copying src/concord/utils/integration_methods.py -> build/lib/concord/utils 2025-09-02T15:35:08,672 copying src/concord/utils/coverage_estimator.py -> build/lib/concord/utils 2025-09-02T15:35:08,674 copying src/concord/utils/importance_analysis.py -> build/lib/concord/utils 2025-09-02T15:35:08,676 copying src/concord/utils/feature_selector.py -> build/lib/concord/utils 2025-09-02T15:35:08,679 creating build/lib/concord/simulation 2025-09-02T15:35:08,681 copying src/concord/simulation/__init__.py -> build/lib/concord/simulation 2025-09-02T15:35:08,683 copying src/concord/simulation/advanced_helper.py -> build/lib/concord/simulation 2025-09-02T15:35:08,686 copying src/concord/simulation/simulation.py -> build/lib/concord/simulation 2025-09-02T15:35:08,690 creating build/lib/concord/plotting 2025-09-02T15:35:08,691 copying src/concord/plotting/palettes.py -> build/lib/concord/plotting 2025-09-02T15:35:08,694 copying src/concord/plotting/__init__.py -> build/lib/concord/plotting 2025-09-02T15:35:08,696 copying src/concord/plotting/pl_tda.py -> build/lib/concord/plotting 2025-09-02T15:35:08,698 copying src/concord/plotting/pl_heatmap.py -> build/lib/concord/plotting 2025-09-02T15:35:08,701 copying src/concord/plotting/pl_model.py -> build/lib/concord/plotting 2025-09-02T15:35:08,704 copying src/concord/plotting/pl_graph.py -> build/lib/concord/plotting 2025-09-02T15:35:08,706 copying src/concord/plotting/pl_enrichment.py -> build/lib/concord/plotting 2025-09-02T15:35:08,709 copying src/concord/plotting/pl_geometry.py -> build/lib/concord/plotting 2025-09-02T15:35:08,711 copying src/concord/plotting/pl_batch.py -> build/lib/concord/plotting 2025-09-02T15:35:08,713 copying src/concord/plotting/pl_benchmark.py -> build/lib/concord/plotting 2025-09-02T15:35:08,716 copying src/concord/plotting/pl_datacoverage.py -> build/lib/concord/plotting 2025-09-02T15:35:08,718 copying src/concord/plotting/pl_general.py -> build/lib/concord/plotting 2025-09-02T15:35:08,720 copying src/concord/plotting/pl_embedding.py -> build/lib/concord/plotting 2025-09-02T15:35:08,723 copying src/concord/plotting/pl_path.py -> build/lib/concord/plotting 2025-09-02T15:35:08,726 creating build/lib/concord/benchmarking 2025-09-02T15:35:08,727 copying src/concord/benchmarking/geometry.py -> build/lib/concord/benchmarking 2025-09-02T15:35:08,729 copying src/concord/benchmarking/time_memory.py -> build/lib/concord/benchmarking 2025-09-02T15:35:08,732 copying src/concord/benchmarking/__init__.py -> build/lib/concord/benchmarking 2025-09-02T15:35:08,734 copying src/concord/benchmarking/linear_probe.py -> build/lib/concord/benchmarking 2025-09-02T15:35:08,736 copying src/concord/benchmarking/benchmark.py -> build/lib/concord/benchmarking 2025-09-02T15:35:08,739 copying src/concord/benchmarking/pipeline_dim_reduction.py -> build/lib/concord/benchmarking 2025-09-02T15:35:08,742 copying src/concord/benchmarking/tda.py -> build/lib/concord/benchmarking 2025-09-02T15:35:08,744 copying src/concord/benchmarking/pipeline_integration.py -> build/lib/concord/benchmarking 2025-09-02T15:35:08,747 copying src/concord/benchmarking/knn_probe.py -> build/lib/concord/benchmarking 2025-09-02T15:35:08,750 creating build/lib/concord/model 2025-09-02T15:35:08,751 copying src/concord/model/augment.py -> build/lib/concord/model 2025-09-02T15:35:08,753 copying src/concord/model/anndataset.py -> build/lib/concord/model 2025-09-02T15:35:08,756 copying src/concord/model/__init__.py -> build/lib/concord/model 2025-09-02T15:35:08,758 copying src/concord/model/sampler.py -> build/lib/concord/model 2025-09-02T15:35:08,761 copying src/concord/model/dataloader.py -> build/lib/concord/model 2025-09-02T15:35:08,763 copying src/concord/model/chunkloader.py -> build/lib/concord/model 2025-09-02T15:35:08,765 copying src/concord/model/trainer.py -> build/lib/concord/model 2025-09-02T15:35:08,768 copying src/concord/model/loss.py -> build/lib/concord/model 2025-09-02T15:35:08,770 copying src/concord/model/knn.py -> build/lib/concord/model 2025-09-02T15:35:08,773 copying src/concord/model/model.py -> build/lib/concord/model 2025-09-02T15:35:08,775 copying src/concord/model/build_layer.py -> build/lib/concord/model 2025-09-02T15:35:08,815 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-02T15:35:08,815 !! 2025-09-02T15:35:08,817 ******************************************************************************** 2025-09-02T15:35:08,817 Please avoid running ``setup.py`` directly. 2025-09-02T15:35:08,818 Instead, use pypa/build, pypa/installer or other 2025-09-02T15:35:08,818 standards-based tools. 2025-09-02T15:35:08,819 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-02T15:35:08,820 or your builds will no longer be supported. 2025-09-02T15:35:08,821 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-02T15:35:08,822 ******************************************************************************** 2025-09-02T15:35:08,823 !! 2025-09-02T15:35:08,823 self.initialize_options() 2025-09-02T15:35:08,843 installing to build/bdist.linux-armv7l/wheel 2025-09-02T15:35:08,844 running install 2025-09-02T15:35:08,868 running install_lib 2025-09-02T15:35:08,895 creating build/bdist.linux-armv7l/wheel 2025-09-02T15:35:08,897 creating build/bdist.linux-armv7l/wheel/concord 2025-09-02T15:35:08,898 copying build/lib/concord/concord.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-02T15:35:08,902 creating build/bdist.linux-armv7l/wheel/concord/utils 2025-09-02T15:35:08,903 copying build/lib/concord/utils/anndata_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,906 copying build/lib/concord/utils/cell_cycle.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,908 copying build/lib/concord/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,910 copying build/lib/concord/utils/dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,912 copying build/lib/concord/utils/batch_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,915 copying build/lib/concord/utils/visCello.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,919 copying build/lib/concord/utils/other_util.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,923 copying build/lib/concord/utils/doublet_utils.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,929 copying build/lib/concord/utils/path_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,933 copying build/lib/concord/utils/enrichment_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,936 copying build/lib/concord/utils/estimate_dropout_rate.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,938 copying build/lib/concord/utils/Hs_Mm_conversion.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,941 copying build/lib/concord/utils/value_check.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,943 copying build/lib/concord/utils/io.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,945 copying build/lib/concord/utils/integration_methods.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,948 copying build/lib/concord/utils/coverage_estimator.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,951 copying build/lib/concord/utils/importance_analysis.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,953 copying build/lib/concord/utils/feature_selector.py -> build/bdist.linux-armv7l/wheel/./concord/utils 2025-09-02T15:35:08,956 copying build/lib/concord/pl.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-02T15:35:08,959 creating build/bdist.linux-armv7l/wheel/concord/simulation 2025-09-02T15:35:08,962 copying build/lib/concord/simulation/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/simulation 2025-09-02T15:35:08,966 copying build/lib/concord/simulation/advanced_helper.py -> build/bdist.linux-armv7l/wheel/./concord/simulation 2025-09-02T15:35:08,972 copying build/lib/concord/simulation/simulation.py -> build/bdist.linux-armv7l/wheel/./concord/simulation 2025-09-02T15:35:08,979 creating build/bdist.linux-armv7l/wheel/concord/plotting 2025-09-02T15:35:08,981 copying build/lib/concord/plotting/palettes.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:08,984 copying build/lib/concord/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:08,986 copying build/lib/concord/plotting/pl_tda.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:08,989 copying build/lib/concord/plotting/pl_heatmap.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:08,992 copying build/lib/concord/plotting/pl_model.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:08,994 copying build/lib/concord/plotting/pl_graph.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:08,997 copying build/lib/concord/plotting/pl_enrichment.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:09,000 copying build/lib/concord/plotting/pl_geometry.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:09,002 copying build/lib/concord/plotting/pl_batch.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:09,004 copying build/lib/concord/plotting/pl_benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:09,007 copying build/lib/concord/plotting/pl_datacoverage.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:09,009 copying build/lib/concord/plotting/pl_general.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:09,011 copying build/lib/concord/plotting/pl_embedding.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:09,014 copying build/lib/concord/plotting/pl_path.py -> build/bdist.linux-armv7l/wheel/./concord/plotting 2025-09-02T15:35:09,016 copying build/lib/concord/__init__.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-02T15:35:09,019 creating build/bdist.linux-armv7l/wheel/concord/benchmarking 2025-09-02T15:35:09,020 copying build/lib/concord/benchmarking/geometry.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-02T15:35:09,023 copying build/lib/concord/benchmarking/time_memory.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-02T15:35:09,025 copying build/lib/concord/benchmarking/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-02T15:35:09,027 copying build/lib/concord/benchmarking/linear_probe.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-02T15:35:09,030 copying build/lib/concord/benchmarking/benchmark.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-02T15:35:09,034 copying build/lib/concord/benchmarking/pipeline_dim_reduction.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-02T15:35:09,037 copying build/lib/concord/benchmarking/tda.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-02T15:35:09,040 copying build/lib/concord/benchmarking/pipeline_integration.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-02T15:35:09,042 copying build/lib/concord/benchmarking/knn_probe.py -> build/bdist.linux-armv7l/wheel/./concord/benchmarking 2025-09-02T15:35:09,045 copying build/lib/concord/ul.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-02T15:35:09,048 copying build/lib/concord/sm.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-02T15:35:09,051 creating build/bdist.linux-armv7l/wheel/concord/model 2025-09-02T15:35:09,052 copying build/lib/concord/model/augment.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-02T15:35:09,055 copying build/lib/concord/model/anndataset.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-02T15:35:09,058 copying build/lib/concord/model/__init__.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-02T15:35:09,061 copying build/lib/concord/model/sampler.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-02T15:35:09,064 copying build/lib/concord/model/dataloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-02T15:35:09,067 copying build/lib/concord/model/chunkloader.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-02T15:35:09,069 copying build/lib/concord/model/trainer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-02T15:35:09,072 copying build/lib/concord/model/loss.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-02T15:35:09,074 copying build/lib/concord/model/knn.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-02T15:35:09,077 copying build/lib/concord/model/model.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-02T15:35:09,080 copying build/lib/concord/model/build_layer.py -> build/bdist.linux-armv7l/wheel/./concord/model 2025-09-02T15:35:09,082 copying build/lib/concord/bm.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-02T15:35:09,084 copying build/lib/concord/ml.py -> build/bdist.linux-armv7l/wheel/./concord 2025-09-02T15:35:09,086 running install_egg_info 2025-09-02T15:35:09,123 running egg_info 2025-09-02T15:35:09,154 writing src/concord_sc.egg-info/PKG-INFO 2025-09-02T15:35:09,160 writing dependency_links to src/concord_sc.egg-info/dependency_links.txt 2025-09-02T15:35:09,165 writing requirements to src/concord_sc.egg-info/requires.txt 2025-09-02T15:35:09,167 writing top-level names to src/concord_sc.egg-info/top_level.txt 2025-09-02T15:35:09,229 reading manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-09-02T15:35:09,235 adding license file 'LICENSE.md' 2025-09-02T15:35:09,241 writing manifest file 'src/concord_sc.egg-info/SOURCES.txt' 2025-09-02T15:35:09,243 Copying src/concord_sc.egg-info to build/bdist.linux-armv7l/wheel/./concord_sc-1.0.8-py3.11.egg-info 2025-09-02T15:35:09,254 running install_scripts 2025-09-02T15:35:09,266 creating build/bdist.linux-armv7l/wheel/concord_sc-1.0.8.dist-info/WHEEL 2025-09-02T15:35:09,269 creating '/tmp/pip-wheel-hos08351/concord_sc-1.0.8-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-02T15:35:09,273 adding 'concord/__init__.py' 2025-09-02T15:35:09,275 adding 'concord/bm.py' 2025-09-02T15:35:09,282 adding 'concord/concord.py' 2025-09-02T15:35:09,285 adding 'concord/ml.py' 2025-09-02T15:35:09,287 adding 'concord/pl.py' 2025-09-02T15:35:09,289 adding 'concord/sm.py' 2025-09-02T15:35:09,291 adding 'concord/ul.py' 2025-09-02T15:35:09,293 adding 'concord/benchmarking/__init__.py' 2025-09-02T15:35:09,299 adding 'concord/benchmarking/benchmark.py' 2025-09-02T15:35:09,301 adding 'concord/benchmarking/geometry.py' 2025-09-02T15:35:09,304 adding 'concord/benchmarking/knn_probe.py' 2025-09-02T15:35:09,306 adding 'concord/benchmarking/linear_probe.py' 2025-09-02T15:35:09,308 adding 'concord/benchmarking/pipeline_dim_reduction.py' 2025-09-02T15:35:09,310 adding 'concord/benchmarking/pipeline_integration.py' 2025-09-02T15:35:09,313 adding 'concord/benchmarking/tda.py' 2025-09-02T15:35:09,315 adding 'concord/benchmarking/time_memory.py' 2025-09-02T15:35:09,317 adding 'concord/model/__init__.py' 2025-09-02T15:35:09,318 adding 'concord/model/anndataset.py' 2025-09-02T15:35:09,320 adding 'concord/model/augment.py' 2025-09-02T15:35:09,322 adding 'concord/model/build_layer.py' 2025-09-02T15:35:09,324 adding 'concord/model/chunkloader.py' 2025-09-02T15:35:09,326 adding 'concord/model/dataloader.py' 2025-09-02T15:35:09,329 adding 'concord/model/knn.py' 2025-09-02T15:35:09,331 adding 'concord/model/loss.py' 2025-09-02T15:35:09,333 adding 'concord/model/model.py' 2025-09-02T15:35:09,335 adding 'concord/model/sampler.py' 2025-09-02T15:35:09,338 adding 'concord/model/trainer.py' 2025-09-02T15:35:09,340 adding 'concord/plotting/__init__.py' 2025-09-02T15:35:09,342 adding 'concord/plotting/palettes.py' 2025-09-02T15:35:09,344 adding 'concord/plotting/pl_batch.py' 2025-09-02T15:35:09,347 adding 'concord/plotting/pl_benchmark.py' 2025-09-02T15:35:09,348 adding 'concord/plotting/pl_datacoverage.py' 2025-09-02T15:35:09,355 adding 'concord/plotting/pl_embedding.py' 2025-09-02T15:35:09,358 adding 'concord/plotting/pl_enrichment.py' 2025-09-02T15:35:09,360 adding 'concord/plotting/pl_general.py' 2025-09-02T15:35:09,362 adding 'concord/plotting/pl_geometry.py' 2025-09-02T15:35:09,365 adding 'concord/plotting/pl_graph.py' 2025-09-02T15:35:09,368 adding 'concord/plotting/pl_heatmap.py' 2025-09-02T15:35:09,371 adding 'concord/plotting/pl_model.py' 2025-09-02T15:35:09,373 adding 'concord/plotting/pl_path.py' 2025-09-02T15:35:09,375 adding 'concord/plotting/pl_tda.py' 2025-09-02T15:35:09,377 adding 'concord/simulation/__init__.py' 2025-09-02T15:35:09,380 adding 'concord/simulation/advanced_helper.py' 2025-09-02T15:35:09,384 adding 'concord/simulation/simulation.py' 2025-09-02T15:35:09,387 adding 'concord/utils/Hs_Mm_conversion.py' 2025-09-02T15:35:09,388 adding 'concord/utils/__init__.py' 2025-09-02T15:35:09,391 adding 'concord/utils/anndata_utils.py' 2025-09-02T15:35:09,392 adding 'concord/utils/batch_analysis.py' 2025-09-02T15:35:09,393 adding 'concord/utils/cell_cycle.py' 2025-09-02T15:35:09,395 adding 'concord/utils/coverage_estimator.py' 2025-09-02T15:35:09,396 adding 'concord/utils/dim_reduction.py' 2025-09-02T15:35:09,398 adding 'concord/utils/doublet_utils.py' 2025-09-02T15:35:09,399 adding 'concord/utils/enrichment_analysis.py' 2025-09-02T15:35:09,401 adding 'concord/utils/estimate_dropout_rate.py' 2025-09-02T15:35:09,403 adding 'concord/utils/feature_selector.py' 2025-09-02T15:35:09,404 adding 'concord/utils/importance_analysis.py' 2025-09-02T15:35:09,406 adding 'concord/utils/integration_methods.py' 2025-09-02T15:35:09,407 adding 'concord/utils/io.py' 2025-09-02T15:35:09,409 adding 'concord/utils/other_util.py' 2025-09-02T15:35:09,410 adding 'concord/utils/path_analysis.py' 2025-09-02T15:35:09,412 adding 'concord/utils/value_check.py' 2025-09-02T15:35:09,413 adding 'concord/utils/visCello.py' 2025-09-02T15:35:09,416 adding 'concord_sc-1.0.8.dist-info/licenses/LICENSE.md' 2025-09-02T15:35:09,418 adding 'concord_sc-1.0.8.dist-info/METADATA' 2025-09-02T15:35:09,419 adding 'concord_sc-1.0.8.dist-info/WHEEL' 2025-09-02T15:35:09,419 adding 'concord_sc-1.0.8.dist-info/top_level.txt' 2025-09-02T15:35:09,421 adding 'concord_sc-1.0.8.dist-info/RECORD' 2025-09-02T15:35:09,425 removing build/bdist.linux-armv7l/wheel 2025-09-02T15:35:09,551 Building wheel for concord-sc (setup.py): finished with status 'done' 2025-09-02T15:35:09,555 Created wheel for concord-sc: filename=concord_sc-1.0.8-py3-none-any.whl size=161846 sha256=391cca75481163cf433645f1514aa26cb5b389b1b777765338d3634d9366b910 2025-09-02T15:35:09,556 Stored in directory: /tmp/pip-ephem-wheel-cache-vukl_hw6/wheels/ba/7c/ec/74cc56809bc7086c1cb6cfdbb2829b978aecd544127f612b35 2025-09-02T15:35:09,572 Successfully built concord-sc 2025-09-02T15:35:09,581 Removed build tracker: '/tmp/pip-build-tracker-4_ibm748'