2025-11-07T19:28:12,889 Created temporary directory: /tmp/pip-ephem-wheel-cache-mkrgkwqc 2025-11-07T19:28:12,891 Created temporary directory: /tmp/pip-build-tracker-i1pk1sgf 2025-11-07T19:28:12,891 Initialized build tracking at /tmp/pip-build-tracker-i1pk1sgf 2025-11-07T19:28:12,892 Created build tracker: /tmp/pip-build-tracker-i1pk1sgf 2025-11-07T19:28:12,892 Entered build tracker: /tmp/pip-build-tracker-i1pk1sgf 2025-11-07T19:28:12,893 Created temporary directory: /tmp/pip-wheel-uvb81luw 2025-11-07T19:28:12,896 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2025-11-07T19:28:12,898 Created temporary directory: /tmp/pip-ephem-wheel-cache-65pytyvb 2025-11-07T19:28:12,920 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-07T19:28:12,923 2 location(s) to search for versions of scunagi: 2025-11-07T19:28:12,923 * https://pypi.org/simple/scunagi/ 2025-11-07T19:28:12,923 * https://www.piwheels.org/simple/scunagi/ 2025-11-07T19:28:12,924 Fetching project page and analyzing links: https://pypi.org/simple/scunagi/ 2025-11-07T19:28:12,925 Getting page https://pypi.org/simple/scunagi/ 2025-11-07T19:28:12,926 Found index url https://pypi.org/simple 2025-11-07T19:28:13,142 Fetched page https://pypi.org/simple/scunagi/ as application/vnd.pypi.simple.v1+json 2025-11-07T19:28:13,148 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/4e/47/f8eadc592806973940740a9417892ce5e870b13f3140d5462b6469f5df29/scUNAGI-0.1-py3-none-any.whl (from https://pypi.org/simple/scunagi/) 2025-11-07T19:28:13,149 Found link https://files.pythonhosted.org/packages/e1/f1/0de90828615ce729086b0bd0040d92816d065d709b8d4cf23aa83212bd12/scUNAGI-0.1.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.1 2025-11-07T19:28:13,149 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/0d/bb/b041310d772ca981d03120f181c4755f44bc2e4088fdd8c19b3f194149cb/scUNAGI-0.1.1-py3-none-any.whl (from https://pypi.org/simple/scunagi/) (requires-python:>=3.9) 2025-11-07T19:28:13,150 Found link https://files.pythonhosted.org/packages/1f/61/ec3d902cc92513faac987d3c96132bca48c123c8367652adb9680071cd26/scUNAGI-0.1.1.tar.gz (from https://pypi.org/simple/scunagi/) (requires-python:>=3.9), version: 0.1.1 2025-11-07T19:28:13,151 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/a1/50/e3172e3800ea043d94ef312db9211b7ebe03d044709ca7ffe5bfe736765c/scUNAGI-0.2-py3-none-any.whl (from https://pypi.org/simple/scunagi/) 2025-11-07T19:28:13,152 Found link https://files.pythonhosted.org/packages/27/25/685283d6b4b5c35f39f23f234c4b69ceb58cfe44d5847fb370d65014efc7/scUNAGI-0.2.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.2 2025-11-07T19:28:13,152 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/75/b1/9ff8fa54ba5a2e2a0102fb3367a6bc4d47606149789cce7f708c9e1ca50b/scUNAGI-0.2.2-py3-none-any.whl (from https://pypi.org/simple/scunagi/) 2025-11-07T19:28:13,153 Found link https://files.pythonhosted.org/packages/56/fc/f64940990310421351ca9414457163eae58f1e9203baf8d1e9c57b606f90/scUNAGI-0.2.2.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.2.2 2025-11-07T19:28:13,154 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/a5/83/521b24d3447fffa8ac0d457271b83a73afeb6e504d97f717554d37b14b3e/scUNAGI-0.2.3-py3-none-any.whl (from https://pypi.org/simple/scunagi/) (requires-python:>=3.9) 2025-11-07T19:28:13,154 Found link https://files.pythonhosted.org/packages/8a/40/03fa3a1a80bdd93652f14ba230ee730619b2c313e0062c0c577e136128f1/scUNAGI-0.2.3.tar.gz (from https://pypi.org/simple/scunagi/) (requires-python:>=3.9), version: 0.2.3 2025-11-07T19:28:13,155 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/97/f1/dddf6a6adea2876f2a15d2497e49c6be90d0635eee858fa599d714c54449/scUNAGI-0.3.0-py3-none-any.whl (from https://pypi.org/simple/scunagi/) (requires-python:>=3.9) 2025-11-07T19:28:13,157 Found link https://files.pythonhosted.org/packages/9b/f1/6c9ddf15ecf960f35e057dcdee9af5eba0d924b24f5a096c3828c0a89ff8/scunagi-0.3.0.tar.gz (from https://pypi.org/simple/scunagi/) (requires-python:>=3.9), version: 0.3.0 2025-11-07T19:28:13,157 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/b0/ec/bb93d0e406214ab78c670676962f30691f31f7c1964d1d0410dd95b00e70/scUNAGI-0.4.0-py3-none-any.whl (from https://pypi.org/simple/scunagi/) (requires-python:>=3.9) 2025-11-07T19:28:13,158 Found link https://files.pythonhosted.org/packages/e7/6e/9e42231afa1a42dc43fff926d723ee50f98192adafc0e65f40ae4d218521/scUNAGI-0.4.0.tar.gz (from https://pypi.org/simple/scunagi/) (requires-python:>=3.9), version: 0.4.0 2025-11-07T19:28:13,159 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/c7/f8/7a87adba85d561b625edfaed2f57642ec5fb48fc7626645298dd92854306/scUNAGI-0.5.0-py3-none-any.whl (from https://pypi.org/simple/scunagi/) 2025-11-07T19:28:13,159 Found link https://files.pythonhosted.org/packages/da/2b/67960203de3c86d8401765dd3a0a427721dfb57b9aaa69f859a5408a5a83/scunagi-0.5.0.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.5.0 2025-11-07T19:28:13,160 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/e4/b8/7fe478bc9e1601e5e9167dc7a016917cf77592ea2dcd231de8d6a0e171f4/scUNAGI-0.5.1-py3-none-any.whl (from https://pypi.org/simple/scunagi/) 2025-11-07T19:28:13,160 Found link https://files.pythonhosted.org/packages/65/78/4705b37b7c895b2f43178c4b5ebe96a9a20b45b4edebda419e0e76194c88/scunagi-0.5.1.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.5.1 2025-11-07T19:28:13,161 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/df/fc/6e900ea410012a56137d8126da4e09b5b1686b0e48d9954229a72da6a4dd/scunagi-0.5.3-py3-none-any.whl (from https://pypi.org/simple/scunagi/) 2025-11-07T19:28:13,161 Found link https://files.pythonhosted.org/packages/18/83/68926b431b80d7ee5a3dd7c14f359cb57304e635c9e5d5a9465f921566db/scunagi-0.5.3.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.5.3 2025-11-07T19:28:13,162 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/1a/3d/16e198e98810d53d47c9146726e8ca77048415ac36f7c5c378825a0144ad/scunagi-0.5.4-py3-none-any.whl (from https://pypi.org/simple/scunagi/) 2025-11-07T19:28:13,162 Found link https://files.pythonhosted.org/packages/0f/b0/7493f395bd61756863f53a8b26f58772d9f21331c3ecc3ac6462c6e5afed/scunagi-0.5.4.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.5.4 2025-11-07T19:28:13,163 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/2d/dc/14dfdd28118150786d2cbe604b627605daa21ab3d59a150a0fdb6af5e5c7/scunagi-0.5.5-py3-none-any.whl (from https://pypi.org/simple/scunagi/) 2025-11-07T19:28:13,163 Found link https://files.pythonhosted.org/packages/1b/00/bdde1081c953ff7918fcd817261cb8d6c0a133074dcd2d619e94bcac3a60/scunagi-0.5.5.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.5.5 2025-11-07T19:28:13,164 Fetching project page and analyzing links: https://www.piwheels.org/simple/scunagi/ 2025-11-07T19:28:13,165 Getting page https://www.piwheels.org/simple/scunagi/ 2025-11-07T19:28:13,166 Found index url https://www.piwheels.org/simple 2025-11-07T19:28:13,322 Fetched page https://www.piwheels.org/simple/scunagi/ as text/html 2025-11-07T19:28:13,325 Skipping link: No binaries permitted for scunagi: https://www.piwheels.org/simple/scunagi/scunagi-0.5.4-py3-none-any.whl#sha256=9a0c0d7b6dac95d998237f9112433275e79649a2aeb7aa97983612e97ca1dcc2 (from https://www.piwheels.org/simple/scunagi/) 2025-11-07T19:28:13,326 Skipping link: No binaries permitted for scunagi: https://www.piwheels.org/simple/scunagi/scunagi-0.5.3-py3-none-any.whl#sha256=bdb9b1b8ad4b0319a8df8fe0c9dc1ce63cb0cf41b9e25f0293ea4461102983c7 (from https://www.piwheels.org/simple/scunagi/) 2025-11-07T19:28:13,326 Skipping link: No binaries permitted for scunagi: https://archive1.piwheels.org/simple/scunagi/scUNAGI-0.5.1-py3-none-any.whl#sha256=5f3e883a98cd74c970d1289df9e51ed74b88c0a2cf717efdc5c031573c803894 (from https://www.piwheels.org/simple/scunagi/) 2025-11-07T19:28:13,328 Skipping link: No binaries permitted for scunagi: https://archive1.piwheels.org/simple/scunagi/scUNAGI-0.5.0-py3-none-any.whl#sha256=8a53da8cb5920cb8e95b06e4e6a95713133b4afdc97813dcaa42784062eef303 (from https://www.piwheels.org/simple/scunagi/) 2025-11-07T19:28:13,328 Skipping link: No binaries permitted for scunagi: https://archive1.piwheels.org/simple/scunagi/scUNAGI-0.2.2-py3-none-any.whl#sha256=7e108ae46749a9bc7ac79a203b412eb58d6ace52ce103f1ae5f48fe3a6d44f8b (from https://www.piwheels.org/simple/scunagi/) 2025-11-07T19:28:13,328 Skipping link: No binaries permitted for scunagi: https://archive1.piwheels.org/simple/scunagi/scUNAGI-0.2-py3-none-any.whl#sha256=e8111234b02add4b4fb4a5b5318c0a308a10633470a5e82a7d3d423438ae509f (from https://www.piwheels.org/simple/scunagi/) 2025-11-07T19:28:13,329 Skipping link: No binaries permitted for scunagi: https://archive1.piwheels.org/simple/scunagi/scUNAGI-0.1-py3-none-any.whl#sha256=129a6ea06ac3e3c1826b3ac39feecff520c456e5688369ffda9c947f39b3a591 (from https://www.piwheels.org/simple/scunagi/) 2025-11-07T19:28:13,329 Skipping link: not a file: https://www.piwheels.org/simple/scunagi/ 2025-11-07T19:28:13,330 Skipping link: not a file: https://pypi.org/simple/scunagi/ 2025-11-07T19:28:13,350 Given no hashes to check 1 links for project 'scunagi': discarding no candidates 2025-11-07T19:28:13,369 Collecting scunagi==0.5.5 2025-11-07T19:28:13,371 Created temporary directory: /tmp/pip-unpack-v5ta468o 2025-11-07T19:28:13,510 Downloading scunagi-0.5.5.tar.gz (7.1 MB) 2025-11-07T19:28:15,523 Added scunagi==0.5.5 from https://files.pythonhosted.org/packages/1b/00/bdde1081c953ff7918fcd817261cb8d6c0a133074dcd2d619e94bcac3a60/scunagi-0.5.5.tar.gz to build tracker '/tmp/pip-build-tracker-i1pk1sgf' 2025-11-07T19:28:15,525 Running setup.py (path:/tmp/pip-wheel-uvb81luw/scunagi_a228a28bee8c4c63ad4d732f5e4ea2cf/setup.py) egg_info for package scunagi 2025-11-07T19:28:15,526 Created temporary directory: /tmp/pip-pip-egg-info-5i7n8h65 2025-11-07T19:28:15,526 Preparing metadata (setup.py): started 2025-11-07T19:28:15,528 Running command python setup.py egg_info 2025-11-07T19:28:16,439 running egg_info 2025-11-07T19:28:16,466 creating /tmp/pip-pip-egg-info-5i7n8h65/scUNAGI.egg-info 2025-11-07T19:28:16,467 writing /tmp/pip-pip-egg-info-5i7n8h65/scUNAGI.egg-info/PKG-INFO 2025-11-07T19:28:16,471 writing dependency_links to /tmp/pip-pip-egg-info-5i7n8h65/scUNAGI.egg-info/dependency_links.txt 2025-11-07T19:28:16,475 writing requirements to /tmp/pip-pip-egg-info-5i7n8h65/scUNAGI.egg-info/requires.txt 2025-11-07T19:28:16,476 writing top-level names to /tmp/pip-pip-egg-info-5i7n8h65/scUNAGI.egg-info/top_level.txt 2025-11-07T19:28:16,478 writing manifest file '/tmp/pip-pip-egg-info-5i7n8h65/scUNAGI.egg-info/SOURCES.txt' 2025-11-07T19:28:16,575 reading manifest file '/tmp/pip-pip-egg-info-5i7n8h65/scUNAGI.egg-info/SOURCES.txt' 2025-11-07T19:28:16,577 reading manifest template 'MANIFEST.in' 2025-11-07T19:28:16,578 warning: no files found matching 'LICENSE' 2025-11-07T19:28:16,579 adding license file 'LICENSE.txt' 2025-11-07T19:28:16,582 writing manifest file '/tmp/pip-pip-egg-info-5i7n8h65/scUNAGI.egg-info/SOURCES.txt' 2025-11-07T19:28:16,686 Preparing metadata (setup.py): finished with status 'done' 2025-11-07T19:28:16,691 Source in /tmp/pip-wheel-uvb81luw/scunagi_a228a28bee8c4c63ad4d732f5e4ea2cf has version 0.5.5, which satisfies requirement scunagi==0.5.5 from https://files.pythonhosted.org/packages/1b/00/bdde1081c953ff7918fcd817261cb8d6c0a133074dcd2d619e94bcac3a60/scunagi-0.5.5.tar.gz 2025-11-07T19:28:16,692 Removed scunagi==0.5.5 from https://files.pythonhosted.org/packages/1b/00/bdde1081c953ff7918fcd817261cb8d6c0a133074dcd2d619e94bcac3a60/scunagi-0.5.5.tar.gz from build tracker '/tmp/pip-build-tracker-i1pk1sgf' 2025-11-07T19:28:16,699 Created temporary directory: /tmp/pip-unpack-pbru2ut9 2025-11-07T19:28:16,699 Building wheels for collected packages: scunagi 2025-11-07T19:28:16,704 Created temporary directory: /tmp/pip-wheel-g6z480cv 2025-11-07T19:28:16,704 Building wheel for scunagi (setup.py): started 2025-11-07T19:28:16,705 Destination directory: /tmp/pip-wheel-g6z480cv 2025-11-07T19:28:16,706 Running command python setup.py bdist_wheel 2025-11-07T19:28:17,545 running bdist_wheel 2025-11-07T19:28:17,676 running build 2025-11-07T19:28:17,676 running build_py 2025-11-07T19:28:17,706 creating build/lib/UNAGI 2025-11-07T19:28:17,708 copying UNAGI/__init__.py -> build/lib/UNAGI 2025-11-07T19:28:17,710 copying UNAGI/UNAGI_tool.py -> build/lib/UNAGI 2025-11-07T19:28:17,713 copying UNAGI/UNAGI_analyst.py -> build/lib/UNAGI 2025-11-07T19:28:17,717 creating build/lib/UNAGI/train 2025-11-07T19:28:17,718 copying UNAGI/train/customized_elbo.py -> build/lib/UNAGI/train 2025-11-07T19:28:17,721 copying UNAGI/train/__init__.py -> build/lib/UNAGI/train 2025-11-07T19:28:17,723 copying UNAGI/train/runner.py -> build/lib/UNAGI/train 2025-11-07T19:28:17,726 copying UNAGI/train/trainer.py -> build/lib/UNAGI/train 2025-11-07T19:28:17,730 creating build/lib/UNAGI/plotting 2025-11-07T19:28:17,731 copying UNAGI/plotting/plot_cell_embeddings.py -> build/lib/UNAGI/plotting 2025-11-07T19:28:17,733 copying UNAGI/plotting/plot_cell_type_composition.py -> build/lib/UNAGI/plotting 2025-11-07T19:28:17,735 copying UNAGI/plotting/plot_hierarchical_markers_heatmap.py -> build/lib/UNAGI/plotting 2025-11-07T19:28:17,737 copying UNAGI/plotting/__init__.py -> build/lib/UNAGI/plotting 2025-11-07T19:28:17,739 copying UNAGI/plotting/plot_stage_dendrogram.py -> build/lib/UNAGI/plotting 2025-11-07T19:28:17,741 creating build/lib/UNAGI/model 2025-11-07T19:28:17,742 copying UNAGI/model/distributions.py -> build/lib/UNAGI/model 2025-11-07T19:28:17,745 copying UNAGI/model/models.py -> build/lib/UNAGI/model 2025-11-07T19:28:17,748 copying UNAGI/model/__init__.py -> build/lib/UNAGI/model 2025-11-07T19:28:17,750 creating build/lib/UNAGI/perturbations 2025-11-07T19:28:17,751 copying UNAGI/perturbations/perturbation.py -> build/lib/UNAGI/perturbations 2025-11-07T19:28:17,754 copying UNAGI/perturbations/pathways.py -> build/lib/UNAGI/perturbations 2025-11-07T19:28:17,756 copying UNAGI/perturbations/__init__.py -> build/lib/UNAGI/perturbations 2025-11-07T19:28:17,758 copying UNAGI/perturbations/normalize_analysis_perturbation.py -> build/lib/UNAGI/perturbations 2025-11-07T19:28:17,761 copying UNAGI/perturbations/compounds.py -> build/lib/UNAGI/perturbations 2025-11-07T19:28:17,764 copying UNAGI/perturbations/new_perturbation_strategy.py -> build/lib/UNAGI/perturbations 2025-11-07T19:28:17,767 copying UNAGI/perturbations/perturbation_centroid.py -> build/lib/UNAGI/perturbations 2025-11-07T19:28:17,771 copying UNAGI/perturbations/analysis_perturbation.py -> build/lib/UNAGI/perturbations 2025-11-07T19:28:17,775 creating build/lib/UNAGI/dynamic_regulatory_networks 2025-11-07T19:28:17,776 copying UNAGI/dynamic_regulatory_networks/processTFs.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-07T19:28:17,779 copying UNAGI/dynamic_regulatory_networks/processIDREM.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-07T19:28:17,782 copying UNAGI/dynamic_regulatory_networks/__init__.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-07T19:28:17,784 creating build/lib/UNAGI/marker_discovery 2025-11-07T19:28:17,785 copying UNAGI/marker_discovery/dynamic_markers_helper.py -> build/lib/UNAGI/marker_discovery 2025-11-07T19:28:17,787 copying UNAGI/marker_discovery/hierachical_static_markers.py -> build/lib/UNAGI/marker_discovery 2025-11-07T19:28:17,790 copying UNAGI/marker_discovery/__init__.py -> build/lib/UNAGI/marker_discovery 2025-11-07T19:28:17,792 copying UNAGI/marker_discovery/dynamic_markers.py -> build/lib/UNAGI/marker_discovery 2025-11-07T19:28:17,795 creating build/lib/UNAGI/dynamic_graphs 2025-11-07T19:28:17,796 copying UNAGI/dynamic_graphs/distDistance.py -> build/lib/UNAGI/dynamic_graphs 2025-11-07T19:28:17,798 copying UNAGI/dynamic_graphs/__init__.py -> build/lib/UNAGI/dynamic_graphs 2025-11-07T19:28:17,799 copying UNAGI/dynamic_graphs/buildGraph.py -> build/lib/UNAGI/dynamic_graphs 2025-11-07T19:28:17,802 creating build/lib/UNAGI/utils 2025-11-07T19:28:17,803 copying UNAGI/utils/h5adReader.py -> build/lib/UNAGI/utils 2025-11-07T19:28:17,805 copying UNAGI/utils/msigdb_data_overlapping.py -> build/lib/UNAGI/utils 2025-11-07T19:28:17,807 copying UNAGI/utils/gcn_utils.py -> build/lib/UNAGI/utils 2025-11-07T19:28:17,809 copying UNAGI/utils/evaluate.py -> build/lib/UNAGI/utils 2025-11-07T19:28:17,811 copying UNAGI/utils/__init__.py -> build/lib/UNAGI/utils 2025-11-07T19:28:17,813 copying UNAGI/utils/analysis_helper.py -> build/lib/UNAGI/utils 2025-11-07T19:28:17,815 copying UNAGI/utils/attribute_utils.py -> build/lib/UNAGI/utils 2025-11-07T19:28:17,818 copying UNAGI/utils/CPO_utils.py -> build/lib/UNAGI/utils 2025-11-07T19:28:17,820 copying UNAGI/utils/idrem_helper.py -> build/lib/UNAGI/utils 2025-11-07T19:28:17,823 copying UNAGI/utils/trainer_utils.py -> build/lib/UNAGI/utils 2025-11-07T19:28:17,824 running egg_info 2025-11-07T19:28:17,852 writing scUNAGI.egg-info/PKG-INFO 2025-11-07T19:28:17,857 writing dependency_links to scUNAGI.egg-info/dependency_links.txt 2025-11-07T19:28:17,860 writing requirements to scUNAGI.egg-info/requires.txt 2025-11-07T19:28:17,861 writing top-level names to scUNAGI.egg-info/top_level.txt 2025-11-07T19:28:17,900 reading manifest file 'scUNAGI.egg-info/SOURCES.txt' 2025-11-07T19:28:17,905 reading manifest template 'MANIFEST.in' 2025-11-07T19:28:17,906 warning: no files found matching 'LICENSE' 2025-11-07T19:28:17,907 adding license file 'LICENSE.txt' 2025-11-07T19:28:17,911 writing manifest file 'scUNAGI.egg-info/SOURCES.txt' 2025-11-07T19:28:17,914 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'UNAGI.data' is absent from the `packages` configuration. 2025-11-07T19:28:17,914 !! 2025-11-07T19:28:17,916 ******************************************************************************** 2025-11-07T19:28:17,916 ############################ 2025-11-07T19:28:17,917 # Package would be ignored # 2025-11-07T19:28:17,917 ############################ 2025-11-07T19:28:17,918 Python recognizes 'UNAGI.data' as an importable package[^1], 2025-11-07T19:28:17,918 but it is absent from setuptools' `packages` configuration. 2025-11-07T19:28:17,920 This leads to an ambiguous overall configuration. If you want to distribute this 2025-11-07T19:28:17,920 package, please make sure that 'UNAGI.data' is explicitly added 2025-11-07T19:28:17,921 to the `packages` configuration field. 2025-11-07T19:28:17,922 Alternatively, you can also rely on setuptools' discovery methods 2025-11-07T19:28:17,922 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-11-07T19:28:17,923 instead of `find_packages(...)`/`find:`). 2025-11-07T19:28:17,924 You can read more about "package discovery" on setuptools documentation page: 2025-11-07T19:28:17,925 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-11-07T19:28:17,926 If you don't want 'UNAGI.data' to be distributed and are 2025-11-07T19:28:17,926 already explicitly excluding 'UNAGI.data' via 2025-11-07T19:28:17,927 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-11-07T19:28:17,927 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-11-07T19:28:17,928 combination with a more fine grained `package-data` configuration. 2025-11-07T19:28:17,929 You can read more about "package data files" on setuptools documentation page: 2025-11-07T19:28:17,930 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-11-07T19:28:17,931 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-11-07T19:28:17,932 even if it does not contain any `.py` files. 2025-11-07T19:28:17,932 On the other hand, currently there is no concept of package data 2025-11-07T19:28:17,933 directory, all directories are treated like packages. 2025-11-07T19:28:17,933 ******************************************************************************** 2025-11-07T19:28:17,934 !! 2025-11-07T19:28:17,935 check.warn(importable) 2025-11-07T19:28:17,941 creating build/lib/UNAGI/data 2025-11-07T19:28:17,948 copying UNAGI/data/brdID2cmapName.npy -> build/lib/UNAGI/data 2025-11-07T19:28:17,956 copying UNAGI/data/cmap_drug_target_genes.npy -> build/lib/UNAGI/data 2025-11-07T19:28:17,961 copying UNAGI/data/gesa_pathways.npy -> build/lib/UNAGI/data 2025-11-07T19:28:18,008 copying UNAGI/data/human_encode.txt -> build/lib/UNAGI/data 2025-11-07T19:28:18,404 copying UNAGI/data/jasper_target_pair.npy -> build/lib/UNAGI/data 2025-11-07T19:28:18,423 copying UNAGI/data/mouse_predicted.txt -> build/lib/UNAGI/data 2025-11-07T19:28:18,678 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-11-07T19:28:18,678 !! 2025-11-07T19:28:18,679 ******************************************************************************** 2025-11-07T19:28:18,680 Please avoid running ``setup.py`` directly. 2025-11-07T19:28:18,681 Instead, use pypa/build, pypa/installer or other 2025-11-07T19:28:18,681 standards-based tools. 2025-11-07T19:28:18,682 This deprecation is overdue, please update your project and remove deprecated 2025-11-07T19:28:18,683 calls to avoid build errors in the future. 2025-11-07T19:28:18,684 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-11-07T19:28:18,685 ******************************************************************************** 2025-11-07T19:28:18,686 !! 2025-11-07T19:28:18,686 self.initialize_options() 2025-11-07T19:28:18,711 installing to build/bdist.linux-armv7l/wheel 2025-11-07T19:28:18,711 running install 2025-11-07T19:28:18,736 running install_lib 2025-11-07T19:28:18,763 creating build/bdist.linux-armv7l/wheel 2025-11-07T19:28:18,766 creating build/bdist.linux-armv7l/wheel/UNAGI 2025-11-07T19:28:18,768 creating build/bdist.linux-armv7l/wheel/UNAGI/data 2025-11-07T19:28:18,769 copying build/lib/UNAGI/data/brdID2cmapName.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-07T19:28:18,799 copying build/lib/UNAGI/data/cmap_drug_target_genes.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-07T19:28:18,803 copying build/lib/UNAGI/data/human_encode.txt -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-07T19:28:19,202 copying build/lib/UNAGI/data/mouse_predicted.txt -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-07T19:28:19,433 copying build/lib/UNAGI/data/gesa_pathways.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-07T19:28:19,470 copying build/lib/UNAGI/data/jasper_target_pair.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-07T19:28:19,490 creating build/bdist.linux-armv7l/wheel/UNAGI/train 2025-11-07T19:28:19,491 copying build/lib/UNAGI/train/customized_elbo.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-07T19:28:19,494 copying build/lib/UNAGI/train/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-07T19:28:19,495 copying build/lib/UNAGI/train/runner.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-07T19:28:19,498 copying build/lib/UNAGI/train/trainer.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-07T19:28:19,501 creating build/bdist.linux-armv7l/wheel/UNAGI/plotting 2025-11-07T19:28:19,502 copying build/lib/UNAGI/plotting/plot_cell_embeddings.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-07T19:28:19,504 copying build/lib/UNAGI/plotting/plot_cell_type_composition.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-07T19:28:19,506 copying build/lib/UNAGI/plotting/plot_hierarchical_markers_heatmap.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-07T19:28:19,508 copying build/lib/UNAGI/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-07T19:28:19,510 copying build/lib/UNAGI/plotting/plot_stage_dendrogram.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-07T19:28:19,512 creating build/bdist.linux-armv7l/wheel/UNAGI/model 2025-11-07T19:28:19,513 copying build/lib/UNAGI/model/distributions.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-07T19:28:19,515 copying build/lib/UNAGI/model/models.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-07T19:28:19,518 copying build/lib/UNAGI/model/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-07T19:28:19,520 creating build/bdist.linux-armv7l/wheel/UNAGI/perturbations 2025-11-07T19:28:19,521 copying build/lib/UNAGI/perturbations/perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-07T19:28:19,524 copying build/lib/UNAGI/perturbations/pathways.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-07T19:28:19,527 copying build/lib/UNAGI/perturbations/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-07T19:28:19,528 copying build/lib/UNAGI/perturbations/normalize_analysis_perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-07T19:28:19,531 copying build/lib/UNAGI/perturbations/compounds.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-07T19:28:19,534 copying build/lib/UNAGI/perturbations/new_perturbation_strategy.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-07T19:28:19,537 copying build/lib/UNAGI/perturbations/perturbation_centroid.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-07T19:28:19,540 copying build/lib/UNAGI/perturbations/analysis_perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-07T19:28:19,544 creating build/bdist.linux-armv7l/wheel/UNAGI/dynamic_regulatory_networks 2025-11-07T19:28:19,545 copying build/lib/UNAGI/dynamic_regulatory_networks/processTFs.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-07T19:28:19,548 copying build/lib/UNAGI/dynamic_regulatory_networks/processIDREM.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-07T19:28:19,551 copying build/lib/UNAGI/dynamic_regulatory_networks/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-07T19:28:19,553 creating build/bdist.linux-armv7l/wheel/UNAGI/marker_discovery 2025-11-07T19:28:19,554 copying build/lib/UNAGI/marker_discovery/dynamic_markers_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-07T19:28:19,556 copying build/lib/UNAGI/marker_discovery/hierachical_static_markers.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-07T19:28:19,559 copying build/lib/UNAGI/marker_discovery/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-07T19:28:19,560 copying build/lib/UNAGI/marker_discovery/dynamic_markers.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-07T19:28:19,563 copying build/lib/UNAGI/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-07T19:28:19,565 creating build/bdist.linux-armv7l/wheel/UNAGI/dynamic_graphs 2025-11-07T19:28:19,566 copying build/lib/UNAGI/dynamic_graphs/distDistance.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-07T19:28:19,569 copying build/lib/UNAGI/dynamic_graphs/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-07T19:28:19,570 copying build/lib/UNAGI/dynamic_graphs/buildGraph.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-07T19:28:19,572 copying build/lib/UNAGI/UNAGI_tool.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-07T19:28:19,576 creating build/bdist.linux-armv7l/wheel/UNAGI/utils 2025-11-07T19:28:19,576 copying build/lib/UNAGI/utils/h5adReader.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-07T19:28:19,578 copying build/lib/UNAGI/utils/msigdb_data_overlapping.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-07T19:28:19,580 copying build/lib/UNAGI/utils/gcn_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-07T19:28:19,582 copying build/lib/UNAGI/utils/evaluate.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-07T19:28:19,584 copying build/lib/UNAGI/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-07T19:28:19,586 copying build/lib/UNAGI/utils/analysis_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-07T19:28:19,588 copying build/lib/UNAGI/utils/attribute_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-07T19:28:19,591 copying build/lib/UNAGI/utils/CPO_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-07T19:28:19,594 copying build/lib/UNAGI/utils/idrem_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-07T19:28:19,596 copying build/lib/UNAGI/utils/trainer_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-07T19:28:19,598 copying build/lib/UNAGI/UNAGI_analyst.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-07T19:28:19,600 running install_egg_info 2025-11-07T19:28:19,634 Copying scUNAGI.egg-info to build/bdist.linux-armv7l/wheel/./scUNAGI-0.5.5-py3.11.egg-info 2025-11-07T19:28:19,645 running install_scripts 2025-11-07T19:28:19,658 creating build/bdist.linux-armv7l/wheel/scunagi-0.5.5.dist-info/WHEEL 2025-11-07T19:28:19,660 creating '/tmp/pip-wheel-g6z480cv/scunagi-0.5.5-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-11-07T19:28:19,664 adding 'UNAGI/UNAGI_analyst.py' 2025-11-07T19:28:19,667 adding 'UNAGI/UNAGI_tool.py' 2025-11-07T19:28:19,668 adding 'UNAGI/__init__.py' 2025-11-07T19:28:19,813 adding 'UNAGI/data/brdID2cmapName.npy' 2025-11-07T19:28:19,849 adding 'UNAGI/data/cmap_drug_target_genes.npy' 2025-11-07T19:28:20,201 adding 'UNAGI/data/gesa_pathways.npy' 2025-11-07T19:28:22,291 adding 'UNAGI/data/human_encode.txt' 2025-11-07T19:28:22,623 adding 'UNAGI/data/jasper_target_pair.npy' 2025-11-07T19:28:23,437 adding 'UNAGI/data/mouse_predicted.txt' 2025-11-07T19:28:23,533 adding 'UNAGI/dynamic_graphs/__init__.py' 2025-11-07T19:28:23,534 adding 'UNAGI/dynamic_graphs/buildGraph.py' 2025-11-07T19:28:23,536 adding 'UNAGI/dynamic_graphs/distDistance.py' 2025-11-07T19:28:23,538 adding 'UNAGI/dynamic_regulatory_networks/__init__.py' 2025-11-07T19:28:23,540 adding 'UNAGI/dynamic_regulatory_networks/processIDREM.py' 2025-11-07T19:28:23,543 adding 'UNAGI/dynamic_regulatory_networks/processTFs.py' 2025-11-07T19:28:23,544 adding 'UNAGI/marker_discovery/__init__.py' 2025-11-07T19:28:23,546 adding 'UNAGI/marker_discovery/dynamic_markers.py' 2025-11-07T19:28:23,548 adding 'UNAGI/marker_discovery/dynamic_markers_helper.py' 2025-11-07T19:28:23,551 adding 'UNAGI/marker_discovery/hierachical_static_markers.py' 2025-11-07T19:28:23,552 adding 'UNAGI/model/__init__.py' 2025-11-07T19:28:23,554 adding 'UNAGI/model/distributions.py' 2025-11-07T19:28:23,556 adding 'UNAGI/model/models.py' 2025-11-07T19:28:23,558 adding 'UNAGI/perturbations/__init__.py' 2025-11-07T19:28:23,562 adding 'UNAGI/perturbations/analysis_perturbation.py' 2025-11-07T19:28:23,564 adding 'UNAGI/perturbations/compounds.py' 2025-11-07T19:28:23,566 adding 'UNAGI/perturbations/new_perturbation_strategy.py' 2025-11-07T19:28:23,571 adding 'UNAGI/perturbations/normalize_analysis_perturbation.py' 2025-11-07T19:28:23,573 adding 'UNAGI/perturbations/pathways.py' 2025-11-07T19:28:23,576 adding 'UNAGI/perturbations/perturbation.py' 2025-11-07T19:28:23,581 adding 'UNAGI/perturbations/perturbation_centroid.py' 2025-11-07T19:28:23,583 adding 'UNAGI/plotting/__init__.py' 2025-11-07T19:28:23,585 adding 'UNAGI/plotting/plot_cell_embeddings.py' 2025-11-07T19:28:23,586 adding 'UNAGI/plotting/plot_cell_type_composition.py' 2025-11-07T19:28:23,587 adding 'UNAGI/plotting/plot_hierarchical_markers_heatmap.py' 2025-11-07T19:28:23,589 adding 'UNAGI/plotting/plot_stage_dendrogram.py' 2025-11-07T19:28:23,590 adding 'UNAGI/train/__init__.py' 2025-11-07T19:28:23,592 adding 'UNAGI/train/customized_elbo.py' 2025-11-07T19:28:23,594 adding 'UNAGI/train/runner.py' 2025-11-07T19:28:23,596 adding 'UNAGI/train/trainer.py' 2025-11-07T19:28:23,598 adding 'UNAGI/utils/CPO_utils.py' 2025-11-07T19:28:23,599 adding 'UNAGI/utils/__init__.py' 2025-11-07T19:28:23,601 adding 'UNAGI/utils/analysis_helper.py' 2025-11-07T19:28:23,603 adding 'UNAGI/utils/attribute_utils.py' 2025-11-07T19:28:23,605 adding 'UNAGI/utils/evaluate.py' 2025-11-07T19:28:23,606 adding 'UNAGI/utils/gcn_utils.py' 2025-11-07T19:28:23,609 adding 'UNAGI/utils/h5adReader.py' 2025-11-07T19:28:23,611 adding 'UNAGI/utils/idrem_helper.py' 2025-11-07T19:28:23,612 adding 'UNAGI/utils/msigdb_data_overlapping.py' 2025-11-07T19:28:23,613 adding 'UNAGI/utils/trainer_utils.py' 2025-11-07T19:28:23,619 adding 'scunagi-0.5.5.dist-info/licenses/LICENSE.txt' 2025-11-07T19:28:23,621 adding 'scunagi-0.5.5.dist-info/METADATA' 2025-11-07T19:28:23,622 adding 'scunagi-0.5.5.dist-info/WHEEL' 2025-11-07T19:28:23,623 adding 'scunagi-0.5.5.dist-info/top_level.txt' 2025-11-07T19:28:23,624 adding 'scunagi-0.5.5.dist-info/RECORD' 2025-11-07T19:28:23,700 removing build/bdist.linux-armv7l/wheel 2025-11-07T19:28:23,840 Building wheel for scunagi (setup.py): finished with status 'done' 2025-11-07T19:28:24,062 Created wheel for scunagi: filename=scunagi-0.5.5-py3-none-any.whl size=7156911 sha256=787ca7aec5fdc7d3730da71d426dc5f7188c517fc06b6e0ae2010782e3da6b18 2025-11-07T19:28:24,063 Stored in directory: /tmp/pip-ephem-wheel-cache-65pytyvb/wheels/57/87/d1/7f725986c59d523cfb3334412c4ea475ffa08da32c8227a8b1 2025-11-07T19:28:25,262 Successfully built scunagi 2025-11-07T19:28:25,470 Removed build tracker: '/tmp/pip-build-tracker-i1pk1sgf'