2025-11-08T01:00:18,656 Created temporary directory: /tmp/pip-ephem-wheel-cache-wgotqri2 2025-11-08T01:00:18,658 Created temporary directory: /tmp/pip-build-tracker-pmbga7f0 2025-11-08T01:00:18,659 Initialized build tracking at /tmp/pip-build-tracker-pmbga7f0 2025-11-08T01:00:18,659 Created build tracker: /tmp/pip-build-tracker-pmbga7f0 2025-11-08T01:00:18,660 Entered build tracker: /tmp/pip-build-tracker-pmbga7f0 2025-11-08T01:00:18,661 Created temporary directory: /tmp/pip-wheel-bbq3imh5 2025-11-08T01:00:18,664 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 2025-11-08T01:00:18,666 Created temporary directory: /tmp/pip-ephem-wheel-cache-cwb2eeyf 2025-11-08T01:00:18,687 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-08T01:00:18,691 2 location(s) to search for versions of scunagi: 2025-11-08T01:00:18,691 * https://pypi.org/simple/scunagi/ 2025-11-08T01:00:18,691 * https://www.piwheels.org/simple/scunagi/ 2025-11-08T01:00:18,692 Fetching project page and analyzing links: https://pypi.org/simple/scunagi/ 2025-11-08T01:00:18,693 Getting page https://pypi.org/simple/scunagi/ 2025-11-08T01:00:18,694 Found index url https://pypi.org/simple 2025-11-08T01:00:18,909 Fetched page https://pypi.org/simple/scunagi/ as application/vnd.pypi.simple.v1+json 2025-11-08T01:00:18,915 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/) 2025-11-08T01:00:18,916 Found link https://files.pythonhosted.org/packages/e1/f1/0de90828615ce729086b0bd0040d92816d065d709b8d4cf23aa83212bd12/scUNAGI-0.1.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.1 2025-11-08T01:00:18,916 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) 2025-11-08T01:00:18,917 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 2025-11-08T01:00:18,918 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/) 2025-11-08T01:00:18,919 Found link https://files.pythonhosted.org/packages/27/25/685283d6b4b5c35f39f23f234c4b69ceb58cfe44d5847fb370d65014efc7/scUNAGI-0.2.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.2 2025-11-08T01:00:18,919 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/) 2025-11-08T01:00:18,920 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 2025-11-08T01:00:18,921 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) 2025-11-08T01:00:18,922 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 2025-11-08T01:00:18,922 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) 2025-11-08T01:00:18,924 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 2025-11-08T01:00:18,924 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) 2025-11-08T01:00:18,925 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 2025-11-08T01:00:18,926 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/) 2025-11-08T01:00:18,926 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 2025-11-08T01:00:18,927 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/) 2025-11-08T01:00:18,927 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 2025-11-08T01:00:18,928 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/) 2025-11-08T01:00:18,928 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 2025-11-08T01:00:18,929 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/) 2025-11-08T01:00:18,930 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 2025-11-08T01:00:18,930 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/) 2025-11-08T01:00:18,931 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 2025-11-08T01:00:18,931 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/b9/c8/496dbbafef280aa8d5a7ddde85667b19a166cbe5147f23f38b453158d282/scunagi-0.5.6-py3-none-any.whl (from https://pypi.org/simple/scunagi/) 2025-11-08T01:00:18,932 Found link https://files.pythonhosted.org/packages/b7/ad/94a2d75c6a914200443bf95780e90047f6b563ffe04a6bf0a3accbb62395/scunagi-0.5.6.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.5.6 2025-11-08T01:00:18,933 Fetching project page and analyzing links: https://www.piwheels.org/simple/scunagi/ 2025-11-08T01:00:18,934 Getting page https://www.piwheels.org/simple/scunagi/ 2025-11-08T01:00:18,935 Found index url https://www.piwheels.org/simple 2025-11-08T01:00:19,101 Fetched page https://www.piwheels.org/simple/scunagi/ as text/html 2025-11-08T01:00:19,105 Skipping link: No binaries permitted for scunagi: https://www.piwheels.org/simple/scunagi/scunagi-0.5.5-py3-none-any.whl#sha256=787ca7aec5fdc7d3730da71d426dc5f7188c517fc06b6e0ae2010782e3da6b18 (from https://www.piwheels.org/simple/scunagi/) 2025-11-08T01:00:19,105 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/) 2025-11-08T01:00:19,106 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/) 2025-11-08T01:00:19,106 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/) 2025-11-08T01:00:19,107 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/) 2025-11-08T01:00:19,107 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/) 2025-11-08T01:00:19,108 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/) 2025-11-08T01:00:19,108 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/) 2025-11-08T01:00:19,109 Skipping link: not a file: https://www.piwheels.org/simple/scunagi/ 2025-11-08T01:00:19,109 Skipping link: not a file: https://pypi.org/simple/scunagi/ 2025-11-08T01:00:19,131 Given no hashes to check 1 links for project 'scunagi': discarding no candidates 2025-11-08T01:00:19,150 Collecting scunagi==0.5.6 2025-11-08T01:00:19,153 Created temporary directory: /tmp/pip-unpack-_4wmrdcu 2025-11-08T01:00:19,371 Downloading scunagi-0.5.6.tar.gz (7.1 MB) 2025-11-08T01:00:21,906 Added scunagi==0.5.6 from https://files.pythonhosted.org/packages/b7/ad/94a2d75c6a914200443bf95780e90047f6b563ffe04a6bf0a3accbb62395/scunagi-0.5.6.tar.gz to build tracker '/tmp/pip-build-tracker-pmbga7f0' 2025-11-08T01:00:21,907 Running setup.py (path:/tmp/pip-wheel-bbq3imh5/scunagi_5c67c2303f0e4488a5f37d1344faa3da/setup.py) egg_info for package scunagi 2025-11-08T01:00:21,908 Created temporary directory: /tmp/pip-pip-egg-info-qx03p0xe 2025-11-08T01:00:21,909 Preparing metadata (setup.py): started 2025-11-08T01:00:21,910 Running command python setup.py egg_info 2025-11-08T01:00:22,783 running egg_info 2025-11-08T01:00:22,811 creating /tmp/pip-pip-egg-info-qx03p0xe/scUNAGI.egg-info 2025-11-08T01:00:22,812 writing /tmp/pip-pip-egg-info-qx03p0xe/scUNAGI.egg-info/PKG-INFO 2025-11-08T01:00:22,816 writing dependency_links to /tmp/pip-pip-egg-info-qx03p0xe/scUNAGI.egg-info/dependency_links.txt 2025-11-08T01:00:22,819 writing requirements to /tmp/pip-pip-egg-info-qx03p0xe/scUNAGI.egg-info/requires.txt 2025-11-08T01:00:22,821 writing top-level names to /tmp/pip-pip-egg-info-qx03p0xe/scUNAGI.egg-info/top_level.txt 2025-11-08T01:00:22,822 writing manifest file '/tmp/pip-pip-egg-info-qx03p0xe/scUNAGI.egg-info/SOURCES.txt' 2025-11-08T01:00:22,975 reading manifest file '/tmp/pip-pip-egg-info-qx03p0xe/scUNAGI.egg-info/SOURCES.txt' 2025-11-08T01:00:22,977 reading manifest template 'MANIFEST.in' 2025-11-08T01:00:22,978 warning: no files found matching 'LICENSE' 2025-11-08T01:00:22,978 adding license file 'LICENSE.txt' 2025-11-08T01:00:23,005 writing manifest file '/tmp/pip-pip-egg-info-qx03p0xe/scUNAGI.egg-info/SOURCES.txt' 2025-11-08T01:00:23,111 Preparing metadata (setup.py): finished with status 'done' 2025-11-08T01:00:23,116 Source in /tmp/pip-wheel-bbq3imh5/scunagi_5c67c2303f0e4488a5f37d1344faa3da has version 0.5.6, which satisfies requirement scunagi==0.5.6 from https://files.pythonhosted.org/packages/b7/ad/94a2d75c6a914200443bf95780e90047f6b563ffe04a6bf0a3accbb62395/scunagi-0.5.6.tar.gz 2025-11-08T01:00:23,117 Removed scunagi==0.5.6 from https://files.pythonhosted.org/packages/b7/ad/94a2d75c6a914200443bf95780e90047f6b563ffe04a6bf0a3accbb62395/scunagi-0.5.6.tar.gz from build tracker '/tmp/pip-build-tracker-pmbga7f0' 2025-11-08T01:00:23,123 Created temporary directory: /tmp/pip-unpack-hqvmvcbs 2025-11-08T01:00:23,124 Building wheels for collected packages: scunagi 2025-11-08T01:00:23,128 Created temporary directory: /tmp/pip-wheel-95qr7z4x 2025-11-08T01:00:23,128 Building wheel for scunagi (setup.py): started 2025-11-08T01:00:23,130 Destination directory: /tmp/pip-wheel-95qr7z4x 2025-11-08T01:00:23,130 Running command python setup.py bdist_wheel 2025-11-08T01:00:23,977 running bdist_wheel 2025-11-08T01:00:24,111 running build 2025-11-08T01:00:24,112 running build_py 2025-11-08T01:00:24,143 creating build/lib/UNAGI 2025-11-08T01:00:24,145 copying UNAGI/__init__.py -> build/lib/UNAGI 2025-11-08T01:00:24,147 copying UNAGI/UNAGI_tool.py -> build/lib/UNAGI 2025-11-08T01:00:24,150 copying UNAGI/UNAGI_analyst.py -> build/lib/UNAGI 2025-11-08T01:00:24,154 creating build/lib/UNAGI/plotting 2025-11-08T01:00:24,156 copying UNAGI/plotting/__init__.py -> build/lib/UNAGI/plotting 2025-11-08T01:00:24,159 copying UNAGI/plotting/plot_cell_embeddings.py -> build/lib/UNAGI/plotting 2025-11-08T01:00:24,161 copying UNAGI/plotting/plot_stage_dendrogram.py -> build/lib/UNAGI/plotting 2025-11-08T01:00:24,163 copying UNAGI/plotting/plot_cell_type_composition.py -> build/lib/UNAGI/plotting 2025-11-08T01:00:24,166 copying UNAGI/plotting/plot_hierarchical_markers_heatmap.py -> build/lib/UNAGI/plotting 2025-11-08T01:00:24,169 creating build/lib/UNAGI/perturbations 2025-11-08T01:00:24,170 copying UNAGI/perturbations/perturbation_centroid.py -> build/lib/UNAGI/perturbations 2025-11-08T01:00:24,174 copying UNAGI/perturbations/compounds.py -> build/lib/UNAGI/perturbations 2025-11-08T01:00:24,177 copying UNAGI/perturbations/perturbation.py -> build/lib/UNAGI/perturbations 2025-11-08T01:00:24,180 copying UNAGI/perturbations/__init__.py -> build/lib/UNAGI/perturbations 2025-11-08T01:00:24,182 copying UNAGI/perturbations/normalize_analysis_perturbation.py -> build/lib/UNAGI/perturbations 2025-11-08T01:00:24,186 copying UNAGI/perturbations/pathways.py -> build/lib/UNAGI/perturbations 2025-11-08T01:00:24,189 copying UNAGI/perturbations/new_perturbation_strategy.py -> build/lib/UNAGI/perturbations 2025-11-08T01:00:24,192 copying UNAGI/perturbations/analysis_perturbation.py -> build/lib/UNAGI/perturbations 2025-11-08T01:00:24,195 creating build/lib/UNAGI/dynamic_regulatory_networks 2025-11-08T01:00:24,197 copying UNAGI/dynamic_regulatory_networks/__init__.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-08T01:00:24,199 copying UNAGI/dynamic_regulatory_networks/processIDREM.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-08T01:00:24,202 copying UNAGI/dynamic_regulatory_networks/processTFs.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-08T01:00:24,205 creating build/lib/UNAGI/dynamic_graphs 2025-11-08T01:00:24,207 copying UNAGI/dynamic_graphs/__init__.py -> build/lib/UNAGI/dynamic_graphs 2025-11-08T01:00:24,208 copying UNAGI/dynamic_graphs/buildGraph.py -> build/lib/UNAGI/dynamic_graphs 2025-11-08T01:00:24,211 copying UNAGI/dynamic_graphs/distDistance.py -> build/lib/UNAGI/dynamic_graphs 2025-11-08T01:00:24,214 creating build/lib/UNAGI/utils 2025-11-08T01:00:24,215 copying UNAGI/utils/evaluate.py -> build/lib/UNAGI/utils 2025-11-08T01:00:24,218 copying UNAGI/utils/msigdb_data_overlapping.py -> build/lib/UNAGI/utils 2025-11-08T01:00:24,220 copying UNAGI/utils/CPO_utils.py -> build/lib/UNAGI/utils 2025-11-08T01:00:24,223 copying UNAGI/utils/trainer_utils.py -> build/lib/UNAGI/utils 2025-11-08T01:00:24,225 copying UNAGI/utils/__init__.py -> build/lib/UNAGI/utils 2025-11-08T01:00:24,227 copying UNAGI/utils/idrem_helper.py -> build/lib/UNAGI/utils 2025-11-08T01:00:24,229 copying UNAGI/utils/gcn_utils.py -> build/lib/UNAGI/utils 2025-11-08T01:00:24,231 copying UNAGI/utils/analysis_helper.py -> build/lib/UNAGI/utils 2025-11-08T01:00:24,234 copying UNAGI/utils/h5adReader.py -> build/lib/UNAGI/utils 2025-11-08T01:00:24,236 copying UNAGI/utils/attribute_utils.py -> build/lib/UNAGI/utils 2025-11-08T01:00:24,240 creating build/lib/UNAGI/marker_discovery 2025-11-08T01:00:24,241 copying UNAGI/marker_discovery/dynamic_markers_helper.py -> build/lib/UNAGI/marker_discovery 2025-11-08T01:00:24,243 copying UNAGI/marker_discovery/__init__.py -> build/lib/UNAGI/marker_discovery 2025-11-08T01:00:24,245 copying UNAGI/marker_discovery/dynamic_markers.py -> build/lib/UNAGI/marker_discovery 2025-11-08T01:00:24,248 copying UNAGI/marker_discovery/hierachical_static_markers.py -> build/lib/UNAGI/marker_discovery 2025-11-08T01:00:24,251 creating build/lib/UNAGI/model 2025-11-08T01:00:24,252 copying UNAGI/model/__init__.py -> build/lib/UNAGI/model 2025-11-08T01:00:24,254 copying UNAGI/model/models.py -> build/lib/UNAGI/model 2025-11-08T01:00:24,257 copying UNAGI/model/distributions.py -> build/lib/UNAGI/model 2025-11-08T01:00:24,260 creating build/lib/UNAGI/train 2025-11-08T01:00:24,262 copying UNAGI/train/__init__.py -> build/lib/UNAGI/train 2025-11-08T01:00:24,264 copying UNAGI/train/trainer.py -> build/lib/UNAGI/train 2025-11-08T01:00:24,267 copying UNAGI/train/runner.py -> build/lib/UNAGI/train 2025-11-08T01:00:24,270 copying UNAGI/train/customized_elbo.py -> build/lib/UNAGI/train 2025-11-08T01:00:24,272 running egg_info 2025-11-08T01:00:24,302 writing scUNAGI.egg-info/PKG-INFO 2025-11-08T01:00:24,307 writing dependency_links to scUNAGI.egg-info/dependency_links.txt 2025-11-08T01:00:24,310 writing requirements to scUNAGI.egg-info/requires.txt 2025-11-08T01:00:24,312 writing top-level names to scUNAGI.egg-info/top_level.txt 2025-11-08T01:00:24,378 reading manifest file 'scUNAGI.egg-info/SOURCES.txt' 2025-11-08T01:00:24,383 reading manifest template 'MANIFEST.in' 2025-11-08T01:00:24,384 warning: no files found matching 'LICENSE' 2025-11-08T01:00:24,384 adding license file 'LICENSE.txt' 2025-11-08T01:00:24,389 writing manifest file 'scUNAGI.egg-info/SOURCES.txt' 2025-11-08T01:00:24,391 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'UNAGI.data' is absent from the `packages` configuration. 2025-11-08T01:00:24,392 !! 2025-11-08T01:00:24,393 ******************************************************************************** 2025-11-08T01:00:24,393 ############################ 2025-11-08T01:00:24,394 # Package would be ignored # 2025-11-08T01:00:24,394 ############################ 2025-11-08T01:00:24,395 Python recognizes 'UNAGI.data' as an importable package[^1], 2025-11-08T01:00:24,395 but it is absent from setuptools' `packages` configuration. 2025-11-08T01:00:24,397 This leads to an ambiguous overall configuration. If you want to distribute this 2025-11-08T01:00:24,397 package, please make sure that 'UNAGI.data' is explicitly added 2025-11-08T01:00:24,398 to the `packages` configuration field. 2025-11-08T01:00:24,399 Alternatively, you can also rely on setuptools' discovery methods 2025-11-08T01:00:24,400 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-11-08T01:00:24,400 instead of `find_packages(...)`/`find:`). 2025-11-08T01:00:24,401 You can read more about "package discovery" on setuptools documentation page: 2025-11-08T01:00:24,402 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-11-08T01:00:24,403 If you don't want 'UNAGI.data' to be distributed and are 2025-11-08T01:00:24,404 already explicitly excluding 'UNAGI.data' via 2025-11-08T01:00:24,404 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-11-08T01:00:24,405 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-11-08T01:00:24,405 combination with a more fine grained `package-data` configuration. 2025-11-08T01:00:24,423 You can read more about "package data files" on setuptools documentation page: 2025-11-08T01:00:24,429 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-11-08T01:00:24,430 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-11-08T01:00:24,431 even if it does not contain any `.py` files. 2025-11-08T01:00:24,431 On the other hand, currently there is no concept of package data 2025-11-08T01:00:24,432 directory, all directories are treated like packages. 2025-11-08T01:00:24,432 ******************************************************************************** 2025-11-08T01:00:24,435 !! 2025-11-08T01:00:24,435 check.warn(importable) 2025-11-08T01:00:24,436 creating build/lib/UNAGI/data 2025-11-08T01:00:24,437 copying UNAGI/data/brdID2cmapName.npy -> build/lib/UNAGI/data 2025-11-08T01:00:24,437 copying UNAGI/data/cmap_drug_target_genes.npy -> build/lib/UNAGI/data 2025-11-08T01:00:24,438 copying UNAGI/data/gesa_pathways.npy -> build/lib/UNAGI/data 2025-11-08T01:00:24,492 copying UNAGI/data/human_encode.txt -> build/lib/UNAGI/data 2025-11-08T01:00:24,897 copying UNAGI/data/jasper_target_pair.npy -> build/lib/UNAGI/data 2025-11-08T01:00:24,917 copying UNAGI/data/mouse_predicted.txt -> build/lib/UNAGI/data 2025-11-08T01:00:25,174 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-11-08T01:00:25,175 !! 2025-11-08T01:00:25,176 ******************************************************************************** 2025-11-08T01:00:25,176 Please avoid running ``setup.py`` directly. 2025-11-08T01:00:25,177 Instead, use pypa/build, pypa/installer or other 2025-11-08T01:00:25,178 standards-based tools. 2025-11-08T01:00:25,179 This deprecation is overdue, please update your project and remove deprecated 2025-11-08T01:00:25,179 calls to avoid build errors in the future. 2025-11-08T01:00:25,180 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-11-08T01:00:25,181 ******************************************************************************** 2025-11-08T01:00:25,182 !! 2025-11-08T01:00:25,182 self.initialize_options() 2025-11-08T01:00:25,203 installing to build/bdist.linux-armv7l/wheel 2025-11-08T01:00:25,204 running install 2025-11-08T01:00:25,228 running install_lib 2025-11-08T01:00:25,255 creating build/bdist.linux-armv7l/wheel 2025-11-08T01:00:25,258 creating build/bdist.linux-armv7l/wheel/UNAGI 2025-11-08T01:00:25,260 creating build/bdist.linux-armv7l/wheel/UNAGI/plotting 2025-11-08T01:00:25,261 copying build/lib/UNAGI/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-08T01:00:25,263 copying build/lib/UNAGI/plotting/plot_cell_embeddings.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-08T01:00:25,265 copying build/lib/UNAGI/plotting/plot_stage_dendrogram.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-08T01:00:25,267 copying build/lib/UNAGI/plotting/plot_cell_type_composition.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-08T01:00:25,269 copying build/lib/UNAGI/plotting/plot_hierarchical_markers_heatmap.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-08T01:00:25,272 creating build/bdist.linux-armv7l/wheel/UNAGI/perturbations 2025-11-08T01:00:25,273 copying build/lib/UNAGI/perturbations/perturbation_centroid.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T01:00:25,276 copying build/lib/UNAGI/perturbations/compounds.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T01:00:25,279 copying build/lib/UNAGI/perturbations/perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T01:00:25,281 copying build/lib/UNAGI/perturbations/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T01:00:25,283 copying build/lib/UNAGI/perturbations/normalize_analysis_perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T01:00:25,286 copying build/lib/UNAGI/perturbations/pathways.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T01:00:25,288 copying build/lib/UNAGI/perturbations/new_perturbation_strategy.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T01:00:25,290 copying build/lib/UNAGI/perturbations/analysis_perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T01:00:25,293 creating build/bdist.linux-armv7l/wheel/UNAGI/dynamic_regulatory_networks 2025-11-08T01:00:25,294 copying build/lib/UNAGI/dynamic_regulatory_networks/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-08T01:00:25,296 copying build/lib/UNAGI/dynamic_regulatory_networks/processIDREM.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-08T01:00:25,298 copying build/lib/UNAGI/dynamic_regulatory_networks/processTFs.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-08T01:00:25,301 creating build/bdist.linux-armv7l/wheel/UNAGI/dynamic_graphs 2025-11-08T01:00:25,303 copying build/lib/UNAGI/dynamic_graphs/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-08T01:00:25,304 copying build/lib/UNAGI/dynamic_graphs/buildGraph.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-08T01:00:25,306 copying build/lib/UNAGI/dynamic_graphs/distDistance.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-08T01:00:25,308 copying build/lib/UNAGI/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-08T01:00:25,311 creating build/bdist.linux-armv7l/wheel/UNAGI/data 2025-11-08T01:00:25,312 copying build/lib/UNAGI/data/mouse_predicted.txt -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-08T01:00:25,526 copying build/lib/UNAGI/data/brdID2cmapName.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-08T01:00:25,564 copying build/lib/UNAGI/data/human_encode.txt -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-08T01:00:25,975 copying build/lib/UNAGI/data/jasper_target_pair.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-08T01:00:25,993 copying build/lib/UNAGI/data/gesa_pathways.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-08T01:00:26,034 copying build/lib/UNAGI/data/cmap_drug_target_genes.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-08T01:00:26,038 copying build/lib/UNAGI/UNAGI_tool.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-08T01:00:26,042 creating build/bdist.linux-armv7l/wheel/UNAGI/utils 2025-11-08T01:00:26,043 copying build/lib/UNAGI/utils/evaluate.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T01:00:26,045 copying build/lib/UNAGI/utils/msigdb_data_overlapping.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T01:00:26,047 copying build/lib/UNAGI/utils/CPO_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T01:00:26,049 copying build/lib/UNAGI/utils/trainer_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T01:00:26,051 copying build/lib/UNAGI/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T01:00:26,053 copying build/lib/UNAGI/utils/idrem_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T01:00:26,055 copying build/lib/UNAGI/utils/gcn_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T01:00:26,056 copying build/lib/UNAGI/utils/analysis_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T01:00:26,059 copying build/lib/UNAGI/utils/h5adReader.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T01:00:26,060 copying build/lib/UNAGI/utils/attribute_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T01:00:26,063 creating build/bdist.linux-armv7l/wheel/UNAGI/marker_discovery 2025-11-08T01:00:26,064 copying build/lib/UNAGI/marker_discovery/dynamic_markers_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-08T01:00:26,066 copying build/lib/UNAGI/marker_discovery/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-08T01:00:26,068 copying build/lib/UNAGI/marker_discovery/dynamic_markers.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-08T01:00:26,070 copying build/lib/UNAGI/marker_discovery/hierachical_static_markers.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-08T01:00:26,073 creating build/bdist.linux-armv7l/wheel/UNAGI/model 2025-11-08T01:00:26,074 copying build/lib/UNAGI/model/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-08T01:00:26,076 copying build/lib/UNAGI/model/models.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-08T01:00:26,078 copying build/lib/UNAGI/model/distributions.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-08T01:00:26,081 creating build/bdist.linux-armv7l/wheel/UNAGI/train 2025-11-08T01:00:26,082 copying build/lib/UNAGI/train/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-08T01:00:26,084 copying build/lib/UNAGI/train/trainer.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-08T01:00:26,086 copying build/lib/UNAGI/train/runner.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-08T01:00:26,089 copying build/lib/UNAGI/train/customized_elbo.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-08T01:00:26,091 copying build/lib/UNAGI/UNAGI_analyst.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-08T01:00:26,093 running install_egg_info 2025-11-08T01:00:26,128 Copying scUNAGI.egg-info to build/bdist.linux-armv7l/wheel/./scUNAGI-0.5.6-py3.11.egg-info 2025-11-08T01:00:26,138 running install_scripts 2025-11-08T01:00:26,151 creating build/bdist.linux-armv7l/wheel/scunagi-0.5.6.dist-info/WHEEL 2025-11-08T01:00:26,154 creating '/tmp/pip-wheel-95qr7z4x/scunagi-0.5.6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-11-08T01:00:26,158 adding 'UNAGI/UNAGI_analyst.py' 2025-11-08T01:00:26,161 adding 'UNAGI/UNAGI_tool.py' 2025-11-08T01:00:26,162 adding 'UNAGI/__init__.py' 2025-11-08T01:00:26,307 adding 'UNAGI/data/brdID2cmapName.npy' 2025-11-08T01:00:26,341 adding 'UNAGI/data/cmap_drug_target_genes.npy' 2025-11-08T01:00:26,725 adding 'UNAGI/data/gesa_pathways.npy' 2025-11-08T01:00:28,822 adding 'UNAGI/data/human_encode.txt' 2025-11-08T01:00:29,158 adding 'UNAGI/data/jasper_target_pair.npy' 2025-11-08T01:00:29,974 adding 'UNAGI/data/mouse_predicted.txt' 2025-11-08T01:00:30,070 adding 'UNAGI/dynamic_graphs/__init__.py' 2025-11-08T01:00:30,071 adding 'UNAGI/dynamic_graphs/buildGraph.py' 2025-11-08T01:00:30,073 adding 'UNAGI/dynamic_graphs/distDistance.py' 2025-11-08T01:00:30,074 adding 'UNAGI/dynamic_regulatory_networks/__init__.py' 2025-11-08T01:00:30,076 adding 'UNAGI/dynamic_regulatory_networks/processIDREM.py' 2025-11-08T01:00:30,079 adding 'UNAGI/dynamic_regulatory_networks/processTFs.py' 2025-11-08T01:00:30,081 adding 'UNAGI/marker_discovery/__init__.py' 2025-11-08T01:00:30,083 adding 'UNAGI/marker_discovery/dynamic_markers.py' 2025-11-08T01:00:30,084 adding 'UNAGI/marker_discovery/dynamic_markers_helper.py' 2025-11-08T01:00:30,087 adding 'UNAGI/marker_discovery/hierachical_static_markers.py' 2025-11-08T01:00:30,089 adding 'UNAGI/model/__init__.py' 2025-11-08T01:00:30,090 adding 'UNAGI/model/distributions.py' 2025-11-08T01:00:30,092 adding 'UNAGI/model/models.py' 2025-11-08T01:00:30,094 adding 'UNAGI/perturbations/__init__.py' 2025-11-08T01:00:30,098 adding 'UNAGI/perturbations/analysis_perturbation.py' 2025-11-08T01:00:30,100 adding 'UNAGI/perturbations/compounds.py' 2025-11-08T01:00:30,103 adding 'UNAGI/perturbations/new_perturbation_strategy.py' 2025-11-08T01:00:30,107 adding 'UNAGI/perturbations/normalize_analysis_perturbation.py' 2025-11-08T01:00:30,109 adding 'UNAGI/perturbations/pathways.py' 2025-11-08T01:00:30,112 adding 'UNAGI/perturbations/perturbation.py' 2025-11-08T01:00:30,118 adding 'UNAGI/perturbations/perturbation_centroid.py' 2025-11-08T01:00:30,120 adding 'UNAGI/plotting/__init__.py' 2025-11-08T01:00:30,121 adding 'UNAGI/plotting/plot_cell_embeddings.py' 2025-11-08T01:00:30,123 adding 'UNAGI/plotting/plot_cell_type_composition.py' 2025-11-08T01:00:30,124 adding 'UNAGI/plotting/plot_hierarchical_markers_heatmap.py' 2025-11-08T01:00:30,126 adding 'UNAGI/plotting/plot_stage_dendrogram.py' 2025-11-08T01:00:30,127 adding 'UNAGI/train/__init__.py' 2025-11-08T01:00:30,129 adding 'UNAGI/train/customized_elbo.py' 2025-11-08T01:00:30,131 adding 'UNAGI/train/runner.py' 2025-11-08T01:00:30,133 adding 'UNAGI/train/trainer.py' 2025-11-08T01:00:30,135 adding 'UNAGI/utils/CPO_utils.py' 2025-11-08T01:00:30,137 adding 'UNAGI/utils/__init__.py' 2025-11-08T01:00:30,139 adding 'UNAGI/utils/analysis_helper.py' 2025-11-08T01:00:30,141 adding 'UNAGI/utils/attribute_utils.py' 2025-11-08T01:00:30,143 adding 'UNAGI/utils/evaluate.py' 2025-11-08T01:00:30,145 adding 'UNAGI/utils/gcn_utils.py' 2025-11-08T01:00:30,146 adding 'UNAGI/utils/h5adReader.py' 2025-11-08T01:00:30,148 adding 'UNAGI/utils/idrem_helper.py' 2025-11-08T01:00:30,149 adding 'UNAGI/utils/msigdb_data_overlapping.py' 2025-11-08T01:00:30,151 adding 'UNAGI/utils/trainer_utils.py' 2025-11-08T01:00:30,157 adding 'scunagi-0.5.6.dist-info/licenses/LICENSE.txt' 2025-11-08T01:00:30,159 adding 'scunagi-0.5.6.dist-info/METADATA' 2025-11-08T01:00:30,160 adding 'scunagi-0.5.6.dist-info/WHEEL' 2025-11-08T01:00:30,161 adding 'scunagi-0.5.6.dist-info/top_level.txt' 2025-11-08T01:00:30,163 adding 'scunagi-0.5.6.dist-info/RECORD' 2025-11-08T01:00:30,244 removing build/bdist.linux-armv7l/wheel 2025-11-08T01:00:30,396 Building wheel for scunagi (setup.py): finished with status 'done' 2025-11-08T01:00:30,469 Created wheel for scunagi: filename=scunagi-0.5.6-py3-none-any.whl size=7158742 sha256=1a9f5aa76347b2eafff106614577b19994460c256ad78e988b00af6a1846ff34 2025-11-08T01:00:30,471 Stored in directory: /tmp/pip-ephem-wheel-cache-cwb2eeyf/wheels/8a/29/85/d0d241b4a115c0a7f4e6442920864c9252adbb897b72540720 2025-11-08T01:00:30,488 Successfully built scunagi 2025-11-08T01:00:30,675 Removed build tracker: '/tmp/pip-build-tracker-pmbga7f0'