2025-11-08T15:25:38,852 Created temporary directory: /tmp/pip-ephem-wheel-cache-bb1w5vb7 2025-11-08T15:25:38,854 Created temporary directory: /tmp/pip-build-tracker-7jez9lkz 2025-11-08T15:25:38,854 Initialized build tracking at /tmp/pip-build-tracker-7jez9lkz 2025-11-08T15:25:38,855 Created build tracker: /tmp/pip-build-tracker-7jez9lkz 2025-11-08T15:25:38,855 Entered build tracker: /tmp/pip-build-tracker-7jez9lkz 2025-11-08T15:25:38,856 Created temporary directory: /tmp/pip-wheel-ojr3qu26 2025-11-08T15:25:38,859 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 2025-11-08T15:25:38,861 Created temporary directory: /tmp/pip-ephem-wheel-cache-cu7k0qlg 2025-11-08T15:25:38,883 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-08T15:25:38,887 2 location(s) to search for versions of scunagi: 2025-11-08T15:25:38,887 * https://pypi.org/simple/scunagi/ 2025-11-08T15:25:38,887 * https://www.piwheels.org/simple/scunagi/ 2025-11-08T15:25:38,888 Fetching project page and analyzing links: https://pypi.org/simple/scunagi/ 2025-11-08T15:25:38,888 Getting page https://pypi.org/simple/scunagi/ 2025-11-08T15:25:38,890 Found index url https://pypi.org/simple 2025-11-08T15:25:39,101 Fetched page https://pypi.org/simple/scunagi/ as application/vnd.pypi.simple.v1+json 2025-11-08T15:25:39,108 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/) 2025-11-08T15:25:39,108 Found link https://files.pythonhosted.org/packages/e1/f1/0de90828615ce729086b0bd0040d92816d065d709b8d4cf23aa83212bd12/scUNAGI-0.1.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.1 2025-11-08T15:25:39,109 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) 2025-11-08T15:25:39,110 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 2025-11-08T15:25:39,111 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/) 2025-11-08T15:25:39,111 Found link https://files.pythonhosted.org/packages/27/25/685283d6b4b5c35f39f23f234c4b69ceb58cfe44d5847fb370d65014efc7/scUNAGI-0.2.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.2 2025-11-08T15:25:39,112 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/) 2025-11-08T15:25:39,113 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 2025-11-08T15:25:39,113 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) 2025-11-08T15:25:39,114 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 2025-11-08T15:25:39,115 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) 2025-11-08T15:25:39,116 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 2025-11-08T15:25:39,117 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) 2025-11-08T15:25:39,118 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 2025-11-08T15:25:39,119 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/) 2025-11-08T15:25:39,119 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 2025-11-08T15:25:39,120 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/) 2025-11-08T15:25:39,120 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 2025-11-08T15:25:39,121 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/) 2025-11-08T15:25:39,122 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 2025-11-08T15:25:39,122 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/) 2025-11-08T15:25:39,123 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 2025-11-08T15:25:39,124 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/) 2025-11-08T15:25:39,125 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 2025-11-08T15:25:39,126 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/) 2025-11-08T15:25:39,126 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 2025-11-08T15:25:39,127 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/31/cf/e1774bb5a883bf02886c2ac4c833e4bbc52dd74e9c132cf93962b9ab8728/scunagi-0.5.7-py3-none-any.whl (from https://pypi.org/simple/scunagi/) 2025-11-08T15:25:39,128 Found link https://files.pythonhosted.org/packages/02/02/0801aea5261eff8a958d2ba32db414202740cfcc5094fcf1baa30d15283a/scunagi-0.5.7.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.5.7 2025-11-08T15:25:39,129 Fetching project page and analyzing links: https://www.piwheels.org/simple/scunagi/ 2025-11-08T15:25:39,130 Getting page https://www.piwheels.org/simple/scunagi/ 2025-11-08T15:25:39,131 Found index url https://www.piwheels.org/simple 2025-11-08T15:25:39,412 Fetched page https://www.piwheels.org/simple/scunagi/ as text/html 2025-11-08T15:25:39,415 Skipping link: No binaries permitted for scunagi: https://www.piwheels.org/simple/scunagi/scunagi-0.5.6-py3-none-any.whl#sha256=1a9f5aa76347b2eafff106614577b19994460c256ad78e988b00af6a1846ff34 (from https://www.piwheels.org/simple/scunagi/) 2025-11-08T15:25:39,416 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/) 2025-11-08T15:25:39,416 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/) 2025-11-08T15:25:39,417 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/) 2025-11-08T15:25:39,417 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/) 2025-11-08T15:25:39,418 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/) 2025-11-08T15:25:39,418 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/) 2025-11-08T15:25:39,419 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/) 2025-11-08T15:25:39,419 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/) 2025-11-08T15:25:39,420 Skipping link: not a file: https://www.piwheels.org/simple/scunagi/ 2025-11-08T15:25:39,421 Skipping link: not a file: https://pypi.org/simple/scunagi/ 2025-11-08T15:25:39,441 Given no hashes to check 1 links for project 'scunagi': discarding no candidates 2025-11-08T15:25:39,458 Collecting scunagi==0.5.7 2025-11-08T15:25:39,461 Created temporary directory: /tmp/pip-unpack-2t3x6zix 2025-11-08T15:25:39,677 Downloading scunagi-0.5.7.tar.gz (7.1 MB) 2025-11-08T15:25:42,340 Added scunagi==0.5.7 from https://files.pythonhosted.org/packages/02/02/0801aea5261eff8a958d2ba32db414202740cfcc5094fcf1baa30d15283a/scunagi-0.5.7.tar.gz to build tracker '/tmp/pip-build-tracker-7jez9lkz' 2025-11-08T15:25:42,341 Running setup.py (path:/tmp/pip-wheel-ojr3qu26/scunagi_1b1a69479dbd479eb179bd94c1368410/setup.py) egg_info for package scunagi 2025-11-08T15:25:42,342 Created temporary directory: /tmp/pip-pip-egg-info-f8nqq6ws 2025-11-08T15:25:42,343 Preparing metadata (setup.py): started 2025-11-08T15:25:42,344 Running command python setup.py egg_info 2025-11-08T15:25:43,277 running egg_info 2025-11-08T15:25:43,305 creating /tmp/pip-pip-egg-info-f8nqq6ws/scUNAGI.egg-info 2025-11-08T15:25:43,306 writing /tmp/pip-pip-egg-info-f8nqq6ws/scUNAGI.egg-info/PKG-INFO 2025-11-08T15:25:43,311 writing dependency_links to /tmp/pip-pip-egg-info-f8nqq6ws/scUNAGI.egg-info/dependency_links.txt 2025-11-08T15:25:43,314 writing requirements to /tmp/pip-pip-egg-info-f8nqq6ws/scUNAGI.egg-info/requires.txt 2025-11-08T15:25:43,315 writing top-level names to /tmp/pip-pip-egg-info-f8nqq6ws/scUNAGI.egg-info/top_level.txt 2025-11-08T15:25:43,317 writing manifest file '/tmp/pip-pip-egg-info-f8nqq6ws/scUNAGI.egg-info/SOURCES.txt' 2025-11-08T15:25:43,416 reading manifest file '/tmp/pip-pip-egg-info-f8nqq6ws/scUNAGI.egg-info/SOURCES.txt' 2025-11-08T15:25:43,417 reading manifest template 'MANIFEST.in' 2025-11-08T15:25:43,419 warning: no files found matching 'LICENSE' 2025-11-08T15:25:43,419 adding license file 'LICENSE.txt' 2025-11-08T15:25:43,423 writing manifest file '/tmp/pip-pip-egg-info-f8nqq6ws/scUNAGI.egg-info/SOURCES.txt' 2025-11-08T15:25:43,528 Preparing metadata (setup.py): finished with status 'done' 2025-11-08T15:25:43,533 Source in /tmp/pip-wheel-ojr3qu26/scunagi_1b1a69479dbd479eb179bd94c1368410 has version 0.5.7, which satisfies requirement scunagi==0.5.7 from https://files.pythonhosted.org/packages/02/02/0801aea5261eff8a958d2ba32db414202740cfcc5094fcf1baa30d15283a/scunagi-0.5.7.tar.gz 2025-11-08T15:25:43,534 Removed scunagi==0.5.7 from https://files.pythonhosted.org/packages/02/02/0801aea5261eff8a958d2ba32db414202740cfcc5094fcf1baa30d15283a/scunagi-0.5.7.tar.gz from build tracker '/tmp/pip-build-tracker-7jez9lkz' 2025-11-08T15:25:43,541 Created temporary directory: /tmp/pip-unpack-hs6bc295 2025-11-08T15:25:43,541 Building wheels for collected packages: scunagi 2025-11-08T15:25:43,546 Created temporary directory: /tmp/pip-wheel-gwyhwhim 2025-11-08T15:25:43,546 Building wheel for scunagi (setup.py): started 2025-11-08T15:25:43,548 Destination directory: /tmp/pip-wheel-gwyhwhim 2025-11-08T15:25:43,548 Running command python setup.py bdist_wheel 2025-11-08T15:25:44,391 running bdist_wheel 2025-11-08T15:25:44,523 running build 2025-11-08T15:25:44,524 running build_py 2025-11-08T15:25:44,554 creating build/lib/UNAGI 2025-11-08T15:25:44,556 copying UNAGI/UNAGI_tool.py -> build/lib/UNAGI 2025-11-08T15:25:44,559 copying UNAGI/UNAGI_analyst.py -> build/lib/UNAGI 2025-11-08T15:25:44,562 copying UNAGI/__init__.py -> build/lib/UNAGI 2025-11-08T15:25:44,565 creating build/lib/UNAGI/perturbations 2025-11-08T15:25:44,566 copying UNAGI/perturbations/perturbation_centroid.py -> build/lib/UNAGI/perturbations 2025-11-08T15:25:44,569 copying UNAGI/perturbations/analysis_perturbation.py -> build/lib/UNAGI/perturbations 2025-11-08T15:25:44,572 copying UNAGI/perturbations/new_perturbation_strategy.py -> build/lib/UNAGI/perturbations 2025-11-08T15:25:44,574 copying UNAGI/perturbations/compounds.py -> build/lib/UNAGI/perturbations 2025-11-08T15:25:44,577 copying UNAGI/perturbations/pathways.py -> build/lib/UNAGI/perturbations 2025-11-08T15:25:44,580 copying UNAGI/perturbations/__init__.py -> build/lib/UNAGI/perturbations 2025-11-08T15:25:44,582 copying UNAGI/perturbations/normalize_analysis_perturbation.py -> build/lib/UNAGI/perturbations 2025-11-08T15:25:44,585 copying UNAGI/perturbations/perturbation.py -> build/lib/UNAGI/perturbations 2025-11-08T15:25:44,589 creating build/lib/UNAGI/model 2025-11-08T15:25:44,590 copying UNAGI/model/distributions.py -> build/lib/UNAGI/model 2025-11-08T15:25:44,593 copying UNAGI/model/models.py -> build/lib/UNAGI/model 2025-11-08T15:25:44,596 copying UNAGI/model/__init__.py -> build/lib/UNAGI/model 2025-11-08T15:25:44,598 creating build/lib/UNAGI/dynamic_graphs 2025-11-08T15:25:44,599 copying UNAGI/dynamic_graphs/distDistance.py -> build/lib/UNAGI/dynamic_graphs 2025-11-08T15:25:44,602 copying UNAGI/dynamic_graphs/buildGraph.py -> build/lib/UNAGI/dynamic_graphs 2025-11-08T15:25:44,605 copying UNAGI/dynamic_graphs/__init__.py -> build/lib/UNAGI/dynamic_graphs 2025-11-08T15:25:44,607 creating build/lib/UNAGI/utils 2025-11-08T15:25:44,608 copying UNAGI/utils/idrem_helper.py -> build/lib/UNAGI/utils 2025-11-08T15:25:44,611 copying UNAGI/utils/evaluate.py -> build/lib/UNAGI/utils 2025-11-08T15:25:44,614 copying UNAGI/utils/gcn_utils.py -> build/lib/UNAGI/utils 2025-11-08T15:25:44,616 copying UNAGI/utils/h5adReader.py -> build/lib/UNAGI/utils 2025-11-08T15:25:44,618 copying UNAGI/utils/CPO_utils.py -> build/lib/UNAGI/utils 2025-11-08T15:25:44,620 copying UNAGI/utils/analysis_helper.py -> build/lib/UNAGI/utils 2025-11-08T15:25:44,623 copying UNAGI/utils/trainer_utils.py -> build/lib/UNAGI/utils 2025-11-08T15:25:44,625 copying UNAGI/utils/attribute_utils.py -> build/lib/UNAGI/utils 2025-11-08T15:25:44,628 copying UNAGI/utils/__init__.py -> build/lib/UNAGI/utils 2025-11-08T15:25:44,630 copying UNAGI/utils/msigdb_data_overlapping.py -> build/lib/UNAGI/utils 2025-11-08T15:25:44,632 creating build/lib/UNAGI/plotting 2025-11-08T15:25:44,633 copying UNAGI/plotting/plot_cell_type_composition.py -> build/lib/UNAGI/plotting 2025-11-08T15:25:44,635 copying UNAGI/plotting/plot_cell_embeddings.py -> build/lib/UNAGI/plotting 2025-11-08T15:25:44,637 copying UNAGI/plotting/plot_hierarchical_markers_heatmap.py -> build/lib/UNAGI/plotting 2025-11-08T15:25:44,639 copying UNAGI/plotting/plot_stage_dendrogram.py -> build/lib/UNAGI/plotting 2025-11-08T15:25:44,641 copying UNAGI/plotting/__init__.py -> build/lib/UNAGI/plotting 2025-11-08T15:25:44,643 creating build/lib/UNAGI/train 2025-11-08T15:25:44,644 copying UNAGI/train/trainer.py -> build/lib/UNAGI/train 2025-11-08T15:25:44,646 copying UNAGI/train/customized_elbo.py -> build/lib/UNAGI/train 2025-11-08T15:25:44,649 copying UNAGI/train/runner.py -> build/lib/UNAGI/train 2025-11-08T15:25:44,651 copying UNAGI/train/__init__.py -> build/lib/UNAGI/train 2025-11-08T15:25:44,653 creating build/lib/UNAGI/marker_discovery 2025-11-08T15:25:44,654 copying UNAGI/marker_discovery/dynamic_markers.py -> build/lib/UNAGI/marker_discovery 2025-11-08T15:25:44,656 copying UNAGI/marker_discovery/hierachical_static_markers.py -> build/lib/UNAGI/marker_discovery 2025-11-08T15:25:44,659 copying UNAGI/marker_discovery/dynamic_markers_helper.py -> build/lib/UNAGI/marker_discovery 2025-11-08T15:25:44,661 copying UNAGI/marker_discovery/__init__.py -> build/lib/UNAGI/marker_discovery 2025-11-08T15:25:44,663 creating build/lib/UNAGI/dynamic_regulatory_networks 2025-11-08T15:25:44,664 copying UNAGI/dynamic_regulatory_networks/processIDREM.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-08T15:25:44,666 copying UNAGI/dynamic_regulatory_networks/__init__.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-08T15:25:44,668 copying UNAGI/dynamic_regulatory_networks/processTFs.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-08T15:25:44,670 running egg_info 2025-11-08T15:25:44,699 writing scUNAGI.egg-info/PKG-INFO 2025-11-08T15:25:44,703 writing dependency_links to scUNAGI.egg-info/dependency_links.txt 2025-11-08T15:25:44,706 writing requirements to scUNAGI.egg-info/requires.txt 2025-11-08T15:25:44,707 writing top-level names to scUNAGI.egg-info/top_level.txt 2025-11-08T15:25:44,746 reading manifest file 'scUNAGI.egg-info/SOURCES.txt' 2025-11-08T15:25:44,750 reading manifest template 'MANIFEST.in' 2025-11-08T15:25:44,751 warning: no files found matching 'LICENSE' 2025-11-08T15:25:44,752 adding license file 'LICENSE.txt' 2025-11-08T15:25:44,756 writing manifest file 'scUNAGI.egg-info/SOURCES.txt' 2025-11-08T15:25:44,758 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'UNAGI.data' is absent from the `packages` configuration. 2025-11-08T15:25:44,759 !! 2025-11-08T15:25:44,760 ******************************************************************************** 2025-11-08T15:25:44,760 ############################ 2025-11-08T15:25:44,761 # Package would be ignored # 2025-11-08T15:25:44,761 ############################ 2025-11-08T15:25:44,762 Python recognizes 'UNAGI.data' as an importable package[^1], 2025-11-08T15:25:44,762 but it is absent from setuptools' `packages` configuration. 2025-11-08T15:25:44,763 This leads to an ambiguous overall configuration. If you want to distribute this 2025-11-08T15:25:44,764 package, please make sure that 'UNAGI.data' is explicitly added 2025-11-08T15:25:44,764 to the `packages` configuration field. 2025-11-08T15:25:44,765 Alternatively, you can also rely on setuptools' discovery methods 2025-11-08T15:25:44,766 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-11-08T15:25:44,766 instead of `find_packages(...)`/`find:`). 2025-11-08T15:25:44,767 You can read more about "package discovery" on setuptools documentation page: 2025-11-08T15:25:44,768 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-11-08T15:25:44,769 If you don't want 'UNAGI.data' to be distributed and are 2025-11-08T15:25:44,769 already explicitly excluding 'UNAGI.data' via 2025-11-08T15:25:44,770 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-11-08T15:25:44,770 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-11-08T15:25:44,771 combination with a more fine grained `package-data` configuration. 2025-11-08T15:25:44,771 You can read more about "package data files" on setuptools documentation page: 2025-11-08T15:25:44,772 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-11-08T15:25:44,774 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-11-08T15:25:44,775 even if it does not contain any `.py` files. 2025-11-08T15:25:44,776 On the other hand, currently there is no concept of package data 2025-11-08T15:25:44,777 directory, all directories are treated like packages. 2025-11-08T15:25:44,777 ******************************************************************************** 2025-11-08T15:25:44,778 !! 2025-11-08T15:25:44,779 check.warn(importable) 2025-11-08T15:25:44,780 creating build/lib/UNAGI/data 2025-11-08T15:25:44,780 copying UNAGI/data/brdID2cmapName.npy -> build/lib/UNAGI/data 2025-11-08T15:25:44,797 copying UNAGI/data/cmap_drug_target_genes.npy -> build/lib/UNAGI/data 2025-11-08T15:25:44,801 copying UNAGI/data/gesa_pathways.npy -> build/lib/UNAGI/data 2025-11-08T15:25:44,895 copying UNAGI/data/human_encode.txt -> build/lib/UNAGI/data 2025-11-08T15:25:45,297 copying UNAGI/data/jasper_target_pair.npy -> build/lib/UNAGI/data 2025-11-08T15:25:45,319 copying UNAGI/data/mouse_predicted.txt -> build/lib/UNAGI/data 2025-11-08T15:25:45,589 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-11-08T15:25:45,589 !! 2025-11-08T15:25:45,590 ******************************************************************************** 2025-11-08T15:25:45,591 Please avoid running ``setup.py`` directly. 2025-11-08T15:25:45,592 Instead, use pypa/build, pypa/installer or other 2025-11-08T15:25:45,592 standards-based tools. 2025-11-08T15:25:45,593 This deprecation is overdue, please update your project and remove deprecated 2025-11-08T15:25:45,594 calls to avoid build errors in the future. 2025-11-08T15:25:45,595 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-11-08T15:25:45,596 ******************************************************************************** 2025-11-08T15:25:45,597 !! 2025-11-08T15:25:45,597 self.initialize_options() 2025-11-08T15:25:45,617 installing to build/bdist.linux-armv7l/wheel 2025-11-08T15:25:45,618 running install 2025-11-08T15:25:45,641 running install_lib 2025-11-08T15:25:45,669 creating build/bdist.linux-armv7l/wheel 2025-11-08T15:25:45,671 creating build/bdist.linux-armv7l/wheel/UNAGI 2025-11-08T15:25:45,673 creating build/bdist.linux-armv7l/wheel/UNAGI/perturbations 2025-11-08T15:25:45,674 copying build/lib/UNAGI/perturbations/perturbation_centroid.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T15:25:45,677 copying build/lib/UNAGI/perturbations/analysis_perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T15:25:45,680 copying build/lib/UNAGI/perturbations/new_perturbation_strategy.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T15:25:45,684 copying build/lib/UNAGI/perturbations/compounds.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T15:25:45,689 copying build/lib/UNAGI/perturbations/pathways.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T15:25:45,691 copying build/lib/UNAGI/perturbations/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T15:25:45,693 copying build/lib/UNAGI/perturbations/normalize_analysis_perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T15:25:45,697 copying build/lib/UNAGI/perturbations/perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-08T15:25:45,700 copying build/lib/UNAGI/UNAGI_tool.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-08T15:25:45,703 creating build/bdist.linux-armv7l/wheel/UNAGI/model 2025-11-08T15:25:45,705 copying build/lib/UNAGI/model/distributions.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-08T15:25:45,708 copying build/lib/UNAGI/model/models.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-08T15:25:45,710 copying build/lib/UNAGI/model/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-08T15:25:45,713 creating build/bdist.linux-armv7l/wheel/UNAGI/dynamic_graphs 2025-11-08T15:25:45,714 copying build/lib/UNAGI/dynamic_graphs/distDistance.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-08T15:25:45,717 copying build/lib/UNAGI/dynamic_graphs/buildGraph.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-08T15:25:45,720 copying build/lib/UNAGI/dynamic_graphs/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-08T15:25:45,722 creating build/bdist.linux-armv7l/wheel/UNAGI/utils 2025-11-08T15:25:45,724 copying build/lib/UNAGI/utils/idrem_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T15:25:45,727 copying build/lib/UNAGI/utils/evaluate.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T15:25:45,729 copying build/lib/UNAGI/utils/gcn_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T15:25:45,732 copying build/lib/UNAGI/utils/h5adReader.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T15:25:45,734 copying build/lib/UNAGI/utils/CPO_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T15:25:45,737 copying build/lib/UNAGI/utils/analysis_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T15:25:45,740 copying build/lib/UNAGI/utils/trainer_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T15:25:45,742 copying build/lib/UNAGI/utils/attribute_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T15:25:45,745 copying build/lib/UNAGI/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T15:25:45,747 copying build/lib/UNAGI/utils/msigdb_data_overlapping.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-08T15:25:45,750 creating build/bdist.linux-armv7l/wheel/UNAGI/plotting 2025-11-08T15:25:45,751 copying build/lib/UNAGI/plotting/plot_cell_type_composition.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-08T15:25:45,754 copying build/lib/UNAGI/plotting/plot_cell_embeddings.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-08T15:25:45,756 copying build/lib/UNAGI/plotting/plot_hierarchical_markers_heatmap.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-08T15:25:45,759 copying build/lib/UNAGI/plotting/plot_stage_dendrogram.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-08T15:25:45,761 copying build/lib/UNAGI/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-08T15:25:45,763 copying build/lib/UNAGI/UNAGI_analyst.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-08T15:25:45,767 creating build/bdist.linux-armv7l/wheel/UNAGI/data 2025-11-08T15:25:45,768 copying build/lib/UNAGI/data/mouse_predicted.txt -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-08T15:25:46,017 copying build/lib/UNAGI/data/brdID2cmapName.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-08T15:25:46,042 copying build/lib/UNAGI/data/human_encode.txt -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-08T15:25:46,486 copying build/lib/UNAGI/data/gesa_pathways.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-08T15:25:46,525 copying build/lib/UNAGI/data/cmap_drug_target_genes.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-08T15:25:46,530 copying build/lib/UNAGI/data/jasper_target_pair.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-08T15:25:46,547 copying build/lib/UNAGI/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-08T15:25:46,549 creating build/bdist.linux-armv7l/wheel/UNAGI/train 2025-11-08T15:25:46,551 copying build/lib/UNAGI/train/trainer.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-08T15:25:46,554 copying build/lib/UNAGI/train/customized_elbo.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-08T15:25:46,557 copying build/lib/UNAGI/train/runner.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-08T15:25:46,559 copying build/lib/UNAGI/train/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-08T15:25:46,562 creating build/bdist.linux-armv7l/wheel/UNAGI/marker_discovery 2025-11-08T15:25:46,563 copying build/lib/UNAGI/marker_discovery/dynamic_markers.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-08T15:25:46,566 copying build/lib/UNAGI/marker_discovery/hierachical_static_markers.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-08T15:25:46,569 copying build/lib/UNAGI/marker_discovery/dynamic_markers_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-08T15:25:46,572 copying build/lib/UNAGI/marker_discovery/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-08T15:25:46,574 creating build/bdist.linux-armv7l/wheel/UNAGI/dynamic_regulatory_networks 2025-11-08T15:25:46,575 copying build/lib/UNAGI/dynamic_regulatory_networks/processIDREM.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-08T15:25:46,578 copying build/lib/UNAGI/dynamic_regulatory_networks/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-08T15:25:46,580 copying build/lib/UNAGI/dynamic_regulatory_networks/processTFs.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-08T15:25:46,583 running install_egg_info 2025-11-08T15:25:46,618 Copying scUNAGI.egg-info to build/bdist.linux-armv7l/wheel/./scUNAGI-0.5.7-py3.11.egg-info 2025-11-08T15:25:46,628 running install_scripts 2025-11-08T15:25:46,641 creating build/bdist.linux-armv7l/wheel/scunagi-0.5.7.dist-info/WHEEL 2025-11-08T15:25:46,644 creating '/tmp/pip-wheel-gwyhwhim/scunagi-0.5.7-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-11-08T15:25:46,648 adding 'UNAGI/UNAGI_analyst.py' 2025-11-08T15:25:46,652 adding 'UNAGI/UNAGI_tool.py' 2025-11-08T15:25:46,653 adding 'UNAGI/__init__.py' 2025-11-08T15:25:46,800 adding 'UNAGI/data/brdID2cmapName.npy' 2025-11-08T15:25:46,835 adding 'UNAGI/data/cmap_drug_target_genes.npy' 2025-11-08T15:25:47,191 adding 'UNAGI/data/gesa_pathways.npy' 2025-11-08T15:25:49,329 adding 'UNAGI/data/human_encode.txt' 2025-11-08T15:25:49,664 adding 'UNAGI/data/jasper_target_pair.npy' 2025-11-08T15:25:50,494 adding 'UNAGI/data/mouse_predicted.txt' 2025-11-08T15:25:50,591 adding 'UNAGI/dynamic_graphs/__init__.py' 2025-11-08T15:25:50,592 adding 'UNAGI/dynamic_graphs/buildGraph.py' 2025-11-08T15:25:50,594 adding 'UNAGI/dynamic_graphs/distDistance.py' 2025-11-08T15:25:50,596 adding 'UNAGI/dynamic_regulatory_networks/__init__.py' 2025-11-08T15:25:50,599 adding 'UNAGI/dynamic_regulatory_networks/processIDREM.py' 2025-11-08T15:25:50,601 adding 'UNAGI/dynamic_regulatory_networks/processTFs.py' 2025-11-08T15:25:50,603 adding 'UNAGI/marker_discovery/__init__.py' 2025-11-08T15:25:50,605 adding 'UNAGI/marker_discovery/dynamic_markers.py' 2025-11-08T15:25:50,607 adding 'UNAGI/marker_discovery/dynamic_markers_helper.py' 2025-11-08T15:25:50,610 adding 'UNAGI/marker_discovery/hierachical_static_markers.py' 2025-11-08T15:25:50,612 adding 'UNAGI/model/__init__.py' 2025-11-08T15:25:50,614 adding 'UNAGI/model/distributions.py' 2025-11-08T15:25:50,616 adding 'UNAGI/model/models.py' 2025-11-08T15:25:50,619 adding 'UNAGI/perturbations/__init__.py' 2025-11-08T15:25:50,623 adding 'UNAGI/perturbations/analysis_perturbation.py' 2025-11-08T15:25:50,626 adding 'UNAGI/perturbations/compounds.py' 2025-11-08T15:25:50,628 adding 'UNAGI/perturbations/new_perturbation_strategy.py' 2025-11-08T15:25:50,633 adding 'UNAGI/perturbations/normalize_analysis_perturbation.py' 2025-11-08T15:25:50,635 adding 'UNAGI/perturbations/pathways.py' 2025-11-08T15:25:50,639 adding 'UNAGI/perturbations/perturbation.py' 2025-11-08T15:25:50,645 adding 'UNAGI/perturbations/perturbation_centroid.py' 2025-11-08T15:25:50,647 adding 'UNAGI/plotting/__init__.py' 2025-11-08T15:25:50,649 adding 'UNAGI/plotting/plot_cell_embeddings.py' 2025-11-08T15:25:50,651 adding 'UNAGI/plotting/plot_cell_type_composition.py' 2025-11-08T15:25:50,653 adding 'UNAGI/plotting/plot_hierarchical_markers_heatmap.py' 2025-11-08T15:25:50,655 adding 'UNAGI/plotting/plot_stage_dendrogram.py' 2025-11-08T15:25:50,657 adding 'UNAGI/train/__init__.py' 2025-11-08T15:25:50,659 adding 'UNAGI/train/customized_elbo.py' 2025-11-08T15:25:50,662 adding 'UNAGI/train/runner.py' 2025-11-08T15:25:50,664 adding 'UNAGI/train/trainer.py' 2025-11-08T15:25:50,666 adding 'UNAGI/utils/CPO_utils.py' 2025-11-08T15:25:50,668 adding 'UNAGI/utils/__init__.py' 2025-11-08T15:25:50,671 adding 'UNAGI/utils/analysis_helper.py' 2025-11-08T15:25:50,674 adding 'UNAGI/utils/attribute_utils.py' 2025-11-08T15:25:50,676 adding 'UNAGI/utils/evaluate.py' 2025-11-08T15:25:50,678 adding 'UNAGI/utils/gcn_utils.py' 2025-11-08T15:25:50,679 adding 'UNAGI/utils/h5adReader.py' 2025-11-08T15:25:50,681 adding 'UNAGI/utils/idrem_helper.py' 2025-11-08T15:25:50,683 adding 'UNAGI/utils/msigdb_data_overlapping.py' 2025-11-08T15:25:50,685 adding 'UNAGI/utils/trainer_utils.py' 2025-11-08T15:25:50,692 adding 'scunagi-0.5.7.dist-info/licenses/LICENSE.txt' 2025-11-08T15:25:50,694 adding 'scunagi-0.5.7.dist-info/METADATA' 2025-11-08T15:25:50,696 adding 'scunagi-0.5.7.dist-info/WHEEL' 2025-11-08T15:25:50,697 adding 'scunagi-0.5.7.dist-info/top_level.txt' 2025-11-08T15:25:50,698 adding 'scunagi-0.5.7.dist-info/RECORD' 2025-11-08T15:25:50,769 removing build/bdist.linux-armv7l/wheel 2025-11-08T15:25:50,912 Building wheel for scunagi (setup.py): finished with status 'done' 2025-11-08T15:25:50,985 Created wheel for scunagi: filename=scunagi-0.5.7-py3-none-any.whl size=7158725 sha256=df6c35b8851efefb276c23a372297ed7fe6b79aa06ab3d2bc1520c078bfab17e 2025-11-08T15:25:50,986 Stored in directory: /tmp/pip-ephem-wheel-cache-cu7k0qlg/wheels/1c/bb/46/208692ffde2137a2bbb4a4108e58e3a70032f3fba341b774df 2025-11-08T15:25:51,003 Successfully built scunagi 2025-11-08T15:25:51,185 Removed build tracker: '/tmp/pip-build-tracker-7jez9lkz'