2025-11-12T05:40:03,892 Created temporary directory: /tmp/pip-ephem-wheel-cache-a4rshri4 2025-11-12T05:40:03,894 Created temporary directory: /tmp/pip-build-tracker-59e7gjga 2025-11-12T05:40:03,895 Initialized build tracking at /tmp/pip-build-tracker-59e7gjga 2025-11-12T05:40:03,895 Created build tracker: /tmp/pip-build-tracker-59e7gjga 2025-11-12T05:40:03,896 Entered build tracker: /tmp/pip-build-tracker-59e7gjga 2025-11-12T05:40:03,897 Created temporary directory: /tmp/pip-wheel-c25tze57 2025-11-12T05:40:03,900 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 2025-11-12T05:40:03,902 Created temporary directory: /tmp/pip-ephem-wheel-cache-l1cqze5n 2025-11-12T05:40:03,924 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-12T05:40:03,927 2 location(s) to search for versions of scunagi: 2025-11-12T05:40:03,927 * https://pypi.org/simple/scunagi/ 2025-11-12T05:40:03,927 * https://www.piwheels.org/simple/scunagi/ 2025-11-12T05:40:03,928 Fetching project page and analyzing links: https://pypi.org/simple/scunagi/ 2025-11-12T05:40:03,929 Getting page https://pypi.org/simple/scunagi/ 2025-11-12T05:40:03,930 Found index url https://pypi.org/simple 2025-11-12T05:40:04,146 Fetched page https://pypi.org/simple/scunagi/ as application/vnd.pypi.simple.v1+json 2025-11-12T05:40:04,152 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/) 2025-11-12T05:40:04,153 Found link https://files.pythonhosted.org/packages/e1/f1/0de90828615ce729086b0bd0040d92816d065d709b8d4cf23aa83212bd12/scUNAGI-0.1.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.1 2025-11-12T05:40:04,154 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) 2025-11-12T05:40:04,155 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 2025-11-12T05:40:04,155 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/) 2025-11-12T05:40:04,156 Found link https://files.pythonhosted.org/packages/27/25/685283d6b4b5c35f39f23f234c4b69ceb58cfe44d5847fb370d65014efc7/scUNAGI-0.2.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.2 2025-11-12T05:40:04,157 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/) 2025-11-12T05:40:04,157 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 2025-11-12T05:40:04,158 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) 2025-11-12T05:40:04,159 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 2025-11-12T05:40:04,160 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) 2025-11-12T05:40:04,161 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 2025-11-12T05:40:04,161 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) 2025-11-12T05:40:04,162 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 2025-11-12T05:40:04,163 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/) 2025-11-12T05:40:04,163 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 2025-11-12T05:40:04,164 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/) 2025-11-12T05:40:04,165 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 2025-11-12T05:40:04,165 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/) 2025-11-12T05:40:04,166 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 2025-11-12T05:40:04,166 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/) 2025-11-12T05:40:04,167 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 2025-11-12T05:40:04,168 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/) 2025-11-12T05:40:04,168 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 2025-11-12T05:40:04,169 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/) 2025-11-12T05:40:04,170 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 2025-11-12T05:40:04,170 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/) 2025-11-12T05:40:04,171 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 2025-11-12T05:40:04,172 Skipping link: No binaries permitted for scunagi: https://files.pythonhosted.org/packages/24/05/b37d0ba32912eb0ba39b8d56ed2c593b2f268ee514c666537691f50a89fe/scunagi-0.5.10-py3-none-any.whl (from https://pypi.org/simple/scunagi/) 2025-11-12T05:40:04,172 Found link https://files.pythonhosted.org/packages/13/35/80f0256986f7124960ec3b9fa0168884d3cf3561acb9795192b0bf46691f/scunagi-0.5.10.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.5.10 2025-11-12T05:40:04,173 Fetching project page and analyzing links: https://www.piwheels.org/simple/scunagi/ 2025-11-12T05:40:04,173 Getting page https://www.piwheels.org/simple/scunagi/ 2025-11-12T05:40:04,175 Found index url https://www.piwheels.org/simple 2025-11-12T05:40:04,330 Fetched page https://www.piwheels.org/simple/scunagi/ as text/html 2025-11-12T05:40:04,334 Skipping link: No binaries permitted for scunagi: https://www.piwheels.org/simple/scunagi/scunagi-0.5.7-py3-none-any.whl#sha256=df6c35b8851efefb276c23a372297ed7fe6b79aa06ab3d2bc1520c078bfab17e (from https://www.piwheels.org/simple/scunagi/) 2025-11-12T05:40:04,335 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/) 2025-11-12T05:40:04,335 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/) 2025-11-12T05:40:04,336 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/) 2025-11-12T05:40:04,337 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/) 2025-11-12T05:40:04,337 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/) 2025-11-12T05:40:04,338 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/) 2025-11-12T05:40:04,339 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/) 2025-11-12T05:40:04,339 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/) 2025-11-12T05:40:04,340 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/) 2025-11-12T05:40:04,341 Skipping link: not a file: https://www.piwheels.org/simple/scunagi/ 2025-11-12T05:40:04,341 Skipping link: not a file: https://pypi.org/simple/scunagi/ 2025-11-12T05:40:04,362 Given no hashes to check 1 links for project 'scunagi': discarding no candidates 2025-11-12T05:40:04,380 Collecting scunagi==0.5.10 2025-11-12T05:40:04,382 Created temporary directory: /tmp/pip-unpack-x4q0936j 2025-11-12T05:40:04,518 Downloading scunagi-0.5.10.tar.gz (6.7 MB) 2025-11-12T05:40:06,424 Added scunagi==0.5.10 from https://files.pythonhosted.org/packages/13/35/80f0256986f7124960ec3b9fa0168884d3cf3561acb9795192b0bf46691f/scunagi-0.5.10.tar.gz to build tracker '/tmp/pip-build-tracker-59e7gjga' 2025-11-12T05:40:06,426 Running setup.py (path:/tmp/pip-wheel-c25tze57/scunagi_fb3c743f4b0a4e299a5f901da4563fb0/setup.py) egg_info for package scunagi 2025-11-12T05:40:06,427 Created temporary directory: /tmp/pip-pip-egg-info-d7nyrbro 2025-11-12T05:40:06,427 Preparing metadata (setup.py): started 2025-11-12T05:40:06,428 Running command python setup.py egg_info 2025-11-12T05:40:07,319 running egg_info 2025-11-12T05:40:07,346 creating /tmp/pip-pip-egg-info-d7nyrbro/scUNAGI.egg-info 2025-11-12T05:40:07,347 writing /tmp/pip-pip-egg-info-d7nyrbro/scUNAGI.egg-info/PKG-INFO 2025-11-12T05:40:07,352 writing dependency_links to /tmp/pip-pip-egg-info-d7nyrbro/scUNAGI.egg-info/dependency_links.txt 2025-11-12T05:40:07,355 writing requirements to /tmp/pip-pip-egg-info-d7nyrbro/scUNAGI.egg-info/requires.txt 2025-11-12T05:40:07,356 writing top-level names to /tmp/pip-pip-egg-info-d7nyrbro/scUNAGI.egg-info/top_level.txt 2025-11-12T05:40:07,357 writing manifest file '/tmp/pip-pip-egg-info-d7nyrbro/scUNAGI.egg-info/SOURCES.txt' 2025-11-12T05:40:07,453 reading manifest file '/tmp/pip-pip-egg-info-d7nyrbro/scUNAGI.egg-info/SOURCES.txt' 2025-11-12T05:40:07,455 reading manifest template 'MANIFEST.in' 2025-11-12T05:40:07,456 warning: no files found matching 'LICENSE' 2025-11-12T05:40:07,456 adding license file 'LICENSE.txt' 2025-11-12T05:40:07,460 writing manifest file '/tmp/pip-pip-egg-info-d7nyrbro/scUNAGI.egg-info/SOURCES.txt' 2025-11-12T05:40:07,562 Preparing metadata (setup.py): finished with status 'done' 2025-11-12T05:40:07,568 Source in /tmp/pip-wheel-c25tze57/scunagi_fb3c743f4b0a4e299a5f901da4563fb0 has version 0.5.10, which satisfies requirement scunagi==0.5.10 from https://files.pythonhosted.org/packages/13/35/80f0256986f7124960ec3b9fa0168884d3cf3561acb9795192b0bf46691f/scunagi-0.5.10.tar.gz 2025-11-12T05:40:07,569 Removed scunagi==0.5.10 from https://files.pythonhosted.org/packages/13/35/80f0256986f7124960ec3b9fa0168884d3cf3561acb9795192b0bf46691f/scunagi-0.5.10.tar.gz from build tracker '/tmp/pip-build-tracker-59e7gjga' 2025-11-12T05:40:07,575 Created temporary directory: /tmp/pip-unpack-nq5rlrhd 2025-11-12T05:40:07,576 Building wheels for collected packages: scunagi 2025-11-12T05:40:07,580 Created temporary directory: /tmp/pip-wheel-1q3poatw 2025-11-12T05:40:07,581 Building wheel for scunagi (setup.py): started 2025-11-12T05:40:07,582 Destination directory: /tmp/pip-wheel-1q3poatw 2025-11-12T05:40:07,583 Running command python setup.py bdist_wheel 2025-11-12T05:40:08,414 running bdist_wheel 2025-11-12T05:40:08,543 running build 2025-11-12T05:40:08,544 running build_py 2025-11-12T05:40:08,573 creating build/lib/UNAGI 2025-11-12T05:40:08,575 copying UNAGI/__init__.py -> build/lib/UNAGI 2025-11-12T05:40:08,577 copying UNAGI/UNAGI_analyst.py -> build/lib/UNAGI 2025-11-12T05:40:08,580 copying UNAGI/UNAGI_tool.py -> build/lib/UNAGI 2025-11-12T05:40:08,583 creating build/lib/UNAGI/perturbations 2025-11-12T05:40:08,584 copying UNAGI/perturbations/new_perturbation_strategy.py -> build/lib/UNAGI/perturbations 2025-11-12T05:40:08,587 copying UNAGI/perturbations/__init__.py -> build/lib/UNAGI/perturbations 2025-11-12T05:40:08,589 copying UNAGI/perturbations/perturbation_centroid.py -> build/lib/UNAGI/perturbations 2025-11-12T05:40:08,592 copying UNAGI/perturbations/normalize_analysis_perturbation.py -> build/lib/UNAGI/perturbations 2025-11-12T05:40:08,595 copying UNAGI/perturbations/pathways.py -> build/lib/UNAGI/perturbations 2025-11-12T05:40:08,598 copying UNAGI/perturbations/analysis_perturbation.py -> build/lib/UNAGI/perturbations 2025-11-12T05:40:08,601 copying UNAGI/perturbations/perturbation.py -> build/lib/UNAGI/perturbations 2025-11-12T05:40:08,603 copying UNAGI/perturbations/compounds.py -> build/lib/UNAGI/perturbations 2025-11-12T05:40:08,607 creating build/lib/UNAGI/utils 2025-11-12T05:40:08,608 copying UNAGI/utils/evaluate.py -> build/lib/UNAGI/utils 2025-11-12T05:40:08,610 copying UNAGI/utils/idrem_helper.py -> build/lib/UNAGI/utils 2025-11-12T05:40:08,613 copying UNAGI/utils/__init__.py -> build/lib/UNAGI/utils 2025-11-12T05:40:08,615 copying UNAGI/utils/msigdb_data_overlapping.py -> build/lib/UNAGI/utils 2025-11-12T05:40:08,616 copying UNAGI/utils/CPO_utils.py -> build/lib/UNAGI/utils 2025-11-12T05:40:08,618 copying UNAGI/utils/attribute_utils.py -> build/lib/UNAGI/utils 2025-11-12T05:40:08,621 copying UNAGI/utils/gcn_utils.py -> build/lib/UNAGI/utils 2025-11-12T05:40:08,622 copying UNAGI/utils/analysis_helper.py -> build/lib/UNAGI/utils 2025-11-12T05:40:08,625 copying UNAGI/utils/trainer_utils.py -> build/lib/UNAGI/utils 2025-11-12T05:40:08,626 copying UNAGI/utils/h5adReader.py -> build/lib/UNAGI/utils 2025-11-12T05:40:08,629 creating build/lib/UNAGI/dynamic_graphs 2025-11-12T05:40:08,630 copying UNAGI/dynamic_graphs/__init__.py -> build/lib/UNAGI/dynamic_graphs 2025-11-12T05:40:08,631 copying UNAGI/dynamic_graphs/buildGraph.py -> build/lib/UNAGI/dynamic_graphs 2025-11-12T05:40:08,634 copying UNAGI/dynamic_graphs/distDistance.py -> build/lib/UNAGI/dynamic_graphs 2025-11-12T05:40:08,636 creating build/lib/UNAGI/model 2025-11-12T05:40:08,637 copying UNAGI/model/__init__.py -> build/lib/UNAGI/model 2025-11-12T05:40:08,639 copying UNAGI/model/models.py -> build/lib/UNAGI/model 2025-11-12T05:40:08,642 copying UNAGI/model/distributions.py -> build/lib/UNAGI/model 2025-11-12T05:40:08,644 creating build/lib/UNAGI/dynamic_regulatory_networks 2025-11-12T05:40:08,645 copying UNAGI/dynamic_regulatory_networks/__init__.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-12T05:40:08,647 copying UNAGI/dynamic_regulatory_networks/processIDREM.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-12T05:40:08,650 copying UNAGI/dynamic_regulatory_networks/processTFs.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-12T05:40:08,653 creating build/lib/UNAGI/marker_discovery 2025-11-12T05:40:08,654 copying UNAGI/marker_discovery/__init__.py -> build/lib/UNAGI/marker_discovery 2025-11-12T05:40:08,656 copying UNAGI/marker_discovery/hierachical_static_markers.py -> build/lib/UNAGI/marker_discovery 2025-11-12T05:40:08,659 copying UNAGI/marker_discovery/dynamic_markers_helper.py -> build/lib/UNAGI/marker_discovery 2025-11-12T05:40:08,661 copying UNAGI/marker_discovery/dynamic_markers.py -> build/lib/UNAGI/marker_discovery 2025-11-12T05:40:08,663 creating build/lib/UNAGI/train 2025-11-12T05:40:08,664 copying UNAGI/train/__init__.py -> build/lib/UNAGI/train 2025-11-12T05:40:08,666 copying UNAGI/train/runner.py -> build/lib/UNAGI/train 2025-11-12T05:40:08,668 copying UNAGI/train/customized_elbo.py -> build/lib/UNAGI/train 2025-11-12T05:40:08,671 copying UNAGI/train/trainer.py -> build/lib/UNAGI/train 2025-11-12T05:40:08,674 creating build/lib/UNAGI/plotting 2025-11-12T05:40:08,675 copying UNAGI/plotting/plot_cell_embeddings.py -> build/lib/UNAGI/plotting 2025-11-12T05:40:08,677 copying UNAGI/plotting/__init__.py -> build/lib/UNAGI/plotting 2025-11-12T05:40:08,679 copying UNAGI/plotting/plot_stage_dendrogram.py -> build/lib/UNAGI/plotting 2025-11-12T05:40:08,681 copying UNAGI/plotting/plot_hierarchical_markers_heatmap.py -> build/lib/UNAGI/plotting 2025-11-12T05:40:08,683 copying UNAGI/plotting/plot_cell_type_composition.py -> build/lib/UNAGI/plotting 2025-11-12T05:40:08,685 running egg_info 2025-11-12T05:40:08,713 writing scUNAGI.egg-info/PKG-INFO 2025-11-12T05:40:08,717 writing dependency_links to scUNAGI.egg-info/dependency_links.txt 2025-11-12T05:40:08,720 writing requirements to scUNAGI.egg-info/requires.txt 2025-11-12T05:40:08,721 writing top-level names to scUNAGI.egg-info/top_level.txt 2025-11-12T05:40:08,760 reading manifest file 'scUNAGI.egg-info/SOURCES.txt' 2025-11-12T05:40:08,764 reading manifest template 'MANIFEST.in' 2025-11-12T05:40:08,765 warning: no files found matching 'LICENSE' 2025-11-12T05:40:08,765 adding license file 'LICENSE.txt' 2025-11-12T05:40:08,770 writing manifest file 'scUNAGI.egg-info/SOURCES.txt' 2025-11-12T05:40:08,772 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'UNAGI.data' is absent from the `packages` configuration. 2025-11-12T05:40:08,772 !! 2025-11-12T05:40:08,773 ******************************************************************************** 2025-11-12T05:40:08,774 ############################ 2025-11-12T05:40:08,774 # Package would be ignored # 2025-11-12T05:40:08,775 ############################ 2025-11-12T05:40:08,775 Python recognizes 'UNAGI.data' as an importable package[^1], 2025-11-12T05:40:08,776 but it is absent from setuptools' `packages` configuration. 2025-11-12T05:40:08,777 This leads to an ambiguous overall configuration. If you want to distribute this 2025-11-12T05:40:08,777 package, please make sure that 'UNAGI.data' is explicitly added 2025-11-12T05:40:08,778 to the `packages` configuration field. 2025-11-12T05:40:08,779 Alternatively, you can also rely on setuptools' discovery methods 2025-11-12T05:40:08,779 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-11-12T05:40:08,780 instead of `find_packages(...)`/`find:`). 2025-11-12T05:40:08,781 You can read more about "package discovery" on setuptools documentation page: 2025-11-12T05:40:08,782 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-11-12T05:40:08,784 If you don't want 'UNAGI.data' to be distributed and are 2025-11-12T05:40:08,784 already explicitly excluding 'UNAGI.data' via 2025-11-12T05:40:08,785 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-11-12T05:40:08,785 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-11-12T05:40:08,786 combination with a more fine grained `package-data` configuration. 2025-11-12T05:40:08,787 You can read more about "package data files" on setuptools documentation page: 2025-11-12T05:40:08,791 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-11-12T05:40:08,805 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-11-12T05:40:08,806 even if it does not contain any `.py` files. 2025-11-12T05:40:08,808 On the other hand, currently there is no concept of package data 2025-11-12T05:40:08,809 directory, all directories are treated like packages. 2025-11-12T05:40:08,815 ******************************************************************************** 2025-11-12T05:40:08,819 !! 2025-11-12T05:40:08,820 check.warn(importable) 2025-11-12T05:40:08,826 creating build/lib/UNAGI/data 2025-11-12T05:40:08,827 copying UNAGI/data/brdID2cmapName.npy -> build/lib/UNAGI/data 2025-11-12T05:40:08,841 copying UNAGI/data/cmap_drug_target_genes.npy -> build/lib/UNAGI/data 2025-11-12T05:40:08,852 copying UNAGI/data/gesa_pathways.npy -> build/lib/UNAGI/data 2025-11-12T05:40:08,901 copying UNAGI/data/human_encode.txt -> build/lib/UNAGI/data 2025-11-12T05:40:09,306 copying UNAGI/data/mouse_predicted.txt -> build/lib/UNAGI/data 2025-11-12T05:40:09,560 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-11-12T05:40:09,560 !! 2025-11-12T05:40:09,562 ******************************************************************************** 2025-11-12T05:40:09,562 Please avoid running ``setup.py`` directly. 2025-11-12T05:40:09,563 Instead, use pypa/build, pypa/installer or other 2025-11-12T05:40:09,564 standards-based tools. 2025-11-12T05:40:09,565 This deprecation is overdue, please update your project and remove deprecated 2025-11-12T05:40:09,565 calls to avoid build errors in the future. 2025-11-12T05:40:09,566 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-11-12T05:40:09,567 ******************************************************************************** 2025-11-12T05:40:09,568 !! 2025-11-12T05:40:09,568 self.initialize_options() 2025-11-12T05:40:09,590 installing to build/bdist.linux-armv7l/wheel 2025-11-12T05:40:09,591 running install 2025-11-12T05:40:09,614 running install_lib 2025-11-12T05:40:09,641 creating build/bdist.linux-armv7l/wheel 2025-11-12T05:40:09,643 creating build/bdist.linux-armv7l/wheel/UNAGI 2025-11-12T05:40:09,645 creating build/bdist.linux-armv7l/wheel/UNAGI/perturbations 2025-11-12T05:40:09,646 copying build/lib/UNAGI/perturbations/new_perturbation_strategy.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-12T05:40:09,648 copying build/lib/UNAGI/perturbations/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-12T05:40:09,650 copying build/lib/UNAGI/perturbations/perturbation_centroid.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-12T05:40:09,653 copying build/lib/UNAGI/perturbations/normalize_analysis_perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-12T05:40:09,656 copying build/lib/UNAGI/perturbations/pathways.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-12T05:40:09,658 copying build/lib/UNAGI/perturbations/analysis_perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-12T05:40:09,661 copying build/lib/UNAGI/perturbations/perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-12T05:40:09,664 copying build/lib/UNAGI/perturbations/compounds.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-12T05:40:09,668 creating build/bdist.linux-armv7l/wheel/UNAGI/utils 2025-11-12T05:40:09,669 copying build/lib/UNAGI/utils/evaluate.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-12T05:40:09,671 copying build/lib/UNAGI/utils/idrem_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-12T05:40:09,673 copying build/lib/UNAGI/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-12T05:40:09,675 copying build/lib/UNAGI/utils/msigdb_data_overlapping.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-12T05:40:09,676 copying build/lib/UNAGI/utils/CPO_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-12T05:40:09,679 copying build/lib/UNAGI/utils/attribute_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-12T05:40:09,681 copying build/lib/UNAGI/utils/gcn_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-12T05:40:09,683 copying build/lib/UNAGI/utils/analysis_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-12T05:40:09,686 copying build/lib/UNAGI/utils/trainer_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-12T05:40:09,687 copying build/lib/UNAGI/utils/h5adReader.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-12T05:40:09,689 copying build/lib/UNAGI/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-12T05:40:09,691 creating build/bdist.linux-armv7l/wheel/UNAGI/dynamic_graphs 2025-11-12T05:40:09,692 copying build/lib/UNAGI/dynamic_graphs/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-12T05:40:09,694 copying build/lib/UNAGI/dynamic_graphs/buildGraph.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-12T05:40:09,697 copying build/lib/UNAGI/dynamic_graphs/distDistance.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-12T05:40:09,699 creating build/bdist.linux-armv7l/wheel/UNAGI/model 2025-11-12T05:40:09,700 copying build/lib/UNAGI/model/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-12T05:40:09,702 copying build/lib/UNAGI/model/models.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-12T05:40:09,705 copying build/lib/UNAGI/model/distributions.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-12T05:40:09,707 creating build/bdist.linux-armv7l/wheel/UNAGI/dynamic_regulatory_networks 2025-11-12T05:40:09,708 copying build/lib/UNAGI/dynamic_regulatory_networks/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-12T05:40:09,710 copying build/lib/UNAGI/dynamic_regulatory_networks/processIDREM.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-12T05:40:09,712 copying build/lib/UNAGI/dynamic_regulatory_networks/processTFs.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-12T05:40:09,715 creating build/bdist.linux-armv7l/wheel/UNAGI/data 2025-11-12T05:40:09,716 copying build/lib/UNAGI/data/human_encode.txt -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-12T05:40:10,162 copying build/lib/UNAGI/data/mouse_predicted.txt -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-12T05:40:10,382 copying build/lib/UNAGI/data/cmap_drug_target_genes.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-12T05:40:10,387 copying build/lib/UNAGI/data/gesa_pathways.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-12T05:40:10,431 copying build/lib/UNAGI/data/brdID2cmapName.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-12T05:40:10,461 creating build/bdist.linux-armv7l/wheel/UNAGI/marker_discovery 2025-11-12T05:40:10,462 copying build/lib/UNAGI/marker_discovery/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-12T05:40:10,464 copying build/lib/UNAGI/marker_discovery/hierachical_static_markers.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-12T05:40:10,466 copying build/lib/UNAGI/marker_discovery/dynamic_markers_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-12T05:40:10,468 copying build/lib/UNAGI/marker_discovery/dynamic_markers.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-12T05:40:10,471 creating build/bdist.linux-armv7l/wheel/UNAGI/train 2025-11-12T05:40:10,472 copying build/lib/UNAGI/train/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-12T05:40:10,474 copying build/lib/UNAGI/train/runner.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-12T05:40:10,477 copying build/lib/UNAGI/train/customized_elbo.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-12T05:40:10,479 copying build/lib/UNAGI/train/trainer.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-12T05:40:10,481 copying build/lib/UNAGI/UNAGI_analyst.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-12T05:40:10,484 copying build/lib/UNAGI/UNAGI_tool.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-12T05:40:10,488 creating build/bdist.linux-armv7l/wheel/UNAGI/plotting 2025-11-12T05:40:10,489 copying build/lib/UNAGI/plotting/plot_cell_embeddings.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-12T05:40:10,491 copying build/lib/UNAGI/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-12T05:40:10,493 copying build/lib/UNAGI/plotting/plot_stage_dendrogram.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-12T05:40:10,495 copying build/lib/UNAGI/plotting/plot_hierarchical_markers_heatmap.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-12T05:40:10,496 copying build/lib/UNAGI/plotting/plot_cell_type_composition.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-12T05:40:10,498 running install_egg_info 2025-11-12T05:40:10,533 Copying scUNAGI.egg-info to build/bdist.linux-armv7l/wheel/./scUNAGI-0.5.10-py3.11.egg-info 2025-11-12T05:40:10,543 running install_scripts 2025-11-12T05:40:10,555 creating build/bdist.linux-armv7l/wheel/scunagi-0.5.10.dist-info/WHEEL 2025-11-12T05:40:10,557 creating '/tmp/pip-wheel-1q3poatw/scunagi-0.5.10-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-11-12T05:40:10,561 adding 'UNAGI/UNAGI_analyst.py' 2025-11-12T05:40:10,565 adding 'UNAGI/UNAGI_tool.py' 2025-11-12T05:40:10,566 adding 'UNAGI/__init__.py' 2025-11-12T05:40:10,710 adding 'UNAGI/data/brdID2cmapName.npy' 2025-11-12T05:40:10,744 adding 'UNAGI/data/cmap_drug_target_genes.npy' 2025-11-12T05:40:11,095 adding 'UNAGI/data/gesa_pathways.npy' 2025-11-12T05:40:13,179 adding 'UNAGI/data/human_encode.txt' 2025-11-12T05:40:14,153 adding 'UNAGI/data/mouse_predicted.txt' 2025-11-12T05:40:14,249 adding 'UNAGI/dynamic_graphs/__init__.py' 2025-11-12T05:40:14,251 adding 'UNAGI/dynamic_graphs/buildGraph.py' 2025-11-12T05:40:14,252 adding 'UNAGI/dynamic_graphs/distDistance.py' 2025-11-12T05:40:14,254 adding 'UNAGI/dynamic_regulatory_networks/__init__.py' 2025-11-12T05:40:14,256 adding 'UNAGI/dynamic_regulatory_networks/processIDREM.py' 2025-11-12T05:40:14,258 adding 'UNAGI/dynamic_regulatory_networks/processTFs.py' 2025-11-12T05:40:14,260 adding 'UNAGI/marker_discovery/__init__.py' 2025-11-12T05:40:14,262 adding 'UNAGI/marker_discovery/dynamic_markers.py' 2025-11-12T05:40:14,263 adding 'UNAGI/marker_discovery/dynamic_markers_helper.py' 2025-11-12T05:40:14,266 adding 'UNAGI/marker_discovery/hierachical_static_markers.py' 2025-11-12T05:40:14,268 adding 'UNAGI/model/__init__.py' 2025-11-12T05:40:14,269 adding 'UNAGI/model/distributions.py' 2025-11-12T05:40:14,271 adding 'UNAGI/model/models.py' 2025-11-12T05:40:14,273 adding 'UNAGI/perturbations/__init__.py' 2025-11-12T05:40:14,277 adding 'UNAGI/perturbations/analysis_perturbation.py' 2025-11-12T05:40:14,279 adding 'UNAGI/perturbations/compounds.py' 2025-11-12T05:40:14,281 adding 'UNAGI/perturbations/new_perturbation_strategy.py' 2025-11-12T05:40:14,285 adding 'UNAGI/perturbations/normalize_analysis_perturbation.py' 2025-11-12T05:40:14,287 adding 'UNAGI/perturbations/pathways.py' 2025-11-12T05:40:14,291 adding 'UNAGI/perturbations/perturbation.py' 2025-11-12T05:40:14,296 adding 'UNAGI/perturbations/perturbation_centroid.py' 2025-11-12T05:40:14,299 adding 'UNAGI/plotting/__init__.py' 2025-11-12T05:40:14,300 adding 'UNAGI/plotting/plot_cell_embeddings.py' 2025-11-12T05:40:14,302 adding 'UNAGI/plotting/plot_cell_type_composition.py' 2025-11-12T05:40:14,303 adding 'UNAGI/plotting/plot_hierarchical_markers_heatmap.py' 2025-11-12T05:40:14,304 adding 'UNAGI/plotting/plot_stage_dendrogram.py' 2025-11-12T05:40:14,306 adding 'UNAGI/train/__init__.py' 2025-11-12T05:40:14,308 adding 'UNAGI/train/customized_elbo.py' 2025-11-12T05:40:14,310 adding 'UNAGI/train/runner.py' 2025-11-12T05:40:14,312 adding 'UNAGI/train/trainer.py' 2025-11-12T05:40:14,314 adding 'UNAGI/utils/CPO_utils.py' 2025-11-12T05:40:14,315 adding 'UNAGI/utils/__init__.py' 2025-11-12T05:40:14,318 adding 'UNAGI/utils/analysis_helper.py' 2025-11-12T05:40:14,320 adding 'UNAGI/utils/attribute_utils.py' 2025-11-12T05:40:14,322 adding 'UNAGI/utils/evaluate.py' 2025-11-12T05:40:14,323 adding 'UNAGI/utils/gcn_utils.py' 2025-11-12T05:40:14,325 adding 'UNAGI/utils/h5adReader.py' 2025-11-12T05:40:14,326 adding 'UNAGI/utils/idrem_helper.py' 2025-11-12T05:40:14,328 adding 'UNAGI/utils/msigdb_data_overlapping.py' 2025-11-12T05:40:14,329 adding 'UNAGI/utils/trainer_utils.py' 2025-11-12T05:40:14,336 adding 'scunagi-0.5.10.dist-info/licenses/LICENSE.txt' 2025-11-12T05:40:14,338 adding 'scunagi-0.5.10.dist-info/METADATA' 2025-11-12T05:40:14,339 adding 'scunagi-0.5.10.dist-info/WHEEL' 2025-11-12T05:40:14,340 adding 'scunagi-0.5.10.dist-info/top_level.txt' 2025-11-12T05:40:14,341 adding 'scunagi-0.5.10.dist-info/RECORD' 2025-11-12T05:40:14,412 removing build/bdist.linux-armv7l/wheel 2025-11-12T05:40:14,550 Building wheel for scunagi (setup.py): finished with status 'done' 2025-11-12T05:40:14,757 Created wheel for scunagi: filename=scunagi-0.5.10-py3-none-any.whl size=6816632 sha256=f173ceeaf326f483851afa17d085272e70fc42c66b71cde795f869679e2a1d48 2025-11-12T05:40:14,759 Stored in directory: /tmp/pip-ephem-wheel-cache-l1cqze5n/wheels/ea/3c/33/e00a3d68254e5ff79306b66b59e1275e2f7949ef1b278d4f31 2025-11-12T05:40:15,929 Successfully built scunagi 2025-11-12T05:40:16,111 Removed build tracker: '/tmp/pip-build-tracker-59e7gjga'