2025-11-02T21:30:23,498 Created temporary directory: /tmp/pip-ephem-wheel-cache-slttanv1 2025-11-02T21:30:23,500 Created temporary directory: /tmp/pip-build-tracker-mn1zy5q5 2025-11-02T21:30:23,501 Initialized build tracking at /tmp/pip-build-tracker-mn1zy5q5 2025-11-02T21:30:23,501 Created build tracker: /tmp/pip-build-tracker-mn1zy5q5 2025-11-02T21:30:23,502 Entered build tracker: /tmp/pip-build-tracker-mn1zy5q5 2025-11-02T21:30:23,503 Created temporary directory: /tmp/pip-wheel-1b6ffg7g 2025-11-02T21:30:23,506 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 2025-11-02T21:30:23,508 Created temporary directory: /tmp/pip-ephem-wheel-cache-8lctd78x 2025-11-02T21:30:23,531 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-11-02T21:30:23,535 2 location(s) to search for versions of scunagi: 2025-11-02T21:30:23,535 * https://pypi.org/simple/scunagi/ 2025-11-02T21:30:23,535 * https://www.piwheels.org/simple/scunagi/ 2025-11-02T21:30:23,536 Fetching project page and analyzing links: https://pypi.org/simple/scunagi/ 2025-11-02T21:30:23,536 Getting page https://pypi.org/simple/scunagi/ 2025-11-02T21:30:23,538 Found index url https://pypi.org/simple 2025-11-02T21:30:23,754 Fetched page https://pypi.org/simple/scunagi/ as application/vnd.pypi.simple.v1+json 2025-11-02T21:30:23,758 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/) 2025-11-02T21:30:23,759 Found link https://files.pythonhosted.org/packages/e1/f1/0de90828615ce729086b0bd0040d92816d065d709b8d4cf23aa83212bd12/scUNAGI-0.1.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.1 2025-11-02T21:30:23,760 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) 2025-11-02T21:30:23,761 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 2025-11-02T21:30:23,761 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/) 2025-11-02T21:30:23,762 Found link https://files.pythonhosted.org/packages/27/25/685283d6b4b5c35f39f23f234c4b69ceb58cfe44d5847fb370d65014efc7/scUNAGI-0.2.tar.gz (from https://pypi.org/simple/scunagi/), version: 0.2 2025-11-02T21:30:23,763 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/) 2025-11-02T21:30:23,763 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 2025-11-02T21:30:23,764 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) 2025-11-02T21:30:23,765 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 2025-11-02T21:30:23,766 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) 2025-11-02T21:30:23,767 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 2025-11-02T21:30:23,768 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) 2025-11-02T21:30:23,769 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 2025-11-02T21:30:23,769 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/) 2025-11-02T21:30:23,770 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 2025-11-02T21:30:23,770 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/) 2025-11-02T21:30:23,771 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 2025-11-02T21:30:23,771 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/) 2025-11-02T21:30:23,772 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 2025-11-02T21:30:23,773 Fetching project page and analyzing links: https://www.piwheels.org/simple/scunagi/ 2025-11-02T21:30:23,774 Getting page https://www.piwheels.org/simple/scunagi/ 2025-11-02T21:30:23,775 Found index url https://www.piwheels.org/simple 2025-11-02T21:30:24,040 Fetched page https://www.piwheels.org/simple/scunagi/ as text/html 2025-11-02T21:30:24,043 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/) 2025-11-02T21:30:24,044 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/) 2025-11-02T21:30:24,044 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/) 2025-11-02T21:30:24,045 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/) 2025-11-02T21:30:24,045 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/) 2025-11-02T21:30:24,046 Skipping link: not a file: https://www.piwheels.org/simple/scunagi/ 2025-11-02T21:30:24,047 Skipping link: not a file: https://pypi.org/simple/scunagi/ 2025-11-02T21:30:24,067 Given no hashes to check 1 links for project 'scunagi': discarding no candidates 2025-11-02T21:30:24,085 Collecting scunagi==0.5.3 2025-11-02T21:30:24,087 Created temporary directory: /tmp/pip-unpack-dth59r6k 2025-11-02T21:30:24,224 Downloading scunagi-0.5.3.tar.gz (7.1 MB) 2025-11-02T21:30:26,579 Added scunagi==0.5.3 from https://files.pythonhosted.org/packages/18/83/68926b431b80d7ee5a3dd7c14f359cb57304e635c9e5d5a9465f921566db/scunagi-0.5.3.tar.gz to build tracker '/tmp/pip-build-tracker-mn1zy5q5' 2025-11-02T21:30:26,580 Running setup.py (path:/tmp/pip-wheel-1b6ffg7g/scunagi_6aed6ca0efa448f89bdcdbed052d2400/setup.py) egg_info for package scunagi 2025-11-02T21:30:26,581 Created temporary directory: /tmp/pip-pip-egg-info-rocwjibu 2025-11-02T21:30:26,582 Preparing metadata (setup.py): started 2025-11-02T21:30:26,583 Running command python setup.py egg_info 2025-11-02T21:30:27,474 running egg_info 2025-11-02T21:30:27,501 creating /tmp/pip-pip-egg-info-rocwjibu/scUNAGI.egg-info 2025-11-02T21:30:27,503 writing /tmp/pip-pip-egg-info-rocwjibu/scUNAGI.egg-info/PKG-INFO 2025-11-02T21:30:27,508 writing dependency_links to /tmp/pip-pip-egg-info-rocwjibu/scUNAGI.egg-info/dependency_links.txt 2025-11-02T21:30:27,511 writing requirements to /tmp/pip-pip-egg-info-rocwjibu/scUNAGI.egg-info/requires.txt 2025-11-02T21:30:27,512 writing top-level names to /tmp/pip-pip-egg-info-rocwjibu/scUNAGI.egg-info/top_level.txt 2025-11-02T21:30:27,513 writing manifest file '/tmp/pip-pip-egg-info-rocwjibu/scUNAGI.egg-info/SOURCES.txt' 2025-11-02T21:30:27,782 reading manifest file '/tmp/pip-pip-egg-info-rocwjibu/scUNAGI.egg-info/SOURCES.txt' 2025-11-02T21:30:27,784 reading manifest template 'MANIFEST.in' 2025-11-02T21:30:27,785 warning: no files found matching 'LICENSE' 2025-11-02T21:30:27,786 adding license file 'LICENSE.txt' 2025-11-02T21:30:27,790 writing manifest file '/tmp/pip-pip-egg-info-rocwjibu/scUNAGI.egg-info/SOURCES.txt' 2025-11-02T21:30:27,895 Preparing metadata (setup.py): finished with status 'done' 2025-11-02T21:30:27,900 Source in /tmp/pip-wheel-1b6ffg7g/scunagi_6aed6ca0efa448f89bdcdbed052d2400 has version 0.5.3, which satisfies requirement scunagi==0.5.3 from https://files.pythonhosted.org/packages/18/83/68926b431b80d7ee5a3dd7c14f359cb57304e635c9e5d5a9465f921566db/scunagi-0.5.3.tar.gz 2025-11-02T21:30:27,901 Removed scunagi==0.5.3 from https://files.pythonhosted.org/packages/18/83/68926b431b80d7ee5a3dd7c14f359cb57304e635c9e5d5a9465f921566db/scunagi-0.5.3.tar.gz from build tracker '/tmp/pip-build-tracker-mn1zy5q5' 2025-11-02T21:30:27,907 Created temporary directory: /tmp/pip-unpack-ywwsk0ip 2025-11-02T21:30:27,907 Building wheels for collected packages: scunagi 2025-11-02T21:30:27,912 Created temporary directory: /tmp/pip-wheel-om5v6v9g 2025-11-02T21:30:27,912 Building wheel for scunagi (setup.py): started 2025-11-02T21:30:27,914 Destination directory: /tmp/pip-wheel-om5v6v9g 2025-11-02T21:30:27,914 Running command python setup.py bdist_wheel 2025-11-02T21:30:28,757 running bdist_wheel 2025-11-02T21:30:28,890 running build 2025-11-02T21:30:28,890 running build_py 2025-11-02T21:30:28,920 creating build/lib/UNAGI 2025-11-02T21:30:28,922 copying UNAGI/UNAGI_tool.py -> build/lib/UNAGI 2025-11-02T21:30:28,925 copying UNAGI/UNAGI_analyst.py -> build/lib/UNAGI 2025-11-02T21:30:28,928 copying UNAGI/__init__.py -> build/lib/UNAGI 2025-11-02T21:30:28,930 creating build/lib/UNAGI/perturbations 2025-11-02T21:30:28,931 copying UNAGI/perturbations/perturbation_centroid.py -> build/lib/UNAGI/perturbations 2025-11-02T21:30:28,935 copying UNAGI/perturbations/analysis_perturbation.py -> build/lib/UNAGI/perturbations 2025-11-02T21:30:28,938 copying UNAGI/perturbations/new_perturbation_strategy.py -> build/lib/UNAGI/perturbations 2025-11-02T21:30:28,940 copying UNAGI/perturbations/compounds.py -> build/lib/UNAGI/perturbations 2025-11-02T21:30:28,943 copying UNAGI/perturbations/pathways.py -> build/lib/UNAGI/perturbations 2025-11-02T21:30:28,945 copying UNAGI/perturbations/__init__.py -> build/lib/UNAGI/perturbations 2025-11-02T21:30:28,947 copying UNAGI/perturbations/normalize_analysis_perturbation.py -> build/lib/UNAGI/perturbations 2025-11-02T21:30:28,949 copying UNAGI/perturbations/perturbation.py -> build/lib/UNAGI/perturbations 2025-11-02T21:30:28,952 creating build/lib/UNAGI/model 2025-11-02T21:30:28,953 copying UNAGI/model/distributions.py -> build/lib/UNAGI/model 2025-11-02T21:30:28,955 copying UNAGI/model/models.py -> build/lib/UNAGI/model 2025-11-02T21:30:28,958 copying UNAGI/model/__init__.py -> build/lib/UNAGI/model 2025-11-02T21:30:28,960 creating build/lib/UNAGI/dynamic_graphs 2025-11-02T21:30:28,961 copying UNAGI/dynamic_graphs/distDistance.py -> build/lib/UNAGI/dynamic_graphs 2025-11-02T21:30:28,963 copying UNAGI/dynamic_graphs/buildGraph.py -> build/lib/UNAGI/dynamic_graphs 2025-11-02T21:30:28,965 copying UNAGI/dynamic_graphs/__init__.py -> build/lib/UNAGI/dynamic_graphs 2025-11-02T21:30:28,967 creating build/lib/UNAGI/utils 2025-11-02T21:30:28,968 copying UNAGI/utils/idrem_helper.py -> build/lib/UNAGI/utils 2025-11-02T21:30:28,971 copying UNAGI/utils/evaluate.py -> build/lib/UNAGI/utils 2025-11-02T21:30:28,973 copying UNAGI/utils/gcn_utils.py -> build/lib/UNAGI/utils 2025-11-02T21:30:28,975 copying UNAGI/utils/h5adReader.py -> build/lib/UNAGI/utils 2025-11-02T21:30:28,977 copying UNAGI/utils/CPO_utils.py -> build/lib/UNAGI/utils 2025-11-02T21:30:28,980 copying UNAGI/utils/analysis_helper.py -> build/lib/UNAGI/utils 2025-11-02T21:30:28,982 copying UNAGI/utils/trainer_utils.py -> build/lib/UNAGI/utils 2025-11-02T21:30:28,984 copying UNAGI/utils/attribute_utils.py -> build/lib/UNAGI/utils 2025-11-02T21:30:28,987 copying UNAGI/utils/__init__.py -> build/lib/UNAGI/utils 2025-11-02T21:30:28,988 copying UNAGI/utils/msigdb_data_overlapping.py -> build/lib/UNAGI/utils 2025-11-02T21:30:28,991 creating build/lib/UNAGI/plotting 2025-11-02T21:30:28,992 copying UNAGI/plotting/plot_cell_type_composition.py -> build/lib/UNAGI/plotting 2025-11-02T21:30:28,994 copying UNAGI/plotting/plot_cell_embeddings.py -> build/lib/UNAGI/plotting 2025-11-02T21:30:28,996 copying UNAGI/plotting/plot_hierarchical_markers_heatmap.py -> build/lib/UNAGI/plotting 2025-11-02T21:30:28,998 copying UNAGI/plotting/plot_stage_dendrogram.py -> build/lib/UNAGI/plotting 2025-11-02T21:30:29,000 copying UNAGI/plotting/__init__.py -> build/lib/UNAGI/plotting 2025-11-02T21:30:29,002 creating build/lib/UNAGI/train 2025-11-02T21:30:29,003 copying UNAGI/train/trainer.py -> build/lib/UNAGI/train 2025-11-02T21:30:29,005 copying UNAGI/train/customized_elbo.py -> build/lib/UNAGI/train 2025-11-02T21:30:29,008 copying UNAGI/train/runner.py -> build/lib/UNAGI/train 2025-11-02T21:30:29,010 copying UNAGI/train/__init__.py -> build/lib/UNAGI/train 2025-11-02T21:30:29,012 creating build/lib/UNAGI/marker_discovery 2025-11-02T21:30:29,013 copying UNAGI/marker_discovery/dynamic_markers.py -> build/lib/UNAGI/marker_discovery 2025-11-02T21:30:29,016 copying UNAGI/marker_discovery/hierachical_static_markers.py -> build/lib/UNAGI/marker_discovery 2025-11-02T21:30:29,018 copying UNAGI/marker_discovery/dynamic_markers_helper.py -> build/lib/UNAGI/marker_discovery 2025-11-02T21:30:29,020 copying UNAGI/marker_discovery/__init__.py -> build/lib/UNAGI/marker_discovery 2025-11-02T21:30:29,022 creating build/lib/UNAGI/dynamic_regulatory_networks 2025-11-02T21:30:29,024 copying UNAGI/dynamic_regulatory_networks/processIDREM.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-02T21:30:29,026 copying UNAGI/dynamic_regulatory_networks/__init__.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-02T21:30:29,028 copying UNAGI/dynamic_regulatory_networks/processTFs.py -> build/lib/UNAGI/dynamic_regulatory_networks 2025-11-02T21:30:29,030 running egg_info 2025-11-02T21:30:29,058 writing scUNAGI.egg-info/PKG-INFO 2025-11-02T21:30:29,063 writing dependency_links to scUNAGI.egg-info/dependency_links.txt 2025-11-02T21:30:29,066 writing requirements to scUNAGI.egg-info/requires.txt 2025-11-02T21:30:29,067 writing top-level names to scUNAGI.egg-info/top_level.txt 2025-11-02T21:30:29,106 reading manifest file 'scUNAGI.egg-info/SOURCES.txt' 2025-11-02T21:30:29,111 reading manifest template 'MANIFEST.in' 2025-11-02T21:30:29,112 warning: no files found matching 'LICENSE' 2025-11-02T21:30:29,113 adding license file 'LICENSE.txt' 2025-11-02T21:30:29,116 writing manifest file 'scUNAGI.egg-info/SOURCES.txt' 2025-11-02T21:30:29,119 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'UNAGI.data' is absent from the `packages` configuration. 2025-11-02T21:30:29,119 !! 2025-11-02T21:30:29,120 ******************************************************************************** 2025-11-02T21:30:29,121 ############################ 2025-11-02T21:30:29,121 # Package would be ignored # 2025-11-02T21:30:29,121 ############################ 2025-11-02T21:30:29,122 Python recognizes 'UNAGI.data' as an importable package[^1], 2025-11-02T21:30:29,122 but it is absent from setuptools' `packages` configuration. 2025-11-02T21:30:29,123 This leads to an ambiguous overall configuration. If you want to distribute this 2025-11-02T21:30:29,124 package, please make sure that 'UNAGI.data' is explicitly added 2025-11-02T21:30:29,124 to the `packages` configuration field. 2025-11-02T21:30:29,125 Alternatively, you can also rely on setuptools' discovery methods 2025-11-02T21:30:29,126 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-11-02T21:30:29,126 instead of `find_packages(...)`/`find:`). 2025-11-02T21:30:29,127 You can read more about "package discovery" on setuptools documentation page: 2025-11-02T21:30:29,128 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-11-02T21:30:29,130 If you don't want 'UNAGI.data' to be distributed and are 2025-11-02T21:30:29,130 already explicitly excluding 'UNAGI.data' via 2025-11-02T21:30:29,131 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-11-02T21:30:29,131 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-11-02T21:30:29,132 combination with a more fine grained `package-data` configuration. 2025-11-02T21:30:29,133 You can read more about "package data files" on setuptools documentation page: 2025-11-02T21:30:29,136 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-11-02T21:30:29,138 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-11-02T21:30:29,139 even if it does not contain any `.py` files. 2025-11-02T21:30:29,140 On the other hand, currently there is no concept of package data 2025-11-02T21:30:29,140 directory, all directories are treated like packages. 2025-11-02T21:30:29,141 ******************************************************************************** 2025-11-02T21:30:29,142 !! 2025-11-02T21:30:29,143 check.warn(importable) 2025-11-02T21:30:29,144 creating build/lib/UNAGI/data 2025-11-02T21:30:29,144 copying UNAGI/data/brdID2cmapName.npy -> build/lib/UNAGI/data 2025-11-02T21:30:29,158 copying UNAGI/data/cmap_drug_target_genes.npy -> build/lib/UNAGI/data 2025-11-02T21:30:29,163 copying UNAGI/data/gesa_pathways.npy -> build/lib/UNAGI/data 2025-11-02T21:30:29,211 copying UNAGI/data/human_encode.txt -> build/lib/UNAGI/data 2025-11-02T21:30:29,628 copying UNAGI/data/jasper_target_pair.npy -> build/lib/UNAGI/data 2025-11-02T21:30:29,646 copying UNAGI/data/mouse_predicted.txt -> build/lib/UNAGI/data 2025-11-02T21:30:29,905 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-11-02T21:30:29,905 !! 2025-11-02T21:30:29,906 ******************************************************************************** 2025-11-02T21:30:29,907 Please avoid running ``setup.py`` directly. 2025-11-02T21:30:29,907 Instead, use pypa/build, pypa/installer or other 2025-11-02T21:30:29,908 standards-based tools. 2025-11-02T21:30:29,908 This deprecation is overdue, please update your project and remove deprecated 2025-11-02T21:30:29,909 calls to avoid build errors in the future. 2025-11-02T21:30:29,910 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-11-02T21:30:29,910 ******************************************************************************** 2025-11-02T21:30:29,911 !! 2025-11-02T21:30:29,911 self.initialize_options() 2025-11-02T21:30:29,936 installing to build/bdist.linux-armv7l/wheel 2025-11-02T21:30:29,936 running install 2025-11-02T21:30:29,960 running install_lib 2025-11-02T21:30:29,988 creating build/bdist.linux-armv7l/wheel 2025-11-02T21:30:29,990 creating build/bdist.linux-armv7l/wheel/UNAGI 2025-11-02T21:30:29,992 creating build/bdist.linux-armv7l/wheel/UNAGI/perturbations 2025-11-02T21:30:29,994 copying build/lib/UNAGI/perturbations/perturbation_centroid.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-02T21:30:29,998 copying build/lib/UNAGI/perturbations/analysis_perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-02T21:30:30,001 copying build/lib/UNAGI/perturbations/new_perturbation_strategy.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-02T21:30:30,003 copying build/lib/UNAGI/perturbations/compounds.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-02T21:30:30,006 copying build/lib/UNAGI/perturbations/pathways.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-02T21:30:30,008 copying build/lib/UNAGI/perturbations/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-02T21:30:30,010 copying build/lib/UNAGI/perturbations/normalize_analysis_perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-02T21:30:30,014 copying build/lib/UNAGI/perturbations/perturbation.py -> build/bdist.linux-armv7l/wheel/./UNAGI/perturbations 2025-11-02T21:30:30,016 copying build/lib/UNAGI/UNAGI_tool.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-02T21:30:30,020 creating build/bdist.linux-armv7l/wheel/UNAGI/model 2025-11-02T21:30:30,021 copying build/lib/UNAGI/model/distributions.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-02T21:30:30,023 copying build/lib/UNAGI/model/models.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-02T21:30:30,026 copying build/lib/UNAGI/model/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/model 2025-11-02T21:30:30,028 creating build/bdist.linux-armv7l/wheel/UNAGI/dynamic_graphs 2025-11-02T21:30:30,029 copying build/lib/UNAGI/dynamic_graphs/distDistance.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-02T21:30:30,032 copying build/lib/UNAGI/dynamic_graphs/buildGraph.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-02T21:30:30,034 copying build/lib/UNAGI/dynamic_graphs/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_graphs 2025-11-02T21:30:30,036 creating build/bdist.linux-armv7l/wheel/UNAGI/utils 2025-11-02T21:30:30,037 copying build/lib/UNAGI/utils/idrem_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-02T21:30:30,040 copying build/lib/UNAGI/utils/evaluate.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-02T21:30:30,042 copying build/lib/UNAGI/utils/gcn_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-02T21:30:30,044 copying build/lib/UNAGI/utils/h5adReader.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-02T21:30:30,046 copying build/lib/UNAGI/utils/CPO_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-02T21:30:30,049 copying build/lib/UNAGI/utils/analysis_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-02T21:30:30,051 copying build/lib/UNAGI/utils/trainer_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-02T21:30:30,053 copying build/lib/UNAGI/utils/attribute_utils.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-02T21:30:30,056 copying build/lib/UNAGI/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-02T21:30:30,058 copying build/lib/UNAGI/utils/msigdb_data_overlapping.py -> build/bdist.linux-armv7l/wheel/./UNAGI/utils 2025-11-02T21:30:30,060 creating build/bdist.linux-armv7l/wheel/UNAGI/plotting 2025-11-02T21:30:30,061 copying build/lib/UNAGI/plotting/plot_cell_type_composition.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-02T21:30:30,063 copying build/lib/UNAGI/plotting/plot_cell_embeddings.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-02T21:30:30,065 copying build/lib/UNAGI/plotting/plot_hierarchical_markers_heatmap.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-02T21:30:30,067 copying build/lib/UNAGI/plotting/plot_stage_dendrogram.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-02T21:30:30,069 copying build/lib/UNAGI/plotting/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/plotting 2025-11-02T21:30:30,071 copying build/lib/UNAGI/UNAGI_analyst.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-02T21:30:30,074 creating build/bdist.linux-armv7l/wheel/UNAGI/data 2025-11-02T21:30:30,075 copying build/lib/UNAGI/data/mouse_predicted.txt -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-02T21:30:30,299 copying build/lib/UNAGI/data/brdID2cmapName.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-02T21:30:30,324 copying build/lib/UNAGI/data/human_encode.txt -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-02T21:30:30,920 copying build/lib/UNAGI/data/gesa_pathways.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-02T21:30:30,958 copying build/lib/UNAGI/data/cmap_drug_target_genes.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-02T21:30:30,963 copying build/lib/UNAGI/data/jasper_target_pair.npy -> build/bdist.linux-armv7l/wheel/./UNAGI/data 2025-11-02T21:30:30,985 copying build/lib/UNAGI/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI 2025-11-02T21:30:30,987 creating build/bdist.linux-armv7l/wheel/UNAGI/train 2025-11-02T21:30:30,989 copying build/lib/UNAGI/train/trainer.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-02T21:30:30,991 copying build/lib/UNAGI/train/customized_elbo.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-02T21:30:30,994 copying build/lib/UNAGI/train/runner.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-02T21:30:30,997 copying build/lib/UNAGI/train/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/train 2025-11-02T21:30:31,000 creating build/bdist.linux-armv7l/wheel/UNAGI/marker_discovery 2025-11-02T21:30:31,002 copying build/lib/UNAGI/marker_discovery/dynamic_markers.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-02T21:30:31,004 copying build/lib/UNAGI/marker_discovery/hierachical_static_markers.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-02T21:30:31,007 copying build/lib/UNAGI/marker_discovery/dynamic_markers_helper.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-02T21:30:31,009 copying build/lib/UNAGI/marker_discovery/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/marker_discovery 2025-11-02T21:30:31,012 creating build/bdist.linux-armv7l/wheel/UNAGI/dynamic_regulatory_networks 2025-11-02T21:30:31,013 copying build/lib/UNAGI/dynamic_regulatory_networks/processIDREM.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-02T21:30:31,016 copying build/lib/UNAGI/dynamic_regulatory_networks/__init__.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-02T21:30:31,018 copying build/lib/UNAGI/dynamic_regulatory_networks/processTFs.py -> build/bdist.linux-armv7l/wheel/./UNAGI/dynamic_regulatory_networks 2025-11-02T21:30:31,020 running install_egg_info 2025-11-02T21:30:31,056 Copying scUNAGI.egg-info to build/bdist.linux-armv7l/wheel/./scUNAGI-0.5.3-py3.11.egg-info 2025-11-02T21:30:31,069 running install_scripts 2025-11-02T21:30:31,082 creating build/bdist.linux-armv7l/wheel/scunagi-0.5.3.dist-info/WHEEL 2025-11-02T21:30:31,085 creating '/tmp/pip-wheel-om5v6v9g/scunagi-0.5.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-11-02T21:30:31,089 adding 'UNAGI/UNAGI_analyst.py' 2025-11-02T21:30:31,092 adding 'UNAGI/UNAGI_tool.py' 2025-11-02T21:30:31,094 adding 'UNAGI/__init__.py' 2025-11-02T21:30:31,239 adding 'UNAGI/data/brdID2cmapName.npy' 2025-11-02T21:30:31,274 adding 'UNAGI/data/cmap_drug_target_genes.npy' 2025-11-02T21:30:31,628 adding 'UNAGI/data/gesa_pathways.npy' 2025-11-02T21:30:33,727 adding 'UNAGI/data/human_encode.txt' 2025-11-02T21:30:34,062 adding 'UNAGI/data/jasper_target_pair.npy' 2025-11-02T21:30:34,881 adding 'UNAGI/data/mouse_predicted.txt' 2025-11-02T21:30:34,978 adding 'UNAGI/dynamic_graphs/__init__.py' 2025-11-02T21:30:34,979 adding 'UNAGI/dynamic_graphs/buildGraph.py' 2025-11-02T21:30:34,982 adding 'UNAGI/dynamic_graphs/distDistance.py' 2025-11-02T21:30:34,983 adding 'UNAGI/dynamic_regulatory_networks/__init__.py' 2025-11-02T21:30:34,986 adding 'UNAGI/dynamic_regulatory_networks/processIDREM.py' 2025-11-02T21:30:34,989 adding 'UNAGI/dynamic_regulatory_networks/processTFs.py' 2025-11-02T21:30:34,991 adding 'UNAGI/marker_discovery/__init__.py' 2025-11-02T21:30:34,993 adding 'UNAGI/marker_discovery/dynamic_markers.py' 2025-11-02T21:30:34,994 adding 'UNAGI/marker_discovery/dynamic_markers_helper.py' 2025-11-02T21:30:34,997 adding 'UNAGI/marker_discovery/hierachical_static_markers.py' 2025-11-02T21:30:35,000 adding 'UNAGI/model/__init__.py' 2025-11-02T21:30:35,001 adding 'UNAGI/model/distributions.py' 2025-11-02T21:30:35,004 adding 'UNAGI/model/models.py' 2025-11-02T21:30:35,006 adding 'UNAGI/perturbations/__init__.py' 2025-11-02T21:30:35,010 adding 'UNAGI/perturbations/analysis_perturbation.py' 2025-11-02T21:30:35,012 adding 'UNAGI/perturbations/compounds.py' 2025-11-02T21:30:35,014 adding 'UNAGI/perturbations/new_perturbation_strategy.py' 2025-11-02T21:30:35,019 adding 'UNAGI/perturbations/normalize_analysis_perturbation.py' 2025-11-02T21:30:35,021 adding 'UNAGI/perturbations/pathways.py' 2025-11-02T21:30:35,025 adding 'UNAGI/perturbations/perturbation.py' 2025-11-02T21:30:35,031 adding 'UNAGI/perturbations/perturbation_centroid.py' 2025-11-02T21:30:35,033 adding 'UNAGI/plotting/__init__.py' 2025-11-02T21:30:35,035 adding 'UNAGI/plotting/plot_cell_embeddings.py' 2025-11-02T21:30:35,037 adding 'UNAGI/plotting/plot_cell_type_composition.py' 2025-11-02T21:30:35,038 adding 'UNAGI/plotting/plot_hierarchical_markers_heatmap.py' 2025-11-02T21:30:35,040 adding 'UNAGI/plotting/plot_stage_dendrogram.py' 2025-11-02T21:30:35,042 adding 'UNAGI/train/__init__.py' 2025-11-02T21:30:35,044 adding 'UNAGI/train/customized_elbo.py' 2025-11-02T21:30:35,047 adding 'UNAGI/train/runner.py' 2025-11-02T21:30:35,049 adding 'UNAGI/train/trainer.py' 2025-11-02T21:30:35,052 adding 'UNAGI/utils/CPO_utils.py' 2025-11-02T21:30:35,054 adding 'UNAGI/utils/__init__.py' 2025-11-02T21:30:35,056 adding 'UNAGI/utils/analysis_helper.py' 2025-11-02T21:30:35,059 adding 'UNAGI/utils/attribute_utils.py' 2025-11-02T21:30:35,061 adding 'UNAGI/utils/evaluate.py' 2025-11-02T21:30:35,063 adding 'UNAGI/utils/gcn_utils.py' 2025-11-02T21:30:35,065 adding 'UNAGI/utils/h5adReader.py' 2025-11-02T21:30:35,067 adding 'UNAGI/utils/idrem_helper.py' 2025-11-02T21:30:35,069 adding 'UNAGI/utils/msigdb_data_overlapping.py' 2025-11-02T21:30:35,070 adding 'UNAGI/utils/trainer_utils.py' 2025-11-02T21:30:35,077 adding 'scunagi-0.5.3.dist-info/licenses/LICENSE.txt' 2025-11-02T21:30:35,080 adding 'scunagi-0.5.3.dist-info/METADATA' 2025-11-02T21:30:35,082 adding 'scunagi-0.5.3.dist-info/WHEEL' 2025-11-02T21:30:35,083 adding 'scunagi-0.5.3.dist-info/top_level.txt' 2025-11-02T21:30:35,085 adding 'scunagi-0.5.3.dist-info/RECORD' 2025-11-02T21:30:35,163 removing build/bdist.linux-armv7l/wheel 2025-11-02T21:30:35,308 Building wheel for scunagi (setup.py): finished with status 'done' 2025-11-02T21:30:35,381 Created wheel for scunagi: filename=scunagi-0.5.3-py3-none-any.whl size=7155753 sha256=bdb9b1b8ad4b0319a8df8fe0c9dc1ce63cb0cf41b9e25f0293ea4461102983c7 2025-11-02T21:30:35,383 Stored in directory: /tmp/pip-ephem-wheel-cache-8lctd78x/wheels/c5/6c/20/84ad3cf43156fe607541bfabd1ff97694abf996bcb6ddca22d 2025-11-02T21:30:35,400 Successfully built scunagi 2025-11-02T21:30:35,566 Removed build tracker: '/tmp/pip-build-tracker-mn1zy5q5'