2026-03-20T14:17:14,094 Created temporary directory: /tmp/pip-ephem-wheel-cache-8byz7wkr 2026-03-20T14:17:14,096 Created temporary directory: /tmp/pip-build-tracker-4ss74n3d 2026-03-20T14:17:14,097 Initialized build tracking at /tmp/pip-build-tracker-4ss74n3d 2026-03-20T14:17:14,097 Created build tracker: /tmp/pip-build-tracker-4ss74n3d 2026-03-20T14:17:14,098 Entered build tracker: /tmp/pip-build-tracker-4ss74n3d 2026-03-20T14:17:14,098 Created temporary directory: /tmp/pip-wheel-d0z5jmh0 2026-03-20T14:17:14,102 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 2026-03-20T14:17:14,104 Created temporary directory: /tmp/pip-ephem-wheel-cache-zbfydaq5 2026-03-20T14:17:14,125 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-03-20T14:17:14,128 2 location(s) to search for versions of spatialformer: 2026-03-20T14:17:14,128 * https://pypi.org/simple/spatialformer/ 2026-03-20T14:17:14,128 * https://www.piwheels.org/simple/spatialformer/ 2026-03-20T14:17:14,129 Fetching project page and analyzing links: https://pypi.org/simple/spatialformer/ 2026-03-20T14:17:14,130 Getting page https://pypi.org/simple/spatialformer/ 2026-03-20T14:17:14,131 Found index url https://pypi.org/simple 2026-03-20T14:17:14,270 Fetched page https://pypi.org/simple/spatialformer/ as application/vnd.pypi.simple.v1+json 2026-03-20T14:17:14,273 Skipping link: No binaries permitted for spatialformer: https://files.pythonhosted.org/packages/67/e8/96287c1d40f52743b8b0d95e7ae7edfa5b3dae9ad193ac4fd283bb0726dd/SpatialFormer-0.0.2-py3-none-any.whl (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.9) 2026-03-20T14:17:14,274 Found link https://files.pythonhosted.org/packages/57/ed/b3d4ff5a83254298007850bde4d0e575dc5ef44c08f0407045a4ddc5143f/SpatialFormer-0.0.2.tar.gz (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.9), version: 0.0.2 2026-03-20T14:17:14,275 Skipping link: No binaries permitted for spatialformer: https://files.pythonhosted.org/packages/61/7f/f281a742e3ef3e3229bb6e6840a45cf151130b28e9ff6ee89f4c01253d42/spatialformer-0.0.20-py3-none-any.whl (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.8) 2026-03-20T14:17:14,276 Found link https://files.pythonhosted.org/packages/04/6a/e64b79f3c0c14d16ba740d29b12b83bf269b5644127814969c6d8fd42a60/spatialformer-0.0.20.tar.gz (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.8), version: 0.0.20 2026-03-20T14:17:14,277 Skipping link: No binaries permitted for spatialformer: https://files.pythonhosted.org/packages/81/4a/28b750ea2236955fa02c2810e513b4bafa33167752e8012e5684718bc76f/spatialformer-0.1.1-py3-none-any.whl (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-20T14:17:14,278 Found link https://files.pythonhosted.org/packages/0b/50/d7ea0775f830fe96b5c47f510f6ed34bb0c576f3ab2316b5558637fbe84a/spatialformer-0.1.1.tar.gz (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10), version: 0.1.1 2026-03-20T14:17:14,279 Skipping link: No binaries permitted for spatialformer: https://files.pythonhosted.org/packages/e6/1c/b53e2ee4988b2290f601f0b0271b20e317a7a67769352cd3b9d79fc58bb3/spatialformer-0.1.2-py3-none-any.whl (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-20T14:17:14,280 Found link https://files.pythonhosted.org/packages/25/86/4f0cdfb8e011e46781ecaa31deb9b07a440302cae6306406e9f394cc62b9/spatialformer-0.1.2.tar.gz (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10), version: 0.1.2 2026-03-20T14:17:14,280 Skipping link: No binaries permitted for spatialformer: https://files.pythonhosted.org/packages/c8/73/c8063afb0735bfa83c6ed0a4f21743b43eb57c90672ccc7f4b27abac4ac2/spatialformer-0.1.3-py3-none-any.whl (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-20T14:17:14,281 Found link https://files.pythonhosted.org/packages/10/f0/b3fe686dc22e745e23209a8892bacd026a9f61cab192a30df2487383b5e5/spatialformer-0.1.3.tar.gz (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10), version: 0.1.3 2026-03-20T14:17:14,282 Skipping link: No binaries permitted for spatialformer: https://files.pythonhosted.org/packages/05/1d/0beedf110bb7a14c7f2289046a38ab2d160af1cb77aed60d03d1d4ad436c/spatialformer-0.1.4-py3-none-any.whl (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-20T14:17:14,283 Found link https://files.pythonhosted.org/packages/94/da/215fc99202870be1445f3dec0de0250bf74faa5276a9b5c40af423231e1c/spatialformer-0.1.4.tar.gz (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10), version: 0.1.4 2026-03-20T14:17:14,283 Skipping link: No binaries permitted for spatialformer: https://files.pythonhosted.org/packages/85/72/fbe9f2043c92b967d39ace23051321e613139f18f0286fb88a35934c8c27/spatialformer-0.1.5-py3-none-any.whl (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-20T14:17:14,284 Found link https://files.pythonhosted.org/packages/88/47/927779624f4a903cac77c86042869bc6686ada6f83d6581c6a5a31d4aff0/spatialformer-0.1.5.tar.gz (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10), version: 0.1.5 2026-03-20T14:17:14,285 Fetching project page and analyzing links: https://www.piwheels.org/simple/spatialformer/ 2026-03-20T14:17:14,286 Getting page https://www.piwheels.org/simple/spatialformer/ 2026-03-20T14:17:14,287 Found index url https://www.piwheels.org/simple 2026-03-20T14:17:14,443 Fetched page https://www.piwheels.org/simple/spatialformer/ as text/html 2026-03-20T14:17:14,445 Skipping link: No binaries permitted for spatialformer: https://www.piwheels.org/simple/spatialformer/spatialformer-0.1.1-py3-none-any.whl#sha256=ea17bdcb84caee63440effbdf751abeb1c4dc6dfcfc98f7cf14964e1198d3046 (from https://www.piwheels.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-20T14:17:14,446 Skipping link: not a file: https://www.piwheels.org/simple/spatialformer/ 2026-03-20T14:17:14,446 Skipping link: not a file: https://pypi.org/simple/spatialformer/ 2026-03-20T14:17:14,467 Given no hashes to check 1 links for project 'spatialformer': discarding no candidates 2026-03-20T14:17:14,487 Collecting spatialformer==0.1.2 2026-03-20T14:17:14,489 Created temporary directory: /tmp/pip-unpack-w40ia471 2026-03-20T14:17:14,713 Downloading spatialformer-0.1.2.tar.gz (3.9 MB) 2026-03-20T14:17:15,529 Added spatialformer==0.1.2 from https://files.pythonhosted.org/packages/25/86/4f0cdfb8e011e46781ecaa31deb9b07a440302cae6306406e9f394cc62b9/spatialformer-0.1.2.tar.gz to build tracker '/tmp/pip-build-tracker-4ss74n3d' 2026-03-20T14:17:15,531 Running setup.py (path:/tmp/pip-wheel-d0z5jmh0/spatialformer_8b8de2b654a84e6090e9fc48f6898868/setup.py) egg_info for package spatialformer 2026-03-20T14:17:15,532 Created temporary directory: /tmp/pip-pip-egg-info-f10fq59o 2026-03-20T14:17:15,532 Preparing metadata (setup.py): started 2026-03-20T14:17:15,533 Running command python setup.py egg_info 2026-03-20T14:17:16,406 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-03-20T14:17:16,406 !! 2026-03-20T14:17:16,407 ******************************************************************************** 2026-03-20T14:17:16,408 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-03-20T14:17:16,409 License :: OSI Approved :: MIT License 2026-03-20T14:17:16,410 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-03-20T14:17:16,411 ******************************************************************************** 2026-03-20T14:17:16,412 !! 2026-03-20T14:17:16,413 self._finalize_license_expression() 2026-03-20T14:17:16,437 running egg_info 2026-03-20T14:17:16,463 creating /tmp/pip-pip-egg-info-f10fq59o/spatialformer.egg-info 2026-03-20T14:17:16,464 writing /tmp/pip-pip-egg-info-f10fq59o/spatialformer.egg-info/PKG-INFO 2026-03-20T14:17:16,468 writing dependency_links to /tmp/pip-pip-egg-info-f10fq59o/spatialformer.egg-info/dependency_links.txt 2026-03-20T14:17:16,470 writing requirements to /tmp/pip-pip-egg-info-f10fq59o/spatialformer.egg-info/requires.txt 2026-03-20T14:17:16,471 writing top-level names to /tmp/pip-pip-egg-info-f10fq59o/spatialformer.egg-info/top_level.txt 2026-03-20T14:17:16,473 writing manifest file '/tmp/pip-pip-egg-info-f10fq59o/spatialformer.egg-info/SOURCES.txt' 2026-03-20T14:17:16,572 reading manifest file '/tmp/pip-pip-egg-info-f10fq59o/spatialformer.egg-info/SOURCES.txt' 2026-03-20T14:17:16,573 reading manifest template 'MANIFEST.in' 2026-03-20T14:17:16,576 warning: no files found matching 'spatialformer/spatial_embeddings/*.json' 2026-03-20T14:17:16,576 adding license file 'LICENSE' 2026-03-20T14:17:16,580 writing manifest file '/tmp/pip-pip-egg-info-f10fq59o/spatialformer.egg-info/SOURCES.txt' 2026-03-20T14:17:16,688 Preparing metadata (setup.py): finished with status 'done' 2026-03-20T14:17:16,693 Source in /tmp/pip-wheel-d0z5jmh0/spatialformer_8b8de2b654a84e6090e9fc48f6898868 has version 0.1.2, which satisfies requirement spatialformer==0.1.2 from https://files.pythonhosted.org/packages/25/86/4f0cdfb8e011e46781ecaa31deb9b07a440302cae6306406e9f394cc62b9/spatialformer-0.1.2.tar.gz 2026-03-20T14:17:16,694 Removed spatialformer==0.1.2 from https://files.pythonhosted.org/packages/25/86/4f0cdfb8e011e46781ecaa31deb9b07a440302cae6306406e9f394cc62b9/spatialformer-0.1.2.tar.gz from build tracker '/tmp/pip-build-tracker-4ss74n3d' 2026-03-20T14:17:16,700 Created temporary directory: /tmp/pip-unpack-4h180ywy 2026-03-20T14:17:16,701 Building wheels for collected packages: spatialformer 2026-03-20T14:17:16,705 Created temporary directory: /tmp/pip-wheel-u0u7w0ko 2026-03-20T14:17:16,706 Building wheel for spatialformer (setup.py): started 2026-03-20T14:17:16,707 Destination directory: /tmp/pip-wheel-u0u7w0ko 2026-03-20T14:17:16,708 Running command python setup.py bdist_wheel 2026-03-20T14:17:17,575 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-03-20T14:17:17,575 !! 2026-03-20T14:17:17,576 ******************************************************************************** 2026-03-20T14:17:17,577 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-03-20T14:17:17,578 License :: OSI Approved :: MIT License 2026-03-20T14:17:17,580 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-03-20T14:17:17,580 ******************************************************************************** 2026-03-20T14:17:17,581 !! 2026-03-20T14:17:17,582 self._finalize_license_expression() 2026-03-20T14:17:17,583 running bdist_wheel 2026-03-20T14:17:17,710 running build 2026-03-20T14:17:17,710 running build_py 2026-03-20T14:17:17,743 creating build/lib/spatialformer 2026-03-20T14:17:17,745 copying spatialformer/utils.py -> build/lib/spatialformer 2026-03-20T14:17:17,748 copying spatialformer/data_loader.py -> build/lib/spatialformer 2026-03-20T14:17:17,751 copying spatialformer/graphsage.py -> build/lib/spatialformer 2026-03-20T14:17:17,754 copying spatialformer/processor.py -> build/lib/spatialformer 2026-03-20T14:17:17,756 copying spatialformer/train.py -> build/lib/spatialformer 2026-03-20T14:17:17,758 copying spatialformer/GraphSAGE.py -> build/lib/spatialformer 2026-03-20T14:17:17,761 copying spatialformer/__init__.py -> build/lib/spatialformer 2026-03-20T14:17:17,763 creating build/lib/spatialformer/spatial_embeddings 2026-03-20T14:17:17,764 copying spatialformer/spatial_embeddings/__init__.py -> build/lib/spatialformer/spatial_embeddings 2026-03-20T14:17:17,767 creating build/lib/spatialformer/dataloader 2026-03-20T14:17:17,768 copying spatialformer/dataloader/dataloader_paired.py -> build/lib/spatialformer/dataloader 2026-03-20T14:17:17,771 copying spatialformer/dataloader/__init__.py -> build/lib/spatialformer/dataloader 2026-03-20T14:17:17,773 creating build/lib/spatialformer/model 2026-03-20T14:17:17,774 copying spatialformer/model/__init__.py -> build/lib/spatialformer/model 2026-03-20T14:17:17,776 copying spatialformer/model/Spaformer_pair.py -> build/lib/spatialformer/model 2026-03-20T14:17:17,779 copying spatialformer/model/model.py -> build/lib/spatialformer/model 2026-03-20T14:17:17,781 copying spatialformer/model/Spaformer.py -> build/lib/spatialformer/model 2026-03-20T14:17:17,783 copying spatialformer/model/settings.py -> build/lib/spatialformer/model 2026-03-20T14:17:17,785 creating build/lib/spatialformer/tools 2026-03-20T14:17:17,786 copying spatialformer/tools/get_embeddings.py -> build/lib/spatialformer/tools 2026-03-20T14:17:17,789 copying spatialformer/tools/__init__.py -> build/lib/spatialformer/tools 2026-03-20T14:17:17,791 creating build/lib/spatialformer/tokenizer 2026-03-20T14:17:17,792 copying spatialformer/tokenizer/__init__.py -> build/lib/spatialformer/tokenizer 2026-03-20T14:17:17,794 creating build/lib/spatialformer/preprocess 2026-03-20T14:17:17,795 copying spatialformer/preprocess/find_gene_interaction.py -> build/lib/spatialformer/preprocess 2026-03-20T14:17:17,797 copying spatialformer/preprocess/__init__.py -> build/lib/spatialformer/preprocess 2026-03-20T14:17:17,799 creating build/lib/spatialformer/config 2026-03-20T14:17:17,800 copying spatialformer/config/__init__.py -> build/lib/spatialformer/config 2026-03-20T14:17:17,803 creating build/lib/spatialformer/gene_gene_calculation 2026-03-20T14:17:17,804 copying spatialformer/gene_gene_calculation/process.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-20T14:17:17,806 copying spatialformer/gene_gene_calculation/find_gene_interaction.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-20T14:17:17,809 copying spatialformer/gene_gene_calculation/__init__.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-20T14:17:17,811 copying spatialformer/gene_gene_calculation/h5toloader.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-20T14:17:17,813 copying spatialformer/gene_gene_calculation/mask_dataset.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-20T14:17:17,816 copying spatialformer/gene_gene_calculation/build_h5ad.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-20T14:17:17,819 creating build/lib/spatialformer/model/submodules 2026-03-20T14:17:17,820 copying spatialformer/model/submodules/modules.py -> build/lib/spatialformer/model/submodules 2026-03-20T14:17:17,823 copying spatialformer/model/submodules/masked_batchnorm.py -> build/lib/spatialformer/model/submodules 2026-03-20T14:17:17,825 copying spatialformer/model/submodules/masked_conv.py -> build/lib/spatialformer/model/submodules 2026-03-20T14:17:17,827 copying spatialformer/model/submodules/__init__.py -> build/lib/spatialformer/model/submodules 2026-03-20T14:17:17,829 copying spatialformer/model/submodules/flash_attention2.py -> build/lib/spatialformer/model/submodules 2026-03-20T14:17:17,832 copying spatialformer/model/submodules/layer_modules.py -> build/lib/spatialformer/model/submodules 2026-03-20T14:17:17,834 copying spatialformer/model/submodules/alibi.py -> build/lib/spatialformer/model/submodules 2026-03-20T14:17:17,836 copying spatialformer/model/submodules/activations.py -> build/lib/spatialformer/model/submodules 2026-03-20T14:17:17,838 running egg_info 2026-03-20T14:17:17,865 writing spatialformer.egg-info/PKG-INFO 2026-03-20T14:17:17,868 writing dependency_links to spatialformer.egg-info/dependency_links.txt 2026-03-20T14:17:17,870 writing requirements to spatialformer.egg-info/requires.txt 2026-03-20T14:17:17,872 writing top-level names to spatialformer.egg-info/top_level.txt 2026-03-20T14:17:17,914 reading manifest file 'spatialformer.egg-info/SOURCES.txt' 2026-03-20T14:17:17,919 reading manifest template 'MANIFEST.in' 2026-03-20T14:17:17,921 warning: no files found matching 'spatialformer/spatial_embeddings/*.json' 2026-03-20T14:17:17,921 adding license file 'LICENSE' 2026-03-20T14:17:17,925 writing manifest file 'spatialformer.egg-info/SOURCES.txt' 2026-03-20T14:17:17,934 copying spatialformer/spatial_embeddings/gene_embeddings_GraphSAGE_pandavid.pkl -> build/lib/spatialformer/spatial_embeddings 2026-03-20T14:17:18,002 copying spatialformer/tokenizer/token.json -> build/lib/spatialformer/tokenizer 2026-03-20T14:17:18,005 copying spatialformer/tokenizer/tokenv2.json -> build/lib/spatialformer/tokenizer 2026-03-20T14:17:18,009 copying spatialformer/tokenizer/tokenv3.json -> build/lib/spatialformer/tokenizer 2026-03-20T14:17:18,013 copying spatialformer/tokenizer/tokenv4.json -> build/lib/spatialformer/tokenizer 2026-03-20T14:17:18,016 copying spatialformer/tokenizer/tokenv5.json -> build/lib/spatialformer/tokenizer 2026-03-20T14:17:18,021 copying spatialformer/config/_config_fine_tune_probe.json -> build/lib/spatialformer/config 2026-03-20T14:17:18,023 copying spatialformer/config/_config_graphsave.json -> build/lib/spatialformer/config 2026-03-20T14:17:18,025 copying spatialformer/config/_config_train.json -> build/lib/spatialformer/config 2026-03-20T14:17:18,027 copying spatialformer/config/_config_train_large_pair.json -> build/lib/spatialformer/config 2026-03-20T14:17:18,029 copying spatialformer/config/_config_train_large_single.json -> build/lib/spatialformer/config 2026-03-20T14:17:18,061 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2026-03-20T14:17:18,062 !! 2026-03-20T14:17:18,063 ******************************************************************************** 2026-03-20T14:17:18,064 Please avoid running ``setup.py`` directly. 2026-03-20T14:17:18,064 Instead, use pypa/build, pypa/installer or other 2026-03-20T14:17:18,065 standards-based tools. 2026-03-20T14:17:18,066 This deprecation is overdue, please update your project and remove deprecated 2026-03-20T14:17:18,067 calls to avoid build errors in the future. 2026-03-20T14:17:18,068 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2026-03-20T14:17:18,069 ******************************************************************************** 2026-03-20T14:17:18,070 !! 2026-03-20T14:17:18,070 self.initialize_options() 2026-03-20T14:17:18,090 installing to build/bdist.linux-armv7l/wheel 2026-03-20T14:17:18,091 running install 2026-03-20T14:17:18,115 running install_lib 2026-03-20T14:17:18,142 creating build/bdist.linux-armv7l/wheel 2026-03-20T14:17:18,145 creating build/bdist.linux-armv7l/wheel/spatialformer 2026-03-20T14:17:18,146 creating build/bdist.linux-armv7l/wheel/spatialformer/spatial_embeddings 2026-03-20T14:17:18,148 copying build/lib/spatialformer/spatial_embeddings/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/spatial_embeddings 2026-03-20T14:17:18,149 copying build/lib/spatialformer/spatial_embeddings/gene_embeddings_GraphSAGE_pandavid.pkl -> build/bdist.linux-armv7l/wheel/./spatialformer/spatial_embeddings 2026-03-20T14:17:18,210 copying build/lib/spatialformer/utils.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-20T14:17:18,213 copying build/lib/spatialformer/data_loader.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-20T14:17:18,216 copying build/lib/spatialformer/graphsage.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-20T14:17:18,219 copying build/lib/spatialformer/processor.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-20T14:17:18,221 copying build/lib/spatialformer/train.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-20T14:17:18,224 creating build/bdist.linux-armv7l/wheel/spatialformer/dataloader 2026-03-20T14:17:18,225 copying build/lib/spatialformer/dataloader/dataloader_paired.py -> build/bdist.linux-armv7l/wheel/./spatialformer/dataloader 2026-03-20T14:17:18,229 copying build/lib/spatialformer/dataloader/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/dataloader 2026-03-20T14:17:18,231 copying build/lib/spatialformer/GraphSAGE.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-20T14:17:18,234 copying build/lib/spatialformer/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-20T14:17:18,237 creating build/bdist.linux-armv7l/wheel/spatialformer/model 2026-03-20T14:17:18,238 creating build/bdist.linux-armv7l/wheel/spatialformer/model/submodules 2026-03-20T14:17:18,239 copying build/lib/spatialformer/model/submodules/modules.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-20T14:17:18,242 copying build/lib/spatialformer/model/submodules/masked_batchnorm.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-20T14:17:18,244 copying build/lib/spatialformer/model/submodules/masked_conv.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-20T14:17:18,246 copying build/lib/spatialformer/model/submodules/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-20T14:17:18,248 copying build/lib/spatialformer/model/submodules/flash_attention2.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-20T14:17:18,251 copying build/lib/spatialformer/model/submodules/layer_modules.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-20T14:17:18,253 copying build/lib/spatialformer/model/submodules/alibi.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-20T14:17:18,255 copying build/lib/spatialformer/model/submodules/activations.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-20T14:17:18,257 copying build/lib/spatialformer/model/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-20T14:17:18,259 copying build/lib/spatialformer/model/Spaformer_pair.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-20T14:17:18,262 copying build/lib/spatialformer/model/model.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-20T14:17:18,264 copying build/lib/spatialformer/model/Spaformer.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-20T14:17:18,267 copying build/lib/spatialformer/model/settings.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-20T14:17:18,270 creating build/bdist.linux-armv7l/wheel/spatialformer/tools 2026-03-20T14:17:18,271 copying build/lib/spatialformer/tools/get_embeddings.py -> build/bdist.linux-armv7l/wheel/./spatialformer/tools 2026-03-20T14:17:18,274 copying build/lib/spatialformer/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/tools 2026-03-20T14:17:18,276 creating build/bdist.linux-armv7l/wheel/spatialformer/tokenizer 2026-03-20T14:17:18,277 copying build/lib/spatialformer/tokenizer/token.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-20T14:17:18,280 copying build/lib/spatialformer/tokenizer/tokenv5.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-20T14:17:18,284 copying build/lib/spatialformer/tokenizer/tokenv4.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-20T14:17:18,287 copying build/lib/spatialformer/tokenizer/tokenv3.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-20T14:17:18,289 copying build/lib/spatialformer/tokenizer/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-20T14:17:18,291 copying build/lib/spatialformer/tokenizer/tokenv2.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-20T14:17:18,295 creating build/bdist.linux-armv7l/wheel/spatialformer/preprocess 2026-03-20T14:17:18,296 copying build/lib/spatialformer/preprocess/find_gene_interaction.py -> build/bdist.linux-armv7l/wheel/./spatialformer/preprocess 2026-03-20T14:17:18,299 copying build/lib/spatialformer/preprocess/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/preprocess 2026-03-20T14:17:18,301 creating build/bdist.linux-armv7l/wheel/spatialformer/config 2026-03-20T14:17:18,302 copying build/lib/spatialformer/config/_config_train_large_pair.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-20T14:17:18,304 copying build/lib/spatialformer/config/_config_train.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-20T14:17:18,306 copying build/lib/spatialformer/config/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-20T14:17:18,307 copying build/lib/spatialformer/config/_config_fine_tune_probe.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-20T14:17:18,309 copying build/lib/spatialformer/config/_config_graphsave.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-20T14:17:18,310 copying build/lib/spatialformer/config/_config_train_large_single.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-20T14:17:18,313 creating build/bdist.linux-armv7l/wheel/spatialformer/gene_gene_calculation 2026-03-20T14:17:18,313 copying build/lib/spatialformer/gene_gene_calculation/process.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-20T14:17:18,316 copying build/lib/spatialformer/gene_gene_calculation/find_gene_interaction.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-20T14:17:18,318 copying build/lib/spatialformer/gene_gene_calculation/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-20T14:17:18,320 copying build/lib/spatialformer/gene_gene_calculation/h5toloader.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-20T14:17:18,322 copying build/lib/spatialformer/gene_gene_calculation/mask_dataset.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-20T14:17:18,325 copying build/lib/spatialformer/gene_gene_calculation/build_h5ad.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-20T14:17:18,327 running install_egg_info 2026-03-20T14:17:18,360 Copying spatialformer.egg-info to build/bdist.linux-armv7l/wheel/./spatialformer-0.1.2-py3.11.egg-info 2026-03-20T14:17:18,369 running install_scripts 2026-03-20T14:17:18,379 creating build/bdist.linux-armv7l/wheel/spatialformer-0.1.2.dist-info/WHEEL 2026-03-20T14:17:18,381 creating '/tmp/pip-wheel-u0u7w0ko/spatialformer-0.1.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-03-20T14:17:18,386 adding 'spatialformer/GraphSAGE.py' 2026-03-20T14:17:18,387 adding 'spatialformer/__init__.py' 2026-03-20T14:17:18,391 adding 'spatialformer/data_loader.py' 2026-03-20T14:17:18,393 adding 'spatialformer/graphsage.py' 2026-03-20T14:17:18,395 adding 'spatialformer/processor.py' 2026-03-20T14:17:18,397 adding 'spatialformer/train.py' 2026-03-20T14:17:18,403 adding 'spatialformer/utils.py' 2026-03-20T14:17:18,405 adding 'spatialformer/config/__init__.py' 2026-03-20T14:17:18,406 adding 'spatialformer/config/_config_fine_tune_probe.json' 2026-03-20T14:17:18,407 adding 'spatialformer/config/_config_graphsave.json' 2026-03-20T14:17:18,409 adding 'spatialformer/config/_config_train.json' 2026-03-20T14:17:18,410 adding 'spatialformer/config/_config_train_large_pair.json' 2026-03-20T14:17:18,411 adding 'spatialformer/config/_config_train_large_single.json' 2026-03-20T14:17:18,413 adding 'spatialformer/dataloader/__init__.py' 2026-03-20T14:17:18,422 adding 'spatialformer/dataloader/dataloader_paired.py' 2026-03-20T14:17:18,424 adding 'spatialformer/gene_gene_calculation/__init__.py' 2026-03-20T14:17:18,426 adding 'spatialformer/gene_gene_calculation/build_h5ad.py' 2026-03-20T14:17:18,428 adding 'spatialformer/gene_gene_calculation/find_gene_interaction.py' 2026-03-20T14:17:18,431 adding 'spatialformer/gene_gene_calculation/h5toloader.py' 2026-03-20T14:17:18,434 adding 'spatialformer/gene_gene_calculation/mask_dataset.py' 2026-03-20T14:17:18,436 adding 'spatialformer/gene_gene_calculation/process.py' 2026-03-20T14:17:18,440 adding 'spatialformer/model/Spaformer.py' 2026-03-20T14:17:18,446 adding 'spatialformer/model/Spaformer_pair.py' 2026-03-20T14:17:18,447 adding 'spatialformer/model/__init__.py' 2026-03-20T14:17:18,449 adding 'spatialformer/model/model.py' 2026-03-20T14:17:18,450 adding 'spatialformer/model/settings.py' 2026-03-20T14:17:18,451 adding 'spatialformer/model/submodules/__init__.py' 2026-03-20T14:17:18,453 adding 'spatialformer/model/submodules/activations.py' 2026-03-20T14:17:18,454 adding 'spatialformer/model/submodules/alibi.py' 2026-03-20T14:17:18,458 adding 'spatialformer/model/submodules/flash_attention2.py' 2026-03-20T14:17:18,460 adding 'spatialformer/model/submodules/layer_modules.py' 2026-03-20T14:17:18,461 adding 'spatialformer/model/submodules/masked_batchnorm.py' 2026-03-20T14:17:18,463 adding 'spatialformer/model/submodules/masked_conv.py' 2026-03-20T14:17:18,465 adding 'spatialformer/model/submodules/modules.py' 2026-03-20T14:17:18,466 adding 'spatialformer/preprocess/__init__.py' 2026-03-20T14:17:18,469 adding 'spatialformer/preprocess/find_gene_interaction.py' 2026-03-20T14:17:18,470 adding 'spatialformer/spatial_embeddings/__init__.py' 2026-03-20T14:17:19,060 adding 'spatialformer/spatial_embeddings/gene_embeddings_GraphSAGE_pandavid.pkl' 2026-03-20T14:17:19,086 adding 'spatialformer/tokenizer/__init__.py' 2026-03-20T14:17:19,089 adding 'spatialformer/tokenizer/token.json' 2026-03-20T14:17:19,116 adding 'spatialformer/tokenizer/tokenv2.json' 2026-03-20T14:17:19,124 adding 'spatialformer/tokenizer/tokenv3.json' 2026-03-20T14:17:19,132 adding 'spatialformer/tokenizer/tokenv4.json' 2026-03-20T14:17:19,156 adding 'spatialformer/tokenizer/tokenv5.json' 2026-03-20T14:17:19,158 adding 'spatialformer/tools/__init__.py' 2026-03-20T14:17:19,165 adding 'spatialformer/tools/get_embeddings.py' 2026-03-20T14:17:19,167 adding 'spatialformer-0.1.2.dist-info/licenses/LICENSE' 2026-03-20T14:17:19,168 adding 'spatialformer-0.1.2.dist-info/METADATA' 2026-03-20T14:17:19,169 adding 'spatialformer-0.1.2.dist-info/WHEEL' 2026-03-20T14:17:19,170 adding 'spatialformer-0.1.2.dist-info/top_level.txt' 2026-03-20T14:17:19,171 adding 'spatialformer-0.1.2.dist-info/RECORD' 2026-03-20T14:17:19,218 error: [Errno 28] No space left on device 2026-03-20T14:17:19,328 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2026-03-20T14:17:19,341 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2026-03-20T14:17:19,341 exec(compile('"'"''"'"''"'"' 2026-03-20T14:17:19,341 # This is -- a caller that pip uses to run setup.py 2026-03-20T14:17:19,341 # 2026-03-20T14:17:19,341 # - It imports setuptools before invoking setup.py, to enable projects that directly 2026-03-20T14:17:19,341 # import from `distutils.core` to work with newer packaging standards. 2026-03-20T14:17:19,341 # - It provides a clear error message when setuptools is not installed. 2026-03-20T14:17:19,341 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2026-03-20T14:17:19,341 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2026-03-20T14:17:19,341 # manifest_maker: standard file '"'"'-c'"'"' not found". 2026-03-20T14:17:19,341 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2026-03-20T14:17:19,341 import os, sys, tokenize 2026-03-20T14:17:19,341 2026-03-20T14:17:19,341 try: 2026-03-20T14:17:19,341 import setuptools 2026-03-20T14:17:19,341 except ImportError as error: 2026-03-20T14:17:19,341 print( 2026-03-20T14:17:19,341 "ERROR: Can not exec2026-03-20T14:17:20,222 running clean 2026-03-20T14:17:20,274 removing 'build/lib' (and everything under it) 2026-03-20T14:17:20,288 removing 'build/bdist.linux-armv7l' (and everything under it) 2026-03-20T14:17:20,304 'build/scripts-3.11' does not exist -- can't clean it 2026-03-20T14:17:20,305 removing 'build' 2026-03-20T14:17:20,946 Failed to build spatialformer 2026-03-20T14:17:20,947 ERROR: Failed to build one or more wheels 2026-03-20T14:17:20,948 Exception information: 2026-03-20T14:17:20,948 Traceback (most recent call last): 2026-03-20T14:17:20,948 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 160, in exc_logging_wrapper 2026-03-20T14:17:20,948 status = run_func(*args) 2026-03-20T14:17:20,948 ^^^^^^^^^^^^^^^ 2026-03-20T14:17:20,948 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 247, in wrapper 2026-03-20T14:17:20,948 return func(self, options, args) 2026-03-20T14:17:20,948 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2026-03-20T14:17:20,948 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 201, in run 2026-03-20T14:17:20,948 raise CommandError("Failed to build one or more wheels") 2026-03-20T14:17:20,948 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2026-03-20T14:17:20,950 Removed build tracker: '/tmp/pip-build-tracker-4ss74n3d'