2026-03-26T19:49:28,376 Created temporary directory: /tmp/pip-ephem-wheel-cache-ki_3l36e 2026-03-26T19:49:28,378 Created temporary directory: /tmp/pip-build-tracker-jjv56y7i 2026-03-26T19:49:28,379 Initialized build tracking at /tmp/pip-build-tracker-jjv56y7i 2026-03-26T19:49:28,379 Created build tracker: /tmp/pip-build-tracker-jjv56y7i 2026-03-26T19:49:28,380 Entered build tracker: /tmp/pip-build-tracker-jjv56y7i 2026-03-26T19:49:28,380 Created temporary directory: /tmp/pip-wheel-1wumma27 2026-03-26T19:49:28,383 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 2026-03-26T19:49:28,386 Created temporary directory: /tmp/pip-ephem-wheel-cache-j3gnueqx 2026-03-26T19:49:28,410 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-03-26T19:49:28,414 2 location(s) to search for versions of spatialformer: 2026-03-26T19:49:28,414 * https://pypi.org/simple/spatialformer/ 2026-03-26T19:49:28,414 * https://www.piwheels.org/simple/spatialformer/ 2026-03-26T19:49:28,414 Fetching project page and analyzing links: https://pypi.org/simple/spatialformer/ 2026-03-26T19:49:28,415 Getting page https://pypi.org/simple/spatialformer/ 2026-03-26T19:49:28,417 Found index url https://pypi.org/simple 2026-03-26T19:49:28,569 Fetched page https://pypi.org/simple/spatialformer/ as application/vnd.pypi.simple.v1+json 2026-03-26T19:49:28,573 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) 2026-03-26T19:49:28,574 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 2026-03-26T19:49:28,575 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) 2026-03-26T19:49:28,576 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 2026-03-26T19:49:28,576 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) 2026-03-26T19:49:28,577 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 2026-03-26T19:49:28,578 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) 2026-03-26T19:49:28,579 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 2026-03-26T19:49:28,580 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) 2026-03-26T19:49:28,581 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 2026-03-26T19:49:28,582 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) 2026-03-26T19:49:28,582 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 2026-03-26T19:49:28,583 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) 2026-03-26T19:49:28,584 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 2026-03-26T19:49:28,585 Skipping link: No binaries permitted for spatialformer: https://files.pythonhosted.org/packages/82/86/3574918e6113f49a9d0bba52b23bb725603e5a8182d4e9637c958d6a4846/spatialformer-0.1.6-py3-none-any.whl (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-26T19:49:28,585 Found link https://files.pythonhosted.org/packages/c5/15/fb3bd5704d9013c4157e0eb3cab6ebb1e7eb9db7ab5a66fd0599c4bd8e40/spatialformer-0.1.6.tar.gz (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10), version: 0.1.6 2026-03-26T19:49:28,586 Skipping link: No binaries permitted for spatialformer: https://files.pythonhosted.org/packages/41/f1/f12767fcbd6997ea51f49966ffb94b923134ae0ae96266aeb7e6bd57066b/spatialformer-0.1.8-py3-none-any.whl (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-26T19:49:28,587 Found link https://files.pythonhosted.org/packages/5a/56/62b2fd12b63f80f29bff02f1c38eccbc10ee5ae6a0666b5bdc870185d07c/spatialformer-0.1.8.tar.gz (from https://pypi.org/simple/spatialformer/) (requires-python:>=3.10), version: 0.1.8 2026-03-26T19:49:28,588 Fetching project page and analyzing links: https://www.piwheels.org/simple/spatialformer/ 2026-03-26T19:49:28,588 Getting page https://www.piwheels.org/simple/spatialformer/ 2026-03-26T19:49:28,589 Found index url https://www.piwheels.org/simple 2026-03-26T19:49:28,756 Fetched page https://www.piwheels.org/simple/spatialformer/ as text/html 2026-03-26T19:49:28,760 Skipping link: No binaries permitted for spatialformer: https://www.piwheels.org/simple/spatialformer/spatialformer-0.1.6-py3-none-any.whl#sha256=1221890b54152fe026ba6186c8c5e2d48fd585be186695c11b30b89cc0957602 (from https://www.piwheels.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-26T19:49:28,760 Skipping link: No binaries permitted for spatialformer: https://www.piwheels.org/simple/spatialformer/spatialformer-0.1.5-py3-none-any.whl#sha256=9037616ea6bfda0e1e8d007b3a84de502ca4516fb1e69ca38048c958990de411 (from https://www.piwheels.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-26T19:49:28,761 Skipping link: No binaries permitted for spatialformer: https://www.piwheels.org/simple/spatialformer/spatialformer-0.1.4-py3-none-any.whl#sha256=4e4bc1bf2ac5d843fa3910d0400af5df9c35f4af59b7414df3ab398c47f16c07 (from https://www.piwheels.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-26T19:49:28,761 Skipping link: No binaries permitted for spatialformer: https://www.piwheels.org/simple/spatialformer/spatialformer-0.1.3-py3-none-any.whl#sha256=8e4adfc89ae0fbbbdbaa3a0d11ea406797372805347a492158d6fbbfba2d292c (from https://www.piwheels.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-26T19:49:28,762 Skipping link: No binaries permitted for spatialformer: https://www.piwheels.org/simple/spatialformer/spatialformer-0.1.2-py3-none-any.whl#sha256=40867d145781926c3287b71e154107f3a67733a28c34e95b2da4ab4e13dc5627 (from https://www.piwheels.org/simple/spatialformer/) (requires-python:>=3.10) 2026-03-26T19:49:28,763 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) 2026-03-26T19:49:28,763 Skipping link: not a file: https://www.piwheels.org/simple/spatialformer/ 2026-03-26T19:49:28,764 Skipping link: not a file: https://pypi.org/simple/spatialformer/ 2026-03-26T19:49:28,783 Given no hashes to check 1 links for project 'spatialformer': discarding no candidates 2026-03-26T19:49:28,801 Collecting spatialformer==0.1.8 2026-03-26T19:49:28,803 Created temporary directory: /tmp/pip-unpack-ye9obkc_ 2026-03-26T19:49:29,033 Downloading spatialformer-0.1.8.tar.gz (10.9 MB) 2026-03-26T19:49:31,929 Added spatialformer==0.1.8 from https://files.pythonhosted.org/packages/5a/56/62b2fd12b63f80f29bff02f1c38eccbc10ee5ae6a0666b5bdc870185d07c/spatialformer-0.1.8.tar.gz to build tracker '/tmp/pip-build-tracker-jjv56y7i' 2026-03-26T19:49:31,931 Running setup.py (path:/tmp/pip-wheel-1wumma27/spatialformer_89daa4d57a29419ab82734773709f02e/setup.py) egg_info for package spatialformer 2026-03-26T19:49:31,932 Created temporary directory: /tmp/pip-pip-egg-info-nrh02tpz 2026-03-26T19:49:31,932 Preparing metadata (setup.py): started 2026-03-26T19:49:31,933 Running command python setup.py egg_info 2026-03-26T19:49:32,806 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-03-26T19:49:32,806 !! 2026-03-26T19:49:32,808 ******************************************************************************** 2026-03-26T19:49:32,808 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-03-26T19:49:32,809 License :: OSI Approved :: MIT License 2026-03-26T19:49:32,811 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-03-26T19:49:32,811 ******************************************************************************** 2026-03-26T19:49:32,812 !! 2026-03-26T19:49:32,813 self._finalize_license_expression() 2026-03-26T19:49:32,836 running egg_info 2026-03-26T19:49:32,863 creating /tmp/pip-pip-egg-info-nrh02tpz/spatialformer.egg-info 2026-03-26T19:49:32,864 writing /tmp/pip-pip-egg-info-nrh02tpz/spatialformer.egg-info/PKG-INFO 2026-03-26T19:49:32,870 writing dependency_links to /tmp/pip-pip-egg-info-nrh02tpz/spatialformer.egg-info/dependency_links.txt 2026-03-26T19:49:32,873 writing requirements to /tmp/pip-pip-egg-info-nrh02tpz/spatialformer.egg-info/requires.txt 2026-03-26T19:49:32,874 writing top-level names to /tmp/pip-pip-egg-info-nrh02tpz/spatialformer.egg-info/top_level.txt 2026-03-26T19:49:32,876 writing manifest file '/tmp/pip-pip-egg-info-nrh02tpz/spatialformer.egg-info/SOURCES.txt' 2026-03-26T19:49:32,976 reading manifest file '/tmp/pip-pip-egg-info-nrh02tpz/spatialformer.egg-info/SOURCES.txt' 2026-03-26T19:49:32,978 reading manifest template 'MANIFEST.in' 2026-03-26T19:49:32,980 adding license file 'LICENSE' 2026-03-26T19:49:32,984 writing manifest file '/tmp/pip-pip-egg-info-nrh02tpz/spatialformer.egg-info/SOURCES.txt' 2026-03-26T19:49:33,090 Preparing metadata (setup.py): finished with status 'done' 2026-03-26T19:49:33,095 Source in /tmp/pip-wheel-1wumma27/spatialformer_89daa4d57a29419ab82734773709f02e has version 0.1.8, which satisfies requirement spatialformer==0.1.8 from https://files.pythonhosted.org/packages/5a/56/62b2fd12b63f80f29bff02f1c38eccbc10ee5ae6a0666b5bdc870185d07c/spatialformer-0.1.8.tar.gz 2026-03-26T19:49:33,096 Removed spatialformer==0.1.8 from https://files.pythonhosted.org/packages/5a/56/62b2fd12b63f80f29bff02f1c38eccbc10ee5ae6a0666b5bdc870185d07c/spatialformer-0.1.8.tar.gz from build tracker '/tmp/pip-build-tracker-jjv56y7i' 2026-03-26T19:49:33,104 Created temporary directory: /tmp/pip-unpack-n8ain3_c 2026-03-26T19:49:33,105 Building wheels for collected packages: spatialformer 2026-03-26T19:49:33,109 Created temporary directory: /tmp/pip-wheel-0v92zn3a 2026-03-26T19:49:33,110 Building wheel for spatialformer (setup.py): started 2026-03-26T19:49:33,111 Destination directory: /tmp/pip-wheel-0v92zn3a 2026-03-26T19:49:33,111 Running command python setup.py bdist_wheel 2026-03-26T19:49:33,943 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-03-26T19:49:33,944 !! 2026-03-26T19:49:33,945 ******************************************************************************** 2026-03-26T19:49:33,945 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-03-26T19:49:33,946 License :: OSI Approved :: MIT License 2026-03-26T19:49:33,947 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-03-26T19:49:33,948 ******************************************************************************** 2026-03-26T19:49:33,949 !! 2026-03-26T19:49:33,949 self._finalize_license_expression() 2026-03-26T19:49:33,950 running bdist_wheel 2026-03-26T19:49:34,080 running build 2026-03-26T19:49:34,081 running build_py 2026-03-26T19:49:34,113 creating build/lib/spatialformer 2026-03-26T19:49:34,115 copying spatialformer/processor.py -> build/lib/spatialformer 2026-03-26T19:49:34,118 copying spatialformer/data_loader.py -> build/lib/spatialformer 2026-03-26T19:49:34,120 copying spatialformer/train.py -> build/lib/spatialformer 2026-03-26T19:49:34,123 copying spatialformer/utils.py -> build/lib/spatialformer 2026-03-26T19:49:34,126 copying spatialformer/GraphSAGE.py -> build/lib/spatialformer 2026-03-26T19:49:34,129 copying spatialformer/__init__.py -> build/lib/spatialformer 2026-03-26T19:49:34,131 copying spatialformer/graphsage.py -> build/lib/spatialformer 2026-03-26T19:49:34,134 creating build/lib/spatialformer/gene_gene_calculation 2026-03-26T19:49:34,135 copying spatialformer/gene_gene_calculation/build_h5ad.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-26T19:49:34,138 copying spatialformer/gene_gene_calculation/process.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-26T19:49:34,140 copying spatialformer/gene_gene_calculation/h5toloader.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-26T19:49:34,143 copying spatialformer/gene_gene_calculation/__init__.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-26T19:49:34,144 copying spatialformer/gene_gene_calculation/find_gene_interaction.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-26T19:49:34,147 copying spatialformer/gene_gene_calculation/mask_dataset.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-26T19:49:34,150 creating build/lib/spatialformer/config 2026-03-26T19:49:34,151 copying spatialformer/config/__init__.py -> build/lib/spatialformer/config 2026-03-26T19:49:34,153 creating build/lib/spatialformer/tokenizer 2026-03-26T19:49:34,154 copying spatialformer/tokenizer/__init__.py -> build/lib/spatialformer/tokenizer 2026-03-26T19:49:34,156 creating build/lib/spatialformer/preprocess 2026-03-26T19:49:34,157 copying spatialformer/preprocess/__init__.py -> build/lib/spatialformer/preprocess 2026-03-26T19:49:34,159 copying spatialformer/preprocess/find_gene_interaction.py -> build/lib/spatialformer/preprocess 2026-03-26T19:49:34,162 creating build/lib/spatialformer/dataloader 2026-03-26T19:49:34,163 copying spatialformer/dataloader/dataloader_paired.py -> build/lib/spatialformer/dataloader 2026-03-26T19:49:34,166 copying spatialformer/dataloader/__init__.py -> build/lib/spatialformer/dataloader 2026-03-26T19:49:34,168 creating build/lib/spatialformer/model 2026-03-26T19:49:34,169 copying spatialformer/model/settings.py -> build/lib/spatialformer/model 2026-03-26T19:49:34,171 copying spatialformer/model/model.py -> build/lib/spatialformer/model 2026-03-26T19:49:34,173 copying spatialformer/model/Spaformer_pair.py -> build/lib/spatialformer/model 2026-03-26T19:49:34,176 copying spatialformer/model/Spaformer.py -> build/lib/spatialformer/model 2026-03-26T19:49:34,179 copying spatialformer/model/__init__.py -> build/lib/spatialformer/model 2026-03-26T19:49:34,181 creating build/lib/spatialformer/tools 2026-03-26T19:49:34,182 copying spatialformer/tools/get_embeddings.py -> build/lib/spatialformer/tools 2026-03-26T19:49:34,185 copying spatialformer/tools/__init__.py -> build/lib/spatialformer/tools 2026-03-26T19:49:34,187 creating build/lib/spatialformer/spatial_embeddings 2026-03-26T19:49:34,188 copying spatialformer/spatial_embeddings/__init__.py -> build/lib/spatialformer/spatial_embeddings 2026-03-26T19:49:34,190 creating build/lib/spatialformer/model/submodules 2026-03-26T19:49:34,191 copying spatialformer/model/submodules/masked_batchnorm.py -> build/lib/spatialformer/model/submodules 2026-03-26T19:49:34,194 copying spatialformer/model/submodules/masked_conv.py -> build/lib/spatialformer/model/submodules 2026-03-26T19:49:34,196 copying spatialformer/model/submodules/layer_modules.py -> build/lib/spatialformer/model/submodules 2026-03-26T19:49:34,198 copying spatialformer/model/submodules/alibi.py -> build/lib/spatialformer/model/submodules 2026-03-26T19:49:34,199 copying spatialformer/model/submodules/flash_attention2.py -> build/lib/spatialformer/model/submodules 2026-03-26T19:49:34,202 copying spatialformer/model/submodules/modules.py -> build/lib/spatialformer/model/submodules 2026-03-26T19:49:34,205 copying spatialformer/model/submodules/activations.py -> build/lib/spatialformer/model/submodules 2026-03-26T19:49:34,207 copying spatialformer/model/submodules/__init__.py -> build/lib/spatialformer/model/submodules 2026-03-26T19:49:34,208 running egg_info 2026-03-26T19:49:34,236 writing spatialformer.egg-info/PKG-INFO 2026-03-26T19:49:34,241 writing dependency_links to spatialformer.egg-info/dependency_links.txt 2026-03-26T19:49:34,245 writing requirements to spatialformer.egg-info/requires.txt 2026-03-26T19:49:34,246 writing top-level names to spatialformer.egg-info/top_level.txt 2026-03-26T19:49:34,287 reading manifest file 'spatialformer.egg-info/SOURCES.txt' 2026-03-26T19:49:34,292 reading manifest template 'MANIFEST.in' 2026-03-26T19:49:34,294 adding license file 'LICENSE' 2026-03-26T19:49:34,299 writing manifest file 'spatialformer.egg-info/SOURCES.txt' 2026-03-26T19:49:34,301 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'spatialformer.data' is absent from the `packages` configuration. 2026-03-26T19:49:34,302 !! 2026-03-26T19:49:34,303 ******************************************************************************** 2026-03-26T19:49:34,303 ############################ 2026-03-26T19:49:34,304 # Package would be ignored # 2026-03-26T19:49:34,304 ############################ 2026-03-26T19:49:34,305 Python recognizes 'spatialformer.data' as an importable package[^1], 2026-03-26T19:49:34,305 but it is absent from setuptools' `packages` configuration. 2026-03-26T19:49:34,306 This leads to an ambiguous overall configuration. If you want to distribute this 2026-03-26T19:49:34,307 package, please make sure that 'spatialformer.data' is explicitly added 2026-03-26T19:49:34,307 to the `packages` configuration field. 2026-03-26T19:49:34,308 Alternatively, you can also rely on setuptools' discovery methods 2026-03-26T19:49:34,309 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2026-03-26T19:49:34,309 instead of `find_packages(...)`/`find:`). 2026-03-26T19:49:34,310 You can read more about "package discovery" on setuptools documentation page: 2026-03-26T19:49:34,311 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2026-03-26T19:49:34,312 If you don't want 'spatialformer.data' to be distributed and are 2026-03-26T19:49:34,312 already explicitly excluding 'spatialformer.data' via 2026-03-26T19:49:34,313 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2026-03-26T19:49:34,314 you can try to use `exclude_package_data`, or `include-package-data=False` in 2026-03-26T19:49:34,315 combination with a more fine grained `package-data` configuration. 2026-03-26T19:49:34,316 You can read more about "package data files" on setuptools documentation page: 2026-03-26T19:49:34,317 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2026-03-26T19:49:34,318 [^1]: For Python, any directory (with suitable naming) can be imported, 2026-03-26T19:49:34,319 even if it does not contain any `.py` files. 2026-03-26T19:49:34,319 On the other hand, currently there is no concept of package data 2026-03-26T19:49:34,320 directory, all directories are treated like packages. 2026-03-26T19:49:34,320 ******************************************************************************** 2026-03-26T19:49:34,321 !! 2026-03-26T19:49:34,322 check.warn(importable) 2026-03-26T19:49:34,322 creating build/lib/spatialformer/data 2026-03-26T19:49:34,323 copying spatialformer/data/gene_median.pkl -> build/lib/spatialformer/data 2026-03-26T19:49:34,323 copying spatialformer/config/_config_fine_tune_probe.json -> build/lib/spatialformer/config 2026-03-26T19:49:34,324 copying spatialformer/config/_config_graphsave.json -> build/lib/spatialformer/config 2026-03-26T19:49:34,324 copying spatialformer/config/_config_train.json -> build/lib/spatialformer/config 2026-03-26T19:49:34,325 copying spatialformer/config/_config_train_large_pair.json -> build/lib/spatialformer/config 2026-03-26T19:49:34,326 copying spatialformer/config/_config_train_large_single.json -> build/lib/spatialformer/config 2026-03-26T19:49:34,328 copying spatialformer/tokenizer/token.json -> build/lib/spatialformer/tokenizer 2026-03-26T19:49:34,331 copying spatialformer/tokenizer/tokenv2.json -> build/lib/spatialformer/tokenizer 2026-03-26T19:49:34,335 copying spatialformer/tokenizer/tokenv3.json -> build/lib/spatialformer/tokenizer 2026-03-26T19:49:34,338 copying spatialformer/tokenizer/tokenv4.json -> build/lib/spatialformer/tokenizer 2026-03-26T19:49:34,342 copying spatialformer/tokenizer/tokenv5.json -> build/lib/spatialformer/tokenizer 2026-03-26T19:49:34,347 copying spatialformer/spatial_embeddings/xenium_5k_pandavid_gene_embeddings.pkl -> build/lib/spatialformer/spatial_embeddings 2026-03-26T19:49:34,564 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2026-03-26T19:49:34,565 !! 2026-03-26T19:49:34,566 ******************************************************************************** 2026-03-26T19:49:34,567 Please avoid running ``setup.py`` directly. 2026-03-26T19:49:34,567 Instead, use pypa/build, pypa/installer or other 2026-03-26T19:49:34,568 standards-based tools. 2026-03-26T19:49:34,569 This deprecation is overdue, please update your project and remove deprecated 2026-03-26T19:49:34,570 calls to avoid build errors in the future. 2026-03-26T19:49:34,571 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2026-03-26T19:49:34,571 ******************************************************************************** 2026-03-26T19:49:34,573 !! 2026-03-26T19:49:34,573 self.initialize_options() 2026-03-26T19:49:34,594 installing to build/bdist.linux-armv7l/wheel 2026-03-26T19:49:34,594 running install 2026-03-26T19:49:34,618 running install_lib 2026-03-26T19:49:34,645 creating build/bdist.linux-armv7l/wheel 2026-03-26T19:49:34,647 creating build/bdist.linux-armv7l/wheel/spatialformer 2026-03-26T19:49:34,649 creating build/bdist.linux-armv7l/wheel/spatialformer/gene_gene_calculation 2026-03-26T19:49:34,650 copying build/lib/spatialformer/gene_gene_calculation/build_h5ad.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-26T19:49:34,652 copying build/lib/spatialformer/gene_gene_calculation/process.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-26T19:49:34,654 copying build/lib/spatialformer/gene_gene_calculation/h5toloader.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-26T19:49:34,657 copying build/lib/spatialformer/gene_gene_calculation/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-26T19:49:34,658 copying build/lib/spatialformer/gene_gene_calculation/find_gene_interaction.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-26T19:49:34,660 copying build/lib/spatialformer/gene_gene_calculation/mask_dataset.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-26T19:49:34,663 creating build/bdist.linux-armv7l/wheel/spatialformer/config 2026-03-26T19:49:34,664 copying build/lib/spatialformer/config/_config_graphsave.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-26T19:49:34,666 copying build/lib/spatialformer/config/_config_train.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-26T19:49:34,668 copying build/lib/spatialformer/config/_config_train_large_single.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-26T19:49:34,670 copying build/lib/spatialformer/config/_config_fine_tune_probe.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-26T19:49:34,672 copying build/lib/spatialformer/config/_config_train_large_pair.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-26T19:49:34,674 copying build/lib/spatialformer/config/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-26T19:49:34,675 copying build/lib/spatialformer/processor.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-26T19:49:34,677 copying build/lib/spatialformer/data_loader.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-26T19:49:34,680 creating build/bdist.linux-armv7l/wheel/spatialformer/data 2026-03-26T19:49:34,681 copying build/lib/spatialformer/data/gene_median.pkl -> build/bdist.linux-armv7l/wheel/./spatialformer/data 2026-03-26T19:49:34,686 copying build/lib/spatialformer/train.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-26T19:49:34,688 copying build/lib/spatialformer/utils.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-26T19:49:34,693 creating build/bdist.linux-armv7l/wheel/spatialformer/tokenizer 2026-03-26T19:49:34,694 copying build/lib/spatialformer/tokenizer/tokenv2.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-26T19:49:34,698 copying build/lib/spatialformer/tokenizer/tokenv3.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-26T19:49:34,701 copying build/lib/spatialformer/tokenizer/tokenv4.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-26T19:49:34,704 copying build/lib/spatialformer/tokenizer/token.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-26T19:49:34,706 copying build/lib/spatialformer/tokenizer/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-26T19:49:34,708 copying build/lib/spatialformer/tokenizer/tokenv5.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-26T19:49:34,713 creating build/bdist.linux-armv7l/wheel/spatialformer/preprocess 2026-03-26T19:49:34,715 copying build/lib/spatialformer/preprocess/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/preprocess 2026-03-26T19:49:34,717 copying build/lib/spatialformer/preprocess/find_gene_interaction.py -> build/bdist.linux-armv7l/wheel/./spatialformer/preprocess 2026-03-26T19:49:34,720 creating build/bdist.linux-armv7l/wheel/spatialformer/dataloader 2026-03-26T19:49:34,721 copying build/lib/spatialformer/dataloader/dataloader_paired.py -> build/bdist.linux-armv7l/wheel/./spatialformer/dataloader 2026-03-26T19:49:34,724 copying build/lib/spatialformer/dataloader/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/dataloader 2026-03-26T19:49:34,727 creating build/bdist.linux-armv7l/wheel/spatialformer/model 2026-03-26T19:49:34,728 copying build/lib/spatialformer/model/settings.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-26T19:49:34,730 copying build/lib/spatialformer/model/model.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-26T19:49:34,733 creating build/bdist.linux-armv7l/wheel/spatialformer/model/submodules 2026-03-26T19:49:34,734 copying build/lib/spatialformer/model/submodules/masked_batchnorm.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-26T19:49:34,737 copying build/lib/spatialformer/model/submodules/masked_conv.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-26T19:49:34,739 copying build/lib/spatialformer/model/submodules/layer_modules.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-26T19:49:34,741 copying build/lib/spatialformer/model/submodules/alibi.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-26T19:49:34,743 copying build/lib/spatialformer/model/submodules/flash_attention2.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-26T19:49:34,746 copying build/lib/spatialformer/model/submodules/modules.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-26T19:49:34,748 copying build/lib/spatialformer/model/submodules/activations.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-26T19:49:34,750 copying build/lib/spatialformer/model/submodules/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-26T19:49:34,752 copying build/lib/spatialformer/model/Spaformer_pair.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-26T19:49:34,755 copying build/lib/spatialformer/model/Spaformer.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-26T19:49:34,758 copying build/lib/spatialformer/model/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-26T19:49:34,760 creating build/bdist.linux-armv7l/wheel/spatialformer/tools 2026-03-26T19:49:34,761 copying build/lib/spatialformer/tools/get_embeddings.py -> build/bdist.linux-armv7l/wheel/./spatialformer/tools 2026-03-26T19:49:34,764 copying build/lib/spatialformer/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/tools 2026-03-26T19:49:34,766 creating build/bdist.linux-armv7l/wheel/spatialformer/spatial_embeddings 2026-03-26T19:49:34,767 copying build/lib/spatialformer/spatial_embeddings/xenium_5k_pandavid_gene_embeddings.pkl -> build/bdist.linux-armv7l/wheel/./spatialformer/spatial_embeddings 2026-03-26T19:49:34,950 copying build/lib/spatialformer/spatial_embeddings/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/spatial_embeddings 2026-03-26T19:49:34,952 copying build/lib/spatialformer/GraphSAGE.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-26T19:49:34,954 copying build/lib/spatialformer/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-26T19:49:34,956 copying build/lib/spatialformer/graphsage.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-26T19:49:34,959 running install_egg_info 2026-03-26T19:49:34,993 Copying spatialformer.egg-info to build/bdist.linux-armv7l/wheel/./spatialformer-0.1.8-py3.11.egg-info 2026-03-26T19:49:35,003 running install_scripts 2026-03-26T19:49:35,014 creating build/bdist.linux-armv7l/wheel/spatialformer-0.1.8.dist-info/WHEEL 2026-03-26T19:49:35,017 creating '/tmp/pip-wheel-0v92zn3a/spatialformer-0.1.8-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-03-26T19:49:35,021 adding 'spatialformer/GraphSAGE.py' 2026-03-26T19:49:35,023 adding 'spatialformer/__init__.py' 2026-03-26T19:49:35,026 adding 'spatialformer/data_loader.py' 2026-03-26T19:49:35,029 adding 'spatialformer/graphsage.py' 2026-03-26T19:49:35,030 adding 'spatialformer/processor.py' 2026-03-26T19:49:35,032 adding 'spatialformer/train.py' 2026-03-26T19:49:35,040 adding 'spatialformer/utils.py' 2026-03-26T19:49:35,042 adding 'spatialformer/config/__init__.py' 2026-03-26T19:49:35,044 adding 'spatialformer/config/_config_fine_tune_probe.json' 2026-03-26T19:49:35,045 adding 'spatialformer/config/_config_graphsave.json' 2026-03-26T19:49:35,046 adding 'spatialformer/config/_config_train.json' 2026-03-26T19:49:35,047 adding 'spatialformer/config/_config_train_large_pair.json' 2026-03-26T19:49:35,049 adding 'spatialformer/config/_config_train_large_single.json' 2026-03-26T19:49:35,060 adding 'spatialformer/data/gene_median.pkl' 2026-03-26T19:49:35,062 adding 'spatialformer/dataloader/__init__.py' 2026-03-26T19:49:35,070 adding 'spatialformer/dataloader/dataloader_paired.py' 2026-03-26T19:49:35,072 adding 'spatialformer/gene_gene_calculation/__init__.py' 2026-03-26T19:49:35,073 adding 'spatialformer/gene_gene_calculation/build_h5ad.py' 2026-03-26T19:49:35,076 adding 'spatialformer/gene_gene_calculation/find_gene_interaction.py' 2026-03-26T19:49:35,078 adding 'spatialformer/gene_gene_calculation/h5toloader.py' 2026-03-26T19:49:35,081 adding 'spatialformer/gene_gene_calculation/mask_dataset.py' 2026-03-26T19:49:35,082 adding 'spatialformer/gene_gene_calculation/process.py' 2026-03-26T19:49:35,086 adding 'spatialformer/model/Spaformer.py' 2026-03-26T19:49:35,092 adding 'spatialformer/model/Spaformer_pair.py' 2026-03-26T19:49:35,094 adding 'spatialformer/model/__init__.py' 2026-03-26T19:49:35,095 adding 'spatialformer/model/model.py' 2026-03-26T19:49:35,097 adding 'spatialformer/model/settings.py' 2026-03-26T19:49:35,098 adding 'spatialformer/model/submodules/__init__.py' 2026-03-26T19:49:35,100 adding 'spatialformer/model/submodules/activations.py' 2026-03-26T19:49:35,101 adding 'spatialformer/model/submodules/alibi.py' 2026-03-26T19:49:35,105 adding 'spatialformer/model/submodules/flash_attention2.py' 2026-03-26T19:49:35,107 adding 'spatialformer/model/submodules/layer_modules.py' 2026-03-26T19:49:35,108 adding 'spatialformer/model/submodules/masked_batchnorm.py' 2026-03-26T19:49:35,110 adding 'spatialformer/model/submodules/masked_conv.py' 2026-03-26T19:49:35,112 adding 'spatialformer/model/submodules/modules.py' 2026-03-26T19:49:35,113 adding 'spatialformer/preprocess/__init__.py' 2026-03-26T19:49:35,115 adding 'spatialformer/preprocess/find_gene_interaction.py' 2026-03-26T19:49:35,117 adding 'spatialformer/spatial_embeddings/__init__.py' 2026-03-26T19:49:36,817 adding 'spatialformer/spatial_embeddings/xenium_5k_pandavid_gene_embeddings.pkl' 2026-03-26T19:49:36,895 adding 'spatialformer/tokenizer/__init__.py' 2026-03-26T19:49:36,898 adding 'spatialformer/tokenizer/token.json' 2026-03-26T19:49:36,922 adding 'spatialformer/tokenizer/tokenv2.json' 2026-03-26T19:49:36,929 adding 'spatialformer/tokenizer/tokenv3.json' 2026-03-26T19:49:36,936 adding 'spatialformer/tokenizer/tokenv4.json' 2026-03-26T19:49:36,961 adding 'spatialformer/tokenizer/tokenv5.json' 2026-03-26T19:49:36,963 adding 'spatialformer/tools/__init__.py' 2026-03-26T19:49:36,969 adding 'spatialformer/tools/get_embeddings.py' 2026-03-26T19:49:36,972 adding 'spatialformer-0.1.8.dist-info/licenses/LICENSE' 2026-03-26T19:49:36,975 adding 'spatialformer-0.1.8.dist-info/METADATA' 2026-03-26T19:49:36,976 adding 'spatialformer-0.1.8.dist-info/WHEEL' 2026-03-26T19:49:36,977 adding 'spatialformer-0.1.8.dist-info/top_level.txt' 2026-03-26T19:49:36,978 adding 'spatialformer-0.1.8.dist-info/RECORD' 2026-03-26T19:49:37,111 removing build/bdist.linux-armv7l/wheel 2026-03-26T19:49:37,238 Building wheel for spatialformer (setup.py): finished with status 'done' 2026-03-26T19:49:37,446 Created wheel for spatialformer: filename=spatialformer-0.1.8-py3-none-any.whl size=10916809 sha256=36004d2a99cf6c6abd761cc2dee9db97e3a9779cb8f27047858cc34f84f6ae42 2026-03-26T19:49:37,447 Stored in directory: /tmp/pip-ephem-wheel-cache-j3gnueqx/wheels/35/f3/18/b1bbe52123904cb181ecdaf87dabc00cd345ac835ee6250d05 2026-03-26T19:49:37,466 Successfully built spatialformer 2026-03-26T19:49:37,726 Removed build tracker: '/tmp/pip-build-tracker-jjv56y7i'