2026-03-25T22:19:30,015 Created temporary directory: /tmp/pip-build-tracker-cz7ucdeg 2026-03-25T22:19:30,016 Initialized build tracking at /tmp/pip-build-tracker-cz7ucdeg 2026-03-25T22:19:30,017 Created build tracker: /tmp/pip-build-tracker-cz7ucdeg 2026-03-25T22:19:30,017 Entered build tracker: /tmp/pip-build-tracker-cz7ucdeg 2026-03-25T22:19:30,017 Created temporary directory: /tmp/pip-wheel-kz75967c 2026-03-25T22:19:30,021 Created temporary directory: /tmp/pip-ephem-wheel-cache-ckl4wird 2026-03-25T22:19:30,077 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-03-25T22:19:30,079 2 location(s) to search for versions of spatialformer: 2026-03-25T22:19:30,079 * https://pypi.org/simple/spatialformer/ 2026-03-25T22:19:30,079 * https://www.piwheels.org/simple/spatialformer/ 2026-03-25T22:19:30,080 Fetching project page and analyzing links: https://pypi.org/simple/spatialformer/ 2026-03-25T22:19:30,080 Getting page https://pypi.org/simple/spatialformer/ 2026-03-25T22:19:30,081 Found index url https://pypi.org/simple/ 2026-03-25T22:19:30,233 Fetched page https://pypi.org/simple/spatialformer/ as application/vnd.pypi.simple.v1+json 2026-03-25T22:19:30,238 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) 2026-03-25T22:19:30,239 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 2026-03-25T22:19:30,240 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) 2026-03-25T22:19:30,241 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 2026-03-25T22:19:30,241 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) 2026-03-25T22:19:30,242 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 2026-03-25T22:19:30,242 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) 2026-03-25T22:19:30,242 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 2026-03-25T22:19:30,243 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) 2026-03-25T22:19:30,243 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 2026-03-25T22:19:30,243 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) 2026-03-25T22:19:30,243 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 2026-03-25T22:19:30,244 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) 2026-03-25T22:19:30,244 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 2026-03-25T22:19:30,244 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) 2026-03-25T22:19:30,244 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 2026-03-25T22:19:30,245 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) 2026-03-25T22:19:30,245 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 2026-03-25T22:19:30,245 Fetching project page and analyzing links: https://www.piwheels.org/simple/spatialformer/ 2026-03-25T22:19:30,246 Getting page https://www.piwheels.org/simple/spatialformer/ 2026-03-25T22:19:30,247 Found index url https://www.piwheels.org/simple/ 2026-03-25T22:19:30,337 Fetched page https://www.piwheels.org/simple/spatialformer/ as text/html 2026-03-25T22:19:30,339 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) 2026-03-25T22:19:30,339 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) 2026-03-25T22:19:30,340 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) 2026-03-25T22:19:30,340 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) 2026-03-25T22:19:30,340 Skipping link: not a file: https://www.piwheels.org/simple/spatialformer/ 2026-03-25T22:19:30,340 Skipping link: not a file: https://pypi.org/simple/spatialformer/ 2026-03-25T22:19:30,365 Given no hashes to check 1 links for project 'spatialformer': discarding no candidates 2026-03-25T22:19:30,367 Collecting spatialformer==0.1.2 2026-03-25T22:19:30,369 Created temporary directory: /tmp/pip-unpack-8qs7xwzs 2026-03-25T22:19:30,522 Downloading spatialformer-0.1.2.tar.gz (3.9 MB) 2026-03-25T22:19:31,415 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-cz7ucdeg' 2026-03-25T22:19:31,419 Running setup.py (path:/tmp/pip-wheel-kz75967c/spatialformer_6d17f5afb558407e972f4129c0ba6bd9/setup.py) egg_info for package spatialformer 2026-03-25T22:19:31,420 Created temporary directory: /tmp/pip-pip-egg-info-3nmtdnvj 2026-03-25T22:19:31,420 Preparing metadata (setup.py): started 2026-03-25T22:19:31,421 Running command python setup.py egg_info 2026-03-25T22:19:32,963 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-03-25T22:19:32,963 !! 2026-03-25T22:19:32,963 ******************************************************************************** 2026-03-25T22:19:32,964 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-03-25T22:19:32,964 License :: OSI Approved :: MIT License 2026-03-25T22:19:32,964 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-03-25T22:19:32,964 ******************************************************************************** 2026-03-25T22:19:32,964 !! 2026-03-25T22:19:32,964 self._finalize_license_expression() 2026-03-25T22:19:33,040 running egg_info 2026-03-25T22:19:33,115 creating /tmp/pip-pip-egg-info-3nmtdnvj/spatialformer.egg-info 2026-03-25T22:19:33,116 writing /tmp/pip-pip-egg-info-3nmtdnvj/spatialformer.egg-info/PKG-INFO 2026-03-25T22:19:33,119 writing dependency_links to /tmp/pip-pip-egg-info-3nmtdnvj/spatialformer.egg-info/dependency_links.txt 2026-03-25T22:19:33,122 writing requirements to /tmp/pip-pip-egg-info-3nmtdnvj/spatialformer.egg-info/requires.txt 2026-03-25T22:19:33,123 writing top-level names to /tmp/pip-pip-egg-info-3nmtdnvj/spatialformer.egg-info/top_level.txt 2026-03-25T22:19:33,124 writing manifest file '/tmp/pip-pip-egg-info-3nmtdnvj/spatialformer.egg-info/SOURCES.txt' 2026-03-25T22:19:33,379 reading manifest file '/tmp/pip-pip-egg-info-3nmtdnvj/spatialformer.egg-info/SOURCES.txt' 2026-03-25T22:19:33,380 reading manifest template 'MANIFEST.in' 2026-03-25T22:19:33,382 warning: no files found matching 'spatialformer/spatial_embeddings/*.json' 2026-03-25T22:19:33,383 adding license file 'LICENSE' 2026-03-25T22:19:33,386 writing manifest file '/tmp/pip-pip-egg-info-3nmtdnvj/spatialformer.egg-info/SOURCES.txt' 2026-03-25T22:19:33,502 Preparing metadata (setup.py): finished with status 'done' 2026-03-25T22:19:33,508 Source in /tmp/pip-wheel-kz75967c/spatialformer_6d17f5afb558407e972f4129c0ba6bd9 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 2026-03-25T22:19:33,509 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-cz7ucdeg' 2026-03-25T22:19:33,520 Created temporary directory: /tmp/pip-unpack-_khyqv8h 2026-03-25T22:19:33,521 Created temporary directory: /tmp/pip-unpack-z040exl5 2026-03-25T22:19:33,521 Building wheels for collected packages: spatialformer 2026-03-25T22:19:33,525 Created temporary directory: /tmp/pip-wheel-zfi1k0m8 2026-03-25T22:19:33,526 DEPRECATION: Building 'spatialformer' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'spatialformer'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2026-03-25T22:19:33,527 Building wheel for spatialformer (setup.py): started 2026-03-25T22:19:33,528 Destination directory: /tmp/pip-wheel-zfi1k0m8 2026-03-25T22:19:33,528 Running command python setup.py bdist_wheel 2026-03-25T22:19:34,694 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-03-25T22:19:34,695 !! 2026-03-25T22:19:34,695 ******************************************************************************** 2026-03-25T22:19:34,695 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-03-25T22:19:34,695 License :: OSI Approved :: MIT License 2026-03-25T22:19:34,696 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-03-25T22:19:34,696 ******************************************************************************** 2026-03-25T22:19:34,696 !! 2026-03-25T22:19:34,696 self._finalize_license_expression() 2026-03-25T22:19:34,697 running bdist_wheel 2026-03-25T22:19:35,078 running build 2026-03-25T22:19:35,078 running build_py 2026-03-25T22:19:35,182 creating build/lib/spatialformer 2026-03-25T22:19:35,185 copying spatialformer/train.py -> build/lib/spatialformer 2026-03-25T22:19:35,187 copying spatialformer/graphsage.py -> build/lib/spatialformer 2026-03-25T22:19:35,189 copying spatialformer/__init__.py -> build/lib/spatialformer 2026-03-25T22:19:35,191 copying spatialformer/utils.py -> build/lib/spatialformer 2026-03-25T22:19:35,194 copying spatialformer/data_loader.py -> build/lib/spatialformer 2026-03-25T22:19:35,198 copying spatialformer/processor.py -> build/lib/spatialformer 2026-03-25T22:19:35,200 copying spatialformer/GraphSAGE.py -> build/lib/spatialformer 2026-03-25T22:19:35,205 creating build/lib/spatialformer/tools 2026-03-25T22:19:35,206 copying spatialformer/tools/__init__.py -> build/lib/spatialformer/tools 2026-03-25T22:19:35,208 copying spatialformer/tools/get_embeddings.py -> build/lib/spatialformer/tools 2026-03-25T22:19:35,212 creating build/lib/spatialformer/spatial_embeddings 2026-03-25T22:19:35,213 copying spatialformer/spatial_embeddings/__init__.py -> build/lib/spatialformer/spatial_embeddings 2026-03-25T22:19:35,216 creating build/lib/spatialformer/model 2026-03-25T22:19:35,217 copying spatialformer/model/Spaformer.py -> build/lib/spatialformer/model 2026-03-25T22:19:35,221 copying spatialformer/model/model.py -> build/lib/spatialformer/model 2026-03-25T22:19:35,224 copying spatialformer/model/__init__.py -> build/lib/spatialformer/model 2026-03-25T22:19:35,227 copying spatialformer/model/settings.py -> build/lib/spatialformer/model 2026-03-25T22:19:35,229 copying spatialformer/model/Spaformer_pair.py -> build/lib/spatialformer/model 2026-03-25T22:19:35,234 creating build/lib/spatialformer/preprocess 2026-03-25T22:19:35,235 copying spatialformer/preprocess/__init__.py -> build/lib/spatialformer/preprocess 2026-03-25T22:19:35,237 copying spatialformer/preprocess/find_gene_interaction.py -> build/lib/spatialformer/preprocess 2026-03-25T22:19:35,241 creating build/lib/spatialformer/tokenizer 2026-03-25T22:19:35,242 copying spatialformer/tokenizer/__init__.py -> build/lib/spatialformer/tokenizer 2026-03-25T22:19:35,245 creating build/lib/spatialformer/gene_gene_calculation 2026-03-25T22:19:35,246 copying spatialformer/gene_gene_calculation/__init__.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-25T22:19:35,248 copying spatialformer/gene_gene_calculation/mask_dataset.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-25T22:19:35,251 copying spatialformer/gene_gene_calculation/h5toloader.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-25T22:19:35,255 copying spatialformer/gene_gene_calculation/build_h5ad.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-25T22:19:35,258 copying spatialformer/gene_gene_calculation/process.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-25T22:19:35,261 copying spatialformer/gene_gene_calculation/find_gene_interaction.py -> build/lib/spatialformer/gene_gene_calculation 2026-03-25T22:19:35,265 creating build/lib/spatialformer/dataloader 2026-03-25T22:19:35,267 copying spatialformer/dataloader/dataloader_paired.py -> build/lib/spatialformer/dataloader 2026-03-25T22:19:35,272 copying spatialformer/dataloader/__init__.py -> build/lib/spatialformer/dataloader 2026-03-25T22:19:35,275 creating build/lib/spatialformer/config 2026-03-25T22:19:35,277 copying spatialformer/config/__init__.py -> build/lib/spatialformer/config 2026-03-25T22:19:35,282 creating build/lib/spatialformer/model/submodules 2026-03-25T22:19:35,284 copying spatialformer/model/submodules/masked_batchnorm.py -> build/lib/spatialformer/model/submodules 2026-03-25T22:19:35,290 copying spatialformer/model/submodules/alibi.py -> build/lib/spatialformer/model/submodules 2026-03-25T22:19:35,293 copying spatialformer/model/submodules/__init__.py -> build/lib/spatialformer/model/submodules 2026-03-25T22:19:35,295 copying spatialformer/model/submodules/masked_conv.py -> build/lib/spatialformer/model/submodules 2026-03-25T22:19:35,298 copying spatialformer/model/submodules/activations.py -> build/lib/spatialformer/model/submodules 2026-03-25T22:19:35,301 copying spatialformer/model/submodules/layer_modules.py -> build/lib/spatialformer/model/submodules 2026-03-25T22:19:35,306 copying spatialformer/model/submodules/flash_attention2.py -> build/lib/spatialformer/model/submodules 2026-03-25T22:19:35,310 copying spatialformer/model/submodules/modules.py -> build/lib/spatialformer/model/submodules 2026-03-25T22:19:35,313 running egg_info 2026-03-25T22:19:35,395 writing spatialformer.egg-info/PKG-INFO 2026-03-25T22:19:35,399 writing dependency_links to spatialformer.egg-info/dependency_links.txt 2026-03-25T22:19:35,401 writing requirements to spatialformer.egg-info/requires.txt 2026-03-25T22:19:35,402 writing top-level names to spatialformer.egg-info/top_level.txt 2026-03-25T22:19:35,507 reading manifest file 'spatialformer.egg-info/SOURCES.txt' 2026-03-25T22:19:35,512 reading manifest template 'MANIFEST.in' 2026-03-25T22:19:35,514 warning: no files found matching 'spatialformer/spatial_embeddings/*.json' 2026-03-25T22:19:35,515 adding license file 'LICENSE' 2026-03-25T22:19:35,519 writing manifest file 'spatialformer.egg-info/SOURCES.txt' 2026-03-25T22:19:35,527 copying spatialformer/spatial_embeddings/gene_embeddings_GraphSAGE_pandavid.pkl -> build/lib/spatialformer/spatial_embeddings 2026-03-25T22:19:35,602 copying spatialformer/tokenizer/token.json -> build/lib/spatialformer/tokenizer 2026-03-25T22:19:35,605 copying spatialformer/tokenizer/tokenv2.json -> build/lib/spatialformer/tokenizer 2026-03-25T22:19:35,609 copying spatialformer/tokenizer/tokenv3.json -> build/lib/spatialformer/tokenizer 2026-03-25T22:19:35,612 copying spatialformer/tokenizer/tokenv4.json -> build/lib/spatialformer/tokenizer 2026-03-25T22:19:35,617 copying spatialformer/tokenizer/tokenv5.json -> build/lib/spatialformer/tokenizer 2026-03-25T22:19:35,624 copying spatialformer/config/_config_fine_tune_probe.json -> build/lib/spatialformer/config 2026-03-25T22:19:35,627 copying spatialformer/config/_config_graphsave.json -> build/lib/spatialformer/config 2026-03-25T22:19:35,630 copying spatialformer/config/_config_train.json -> build/lib/spatialformer/config 2026-03-25T22:19:35,632 copying spatialformer/config/_config_train_large_pair.json -> build/lib/spatialformer/config 2026-03-25T22:19:35,635 copying spatialformer/config/_config_train_large_single.json -> build/lib/spatialformer/config 2026-03-25T22:19:35,724 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2026-03-25T22:19:35,724 !! 2026-03-25T22:19:35,725 ******************************************************************************** 2026-03-25T22:19:35,725 Please avoid running ``setup.py`` directly. 2026-03-25T22:19:35,725 Instead, use pypa/build, pypa/installer or other 2026-03-25T22:19:35,725 standards-based tools. 2026-03-25T22:19:35,725 This deprecation is overdue, please update your project and remove deprecated 2026-03-25T22:19:35,725 calls to avoid build errors in the future. 2026-03-25T22:19:35,725 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2026-03-25T22:19:35,726 ******************************************************************************** 2026-03-25T22:19:35,726 !! 2026-03-25T22:19:35,726 self.initialize_options() 2026-03-25T22:19:35,801 installing to build/bdist.linux-armv7l/wheel 2026-03-25T22:19:35,801 running install 2026-03-25T22:19:35,824 running install_lib 2026-03-25T22:19:35,907 creating build/bdist.linux-armv7l/wheel 2026-03-25T22:19:35,909 creating build/bdist.linux-armv7l/wheel/spatialformer 2026-03-25T22:19:35,911 copying build/lib/spatialformer/train.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-25T22:19:35,913 creating build/bdist.linux-armv7l/wheel/spatialformer/tools 2026-03-25T22:19:35,914 copying build/lib/spatialformer/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/tools 2026-03-25T22:19:35,916 copying build/lib/spatialformer/tools/get_embeddings.py -> build/bdist.linux-armv7l/wheel/./spatialformer/tools 2026-03-25T22:19:35,920 creating build/bdist.linux-armv7l/wheel/spatialformer/spatial_embeddings 2026-03-25T22:19:35,921 copying build/lib/spatialformer/spatial_embeddings/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/spatial_embeddings 2026-03-25T22:19:35,923 copying build/lib/spatialformer/spatial_embeddings/gene_embeddings_GraphSAGE_pandavid.pkl -> build/bdist.linux-armv7l/wheel/./spatialformer/spatial_embeddings 2026-03-25T22:19:36,034 copying build/lib/spatialformer/graphsage.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-25T22:19:36,039 copying build/lib/spatialformer/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-25T22:19:36,043 creating build/bdist.linux-armv7l/wheel/spatialformer/model 2026-03-25T22:19:36,044 copying build/lib/spatialformer/model/Spaformer.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-25T22:19:36,048 copying build/lib/spatialformer/model/model.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-25T22:19:36,051 copying build/lib/spatialformer/model/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-25T22:19:36,053 copying build/lib/spatialformer/model/settings.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-25T22:19:36,056 copying build/lib/spatialformer/model/Spaformer_pair.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model 2026-03-25T22:19:36,061 creating build/bdist.linux-armv7l/wheel/spatialformer/model/submodules 2026-03-25T22:19:36,062 copying build/lib/spatialformer/model/submodules/masked_batchnorm.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-25T22:19:36,065 copying build/lib/spatialformer/model/submodules/alibi.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-25T22:19:36,068 copying build/lib/spatialformer/model/submodules/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-25T22:19:36,070 copying build/lib/spatialformer/model/submodules/masked_conv.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-25T22:19:36,072 copying build/lib/spatialformer/model/submodules/activations.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-25T22:19:36,076 copying build/lib/spatialformer/model/submodules/layer_modules.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-25T22:19:36,079 copying build/lib/spatialformer/model/submodules/flash_attention2.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-25T22:19:36,085 copying build/lib/spatialformer/model/submodules/modules.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules 2026-03-25T22:19:36,090 copying build/lib/spatialformer/utils.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-25T22:19:36,097 copying build/lib/spatialformer/data_loader.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-25T22:19:36,108 creating build/bdist.linux-armv7l/wheel/spatialformer/preprocess 2026-03-25T22:19:36,112 copying build/lib/spatialformer/preprocess/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/preprocess 2026-03-25T22:19:36,123 copying build/lib/spatialformer/preprocess/find_gene_interaction.py -> build/bdist.linux-armv7l/wheel/./spatialformer/preprocess 2026-03-25T22:19:36,142 creating build/bdist.linux-armv7l/wheel/spatialformer/tokenizer 2026-03-25T22:19:36,144 copying build/lib/spatialformer/tokenizer/tokenv3.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-25T22:19:36,148 copying build/lib/spatialformer/tokenizer/token.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-25T22:19:36,151 copying build/lib/spatialformer/tokenizer/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-25T22:19:36,153 copying build/lib/spatialformer/tokenizer/tokenv5.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-25T22:19:36,160 copying build/lib/spatialformer/tokenizer/tokenv2.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-25T22:19:36,166 copying build/lib/spatialformer/tokenizer/tokenv4.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer 2026-03-25T22:19:36,170 creating build/bdist.linux-armv7l/wheel/spatialformer/gene_gene_calculation 2026-03-25T22:19:36,171 copying build/lib/spatialformer/gene_gene_calculation/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-25T22:19:36,173 copying build/lib/spatialformer/gene_gene_calculation/mask_dataset.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-25T22:19:36,175 copying build/lib/spatialformer/gene_gene_calculation/h5toloader.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-25T22:19:36,178 copying build/lib/spatialformer/gene_gene_calculation/build_h5ad.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-25T22:19:36,181 copying build/lib/spatialformer/gene_gene_calculation/process.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-25T22:19:36,184 copying build/lib/spatialformer/gene_gene_calculation/find_gene_interaction.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation 2026-03-25T22:19:36,187 copying build/lib/spatialformer/processor.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-25T22:19:36,189 creating build/bdist.linux-armv7l/wheel/spatialformer/dataloader 2026-03-25T22:19:36,191 copying build/lib/spatialformer/dataloader/dataloader_paired.py -> build/bdist.linux-armv7l/wheel/./spatialformer/dataloader 2026-03-25T22:19:36,195 copying build/lib/spatialformer/dataloader/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/dataloader 2026-03-25T22:19:36,197 creating build/bdist.linux-armv7l/wheel/spatialformer/config 2026-03-25T22:19:36,199 copying build/lib/spatialformer/config/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-25T22:19:36,201 copying build/lib/spatialformer/config/_config_train_large_single.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-25T22:19:36,203 copying build/lib/spatialformer/config/_config_train.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-25T22:19:36,205 copying build/lib/spatialformer/config/_config_graphsave.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-25T22:19:36,207 copying build/lib/spatialformer/config/_config_fine_tune_probe.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-25T22:19:36,209 copying build/lib/spatialformer/config/_config_train_large_pair.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config 2026-03-25T22:19:36,211 copying build/lib/spatialformer/GraphSAGE.py -> build/bdist.linux-armv7l/wheel/./spatialformer 2026-03-25T22:19:36,214 running install_egg_info 2026-03-25T22:19:36,299 Copying spatialformer.egg-info to build/bdist.linux-armv7l/wheel/./spatialformer-0.1.2-py3.13.egg-info 2026-03-25T22:19:36,308 running install_scripts 2026-03-25T22:19:36,320 creating build/bdist.linux-armv7l/wheel/spatialformer-0.1.2.dist-info/WHEEL 2026-03-25T22:19:36,324 creating '/tmp/pip-wheel-zfi1k0m8/spatialformer-0.1.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-03-25T22:19:36,330 adding 'spatialformer/GraphSAGE.py' 2026-03-25T22:19:36,332 adding 'spatialformer/__init__.py' 2026-03-25T22:19:36,336 adding 'spatialformer/data_loader.py' 2026-03-25T22:19:36,340 adding 'spatialformer/graphsage.py' 2026-03-25T22:19:36,342 adding 'spatialformer/processor.py' 2026-03-25T22:19:36,344 adding 'spatialformer/train.py' 2026-03-25T22:19:36,351 adding 'spatialformer/utils.py' 2026-03-25T22:19:36,354 adding 'spatialformer/config/__init__.py' 2026-03-25T22:19:36,356 adding 'spatialformer/config/_config_fine_tune_probe.json' 2026-03-25T22:19:36,358 adding 'spatialformer/config/_config_graphsave.json' 2026-03-25T22:19:36,360 adding 'spatialformer/config/_config_train.json' 2026-03-25T22:19:36,362 adding 'spatialformer/config/_config_train_large_pair.json' 2026-03-25T22:19:36,364 adding 'spatialformer/config/_config_train_large_single.json' 2026-03-25T22:19:36,367 adding 'spatialformer/dataloader/__init__.py' 2026-03-25T22:19:36,377 adding 'spatialformer/dataloader/dataloader_paired.py' 2026-03-25T22:19:36,379 adding 'spatialformer/gene_gene_calculation/__init__.py' 2026-03-25T22:19:36,382 adding 'spatialformer/gene_gene_calculation/build_h5ad.py' 2026-03-25T22:19:36,385 adding 'spatialformer/gene_gene_calculation/find_gene_interaction.py' 2026-03-25T22:19:36,388 adding 'spatialformer/gene_gene_calculation/h5toloader.py' 2026-03-25T22:19:36,391 adding 'spatialformer/gene_gene_calculation/mask_dataset.py' 2026-03-25T22:19:36,393 adding 'spatialformer/gene_gene_calculation/process.py' 2026-03-25T22:19:36,397 adding 'spatialformer/model/Spaformer.py' 2026-03-25T22:19:36,404 adding 'spatialformer/model/Spaformer_pair.py' 2026-03-25T22:19:36,406 adding 'spatialformer/model/__init__.py' 2026-03-25T22:19:36,408 adding 'spatialformer/model/model.py' 2026-03-25T22:19:36,409 adding 'spatialformer/model/settings.py' 2026-03-25T22:19:36,411 adding 'spatialformer/model/submodules/__init__.py' 2026-03-25T22:19:36,413 adding 'spatialformer/model/submodules/activations.py' 2026-03-25T22:19:36,415 adding 'spatialformer/model/submodules/alibi.py' 2026-03-25T22:19:36,419 adding 'spatialformer/model/submodules/flash_attention2.py' 2026-03-25T22:19:36,421 adding 'spatialformer/model/submodules/layer_modules.py' 2026-03-25T22:19:36,422 adding 'spatialformer/model/submodules/masked_batchnorm.py' 2026-03-25T22:19:36,424 adding 'spatialformer/model/submodules/masked_conv.py' 2026-03-25T22:19:36,426 adding 'spatialformer/model/submodules/modules.py' 2026-03-25T22:19:36,428 adding 'spatialformer/preprocess/__init__.py' 2026-03-25T22:19:36,431 adding 'spatialformer/preprocess/find_gene_interaction.py' 2026-03-25T22:19:36,433 adding 'spatialformer/spatial_embeddings/__init__.py' 2026-03-25T22:19:37,026 adding 'spatialformer/spatial_embeddings/gene_embeddings_GraphSAGE_pandavid.pkl' 2026-03-25T22:19:37,052 adding 'spatialformer/tokenizer/__init__.py' 2026-03-25T22:19:37,055 adding 'spatialformer/tokenizer/token.json' 2026-03-25T22:19:37,078 adding 'spatialformer/tokenizer/tokenv2.json' 2026-03-25T22:19:37,086 adding 'spatialformer/tokenizer/tokenv3.json' 2026-03-25T22:19:37,093 adding 'spatialformer/tokenizer/tokenv4.json' 2026-03-25T22:19:37,117 adding 'spatialformer/tokenizer/tokenv5.json' 2026-03-25T22:19:37,119 adding 'spatialformer/tools/__init__.py' 2026-03-25T22:19:37,125 adding 'spatialformer/tools/get_embeddings.py' 2026-03-25T22:19:37,128 adding 'spatialformer-0.1.2.dist-info/licenses/LICENSE' 2026-03-25T22:19:37,129 adding 'spatialformer-0.1.2.dist-info/METADATA' 2026-03-25T22:19:37,129 adding 'spatialformer-0.1.2.dist-info/WHEEL' 2026-03-25T22:19:37,130 adding 'spatialformer-0.1.2.dist-info/top_level.txt' 2026-03-25T22:19:37,131 adding 'spatialformer-0.1.2.dist-info/RECORD' 2026-03-25T22:19:37,219 removing build/bdist.linux-armv7l/wheel 2026-03-25T22:19:37,378 Building wheel for spatialformer (setup.py): finished with status 'done' 2026-03-25T22:19:37,429 Created wheel for spatialformer: filename=spatialformer-0.1.2-py3-none-any.whl size=3936147 sha256=40867d145781926c3287b71e154107f3a67733a28c34e95b2da4ab4e13dc5627 2026-03-25T22:19:37,430 Stored in directory: /tmp/pip-ephem-wheel-cache-ckl4wird/wheels/74/75/9f/79f96b8028ecc0b00a54054d4f338daeecf77e82d05730be0e 2026-03-25T22:19:37,444 Successfully built spatialformer 2026-03-25T22:19:37,584 Removed build tracker: '/tmp/pip-build-tracker-cz7ucdeg'