2026-03-26T19:16:44,697 Created temporary directory: /tmp/pip-ephem-wheel-cache-ojrs34r0
2026-03-26T19:16:44,699 Created temporary directory: /tmp/pip-build-tracker-f9l10zup
2026-03-26T19:16:44,699 Initialized build tracking at /tmp/pip-build-tracker-f9l10zup
2026-03-26T19:16:44,700 Created build tracker: /tmp/pip-build-tracker-f9l10zup
2026-03-26T19:16:44,700 Entered build tracker: /tmp/pip-build-tracker-f9l10zup
2026-03-26T19:16:44,701 Created temporary directory: /tmp/pip-wheel-ewep0psw
2026-03-26T19:16:44,704 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
2026-03-26T19:16:44,706 Created temporary directory: /tmp/pip-ephem-wheel-cache-96uvwmqm
2026-03-26T19:16:44,733 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-03-26T19:16:44,736 2 location(s) to search for versions of spatialformer:
2026-03-26T19:16:44,736 * https://pypi.org/simple/spatialformer/
2026-03-26T19:16:44,736 * https://www.piwheels.org/simple/spatialformer/
2026-03-26T19:16:44,737 Fetching project page and analyzing links: https://pypi.org/simple/spatialformer/
2026-03-26T19:16:44,738 Getting page https://pypi.org/simple/spatialformer/
2026-03-26T19:16:44,739 Found index url https://pypi.org/simple
2026-03-26T19:16:44,891 Fetched page https://pypi.org/simple/spatialformer/ as application/vnd.pypi.simple.v1+json
2026-03-26T19:16:44,896   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)
2026-03-26T19:16:44,897   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
2026-03-26T19:16:44,898   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)
2026-03-26T19:16:44,899   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
2026-03-26T19:16:44,899   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)
2026-03-26T19:16:44,900   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
2026-03-26T19:16:44,901   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)
2026-03-26T19:16:44,902   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
2026-03-26T19:16:44,903   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)
2026-03-26T19:16:44,904   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
2026-03-26T19:16:44,905   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)
2026-03-26T19:16:44,905   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
2026-03-26T19:16:44,906   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)
2026-03-26T19:16:44,907   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
2026-03-26T19:16:44,907   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)
2026-03-26T19:16:44,908   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
2026-03-26T19:16:44,909   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)
2026-03-26T19:16:44,910   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
2026-03-26T19:16:44,911 Fetching project page and analyzing links: https://www.piwheels.org/simple/spatialformer/
2026-03-26T19:16:44,911 Getting page https://www.piwheels.org/simple/spatialformer/
2026-03-26T19:16:44,913 Found index url https://www.piwheels.org/simple
2026-03-26T19:16:45,086 Fetched page https://www.piwheels.org/simple/spatialformer/ as text/html
2026-03-26T19:16:45,089   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)
2026-03-26T19:16:45,089   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)
2026-03-26T19:16:45,090   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)
2026-03-26T19:16:45,091   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)
2026-03-26T19:16:45,091   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)
2026-03-26T19:16:45,092 Skipping link: not a file: https://www.piwheels.org/simple/spatialformer/
2026-03-26T19:16:45,093 Skipping link: not a file: https://pypi.org/simple/spatialformer/
2026-03-26T19:16:45,112 Given no hashes to check 1 links for project 'spatialformer': discarding no candidates
2026-03-26T19:16:45,130 Collecting spatialformer==0.1.6
2026-03-26T19:16:45,132   Created temporary directory: /tmp/pip-unpack-l01_k1ei
2026-03-26T19:16:45,279   Downloading spatialformer-0.1.6.tar.gz (10.9 MB)
2026-03-26T19:16:47,166   Added spatialformer==0.1.6 from https://files.pythonhosted.org/packages/c5/15/fb3bd5704d9013c4157e0eb3cab6ebb1e7eb9db7ab5a66fd0599c4bd8e40/spatialformer-0.1.6.tar.gz to build tracker '/tmp/pip-build-tracker-f9l10zup'
2026-03-26T19:16:47,167   Running setup.py (path:/tmp/pip-wheel-ewep0psw/spatialformer_82f51ee0a1fc4e73bf2081a2672c7f5e/setup.py) egg_info for package spatialformer
2026-03-26T19:16:47,168   Created temporary directory: /tmp/pip-pip-egg-info-xmvxyh7l
2026-03-26T19:16:47,168   Preparing metadata (setup.py): started
2026-03-26T19:16:47,169   Running command python setup.py egg_info
2026-03-26T19:16:48,030   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-03-26T19:16:48,031   !!

2026-03-26T19:16:48,032           ********************************************************************************
2026-03-26T19:16:48,032           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-03-26T19:16:48,033           License :: OSI Approved :: MIT License

2026-03-26T19:16:48,035           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-03-26T19:16:48,035           ********************************************************************************

2026-03-26T19:16:48,037   !!
2026-03-26T19:16:48,037     self._finalize_license_expression()
2026-03-26T19:16:48,060   running egg_info
2026-03-26T19:16:48,086   creating /tmp/pip-pip-egg-info-xmvxyh7l/spatialformer.egg-info
2026-03-26T19:16:48,087   writing /tmp/pip-pip-egg-info-xmvxyh7l/spatialformer.egg-info/PKG-INFO
2026-03-26T19:16:48,092   writing dependency_links to /tmp/pip-pip-egg-info-xmvxyh7l/spatialformer.egg-info/dependency_links.txt
2026-03-26T19:16:48,095   writing requirements to /tmp/pip-pip-egg-info-xmvxyh7l/spatialformer.egg-info/requires.txt
2026-03-26T19:16:48,096   writing top-level names to /tmp/pip-pip-egg-info-xmvxyh7l/spatialformer.egg-info/top_level.txt
2026-03-26T19:16:48,098   writing manifest file '/tmp/pip-pip-egg-info-xmvxyh7l/spatialformer.egg-info/SOURCES.txt'
2026-03-26T19:16:48,327   reading manifest file '/tmp/pip-pip-egg-info-xmvxyh7l/spatialformer.egg-info/SOURCES.txt'
2026-03-26T19:16:48,328   reading manifest template 'MANIFEST.in'
2026-03-26T19:16:48,331   warning: no files found matching 'spatialformer/spatial_embeddings/*.json'
2026-03-26T19:16:48,331   adding license file 'LICENSE'
2026-03-26T19:16:48,335   writing manifest file '/tmp/pip-pip-egg-info-xmvxyh7l/spatialformer.egg-info/SOURCES.txt'
2026-03-26T19:16:48,445   Preparing metadata (setup.py): finished with status 'done'
2026-03-26T19:16:48,448   Source in /tmp/pip-wheel-ewep0psw/spatialformer_82f51ee0a1fc4e73bf2081a2672c7f5e has version 0.1.6, which satisfies requirement spatialformer==0.1.6 from https://files.pythonhosted.org/packages/c5/15/fb3bd5704d9013c4157e0eb3cab6ebb1e7eb9db7ab5a66fd0599c4bd8e40/spatialformer-0.1.6.tar.gz
2026-03-26T19:16:48,449   Removed spatialformer==0.1.6 from https://files.pythonhosted.org/packages/c5/15/fb3bd5704d9013c4157e0eb3cab6ebb1e7eb9db7ab5a66fd0599c4bd8e40/spatialformer-0.1.6.tar.gz from build tracker '/tmp/pip-build-tracker-f9l10zup'
2026-03-26T19:16:48,455 Created temporary directory: /tmp/pip-unpack-qlikuv9e
2026-03-26T19:16:48,456 Building wheels for collected packages: spatialformer
2026-03-26T19:16:48,460   Created temporary directory: /tmp/pip-wheel-891wtgw8
2026-03-26T19:16:48,460   Building wheel for spatialformer (setup.py): started
2026-03-26T19:16:48,462   Destination directory: /tmp/pip-wheel-891wtgw8
2026-03-26T19:16:48,462   Running command python setup.py bdist_wheel
2026-03-26T19:16:49,296   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-03-26T19:16:49,296   !!

2026-03-26T19:16:49,297           ********************************************************************************
2026-03-26T19:16:49,298           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-03-26T19:16:49,299           License :: OSI Approved :: MIT License

2026-03-26T19:16:49,300           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-03-26T19:16:49,300           ********************************************************************************

2026-03-26T19:16:49,301   !!
2026-03-26T19:16:49,302     self._finalize_license_expression()
2026-03-26T19:16:49,302   running bdist_wheel
2026-03-26T19:16:49,463   running build
2026-03-26T19:16:49,465   running build_py
2026-03-26T19:16:49,536   creating build/lib/spatialformer
2026-03-26T19:16:49,538   copying spatialformer/data_loader.py -> build/lib/spatialformer
2026-03-26T19:16:49,541   copying spatialformer/__init__.py -> build/lib/spatialformer
2026-03-26T19:16:49,543   copying spatialformer/processor.py -> build/lib/spatialformer
2026-03-26T19:16:49,545   copying spatialformer/graphsage.py -> build/lib/spatialformer
2026-03-26T19:16:49,548   copying spatialformer/GraphSAGE.py -> build/lib/spatialformer
2026-03-26T19:16:49,550   copying spatialformer/train.py -> build/lib/spatialformer
2026-03-26T19:16:49,553   copying spatialformer/utils.py -> build/lib/spatialformer
2026-03-26T19:16:49,556   creating build/lib/spatialformer/preprocess
2026-03-26T19:16:49,557   copying spatialformer/preprocess/__init__.py -> build/lib/spatialformer/preprocess
2026-03-26T19:16:49,559   copying spatialformer/preprocess/find_gene_interaction.py -> build/lib/spatialformer/preprocess
2026-03-26T19:16:49,562   creating build/lib/spatialformer/spatial_embeddings
2026-03-26T19:16:49,563   copying spatialformer/spatial_embeddings/__init__.py -> build/lib/spatialformer/spatial_embeddings
2026-03-26T19:16:49,565   creating build/lib/spatialformer/config
2026-03-26T19:16:49,566   copying spatialformer/config/__init__.py -> build/lib/spatialformer/config
2026-03-26T19:16:49,568   creating build/lib/spatialformer/dataloader
2026-03-26T19:16:49,569   copying spatialformer/dataloader/__init__.py -> build/lib/spatialformer/dataloader
2026-03-26T19:16:49,571   copying spatialformer/dataloader/dataloader_paired.py -> build/lib/spatialformer/dataloader
2026-03-26T19:16:49,575   creating build/lib/spatialformer/tokenizer
2026-03-26T19:16:49,576   copying spatialformer/tokenizer/__init__.py -> build/lib/spatialformer/tokenizer
2026-03-26T19:16:49,578   creating build/lib/spatialformer/model
2026-03-26T19:16:49,579   copying spatialformer/model/__init__.py -> build/lib/spatialformer/model
2026-03-26T19:16:49,581   copying spatialformer/model/Spaformer_pair.py -> build/lib/spatialformer/model
2026-03-26T19:16:49,585   copying spatialformer/model/model.py -> build/lib/spatialformer/model
2026-03-26T19:16:49,587   copying spatialformer/model/Spaformer.py -> build/lib/spatialformer/model
2026-03-26T19:16:49,589   copying spatialformer/model/settings.py -> build/lib/spatialformer/model
2026-03-26T19:16:49,592   creating build/lib/spatialformer/gene_gene_calculation
2026-03-26T19:16:49,593   copying spatialformer/gene_gene_calculation/__init__.py -> build/lib/spatialformer/gene_gene_calculation
2026-03-26T19:16:49,595   copying spatialformer/gene_gene_calculation/process.py -> build/lib/spatialformer/gene_gene_calculation
2026-03-26T19:16:49,597   copying spatialformer/gene_gene_calculation/h5toloader.py -> build/lib/spatialformer/gene_gene_calculation
2026-03-26T19:16:49,600   copying spatialformer/gene_gene_calculation/find_gene_interaction.py -> build/lib/spatialformer/gene_gene_calculation
2026-03-26T19:16:49,602   copying spatialformer/gene_gene_calculation/build_h5ad.py -> build/lib/spatialformer/gene_gene_calculation
2026-03-26T19:16:49,605   copying spatialformer/gene_gene_calculation/mask_dataset.py -> build/lib/spatialformer/gene_gene_calculation
2026-03-26T19:16:49,608   creating build/lib/spatialformer/tools
2026-03-26T19:16:49,609   copying spatialformer/tools/__init__.py -> build/lib/spatialformer/tools
2026-03-26T19:16:49,611   copying spatialformer/tools/get_embeddings.py -> build/lib/spatialformer/tools
2026-03-26T19:16:49,615   creating build/lib/spatialformer/model/submodules
2026-03-26T19:16:49,616   copying spatialformer/model/submodules/__init__.py -> build/lib/spatialformer/model/submodules
2026-03-26T19:16:49,618   copying spatialformer/model/submodules/flash_attention2.py -> build/lib/spatialformer/model/submodules
2026-03-26T19:16:49,621   copying spatialformer/model/submodules/masked_conv.py -> build/lib/spatialformer/model/submodules
2026-03-26T19:16:49,623   copying spatialformer/model/submodules/masked_batchnorm.py -> build/lib/spatialformer/model/submodules
2026-03-26T19:16:49,625   copying spatialformer/model/submodules/modules.py -> build/lib/spatialformer/model/submodules
2026-03-26T19:16:49,628   copying spatialformer/model/submodules/layer_modules.py -> build/lib/spatialformer/model/submodules
2026-03-26T19:16:49,629   copying spatialformer/model/submodules/alibi.py -> build/lib/spatialformer/model/submodules
2026-03-26T19:16:49,631   copying spatialformer/model/submodules/activations.py -> build/lib/spatialformer/model/submodules
2026-03-26T19:16:49,633   running egg_info
2026-03-26T19:16:49,661   writing spatialformer.egg-info/PKG-INFO
2026-03-26T19:16:49,666   writing dependency_links to spatialformer.egg-info/dependency_links.txt
2026-03-26T19:16:49,669   writing requirements to spatialformer.egg-info/requires.txt
2026-03-26T19:16:49,670   writing top-level names to spatialformer.egg-info/top_level.txt
2026-03-26T19:16:49,712   reading manifest file 'spatialformer.egg-info/SOURCES.txt'
2026-03-26T19:16:49,717   reading manifest template 'MANIFEST.in'
2026-03-26T19:16:49,719   warning: no files found matching 'spatialformer/spatial_embeddings/*.json'
2026-03-26T19:16:49,720   adding license file 'LICENSE'
2026-03-26T19:16:49,724   writing manifest file 'spatialformer.egg-info/SOURCES.txt'
2026-03-26T19:16:49,732   copying spatialformer/spatial_embeddings/xenium_5k_pandavid_gene_embeddings.pkl -> build/lib/spatialformer/spatial_embeddings
2026-03-26T19:16:49,936   copying spatialformer/config/_config_fine_tune_probe.json -> build/lib/spatialformer/config
2026-03-26T19:16:49,939   copying spatialformer/config/_config_graphsave.json -> build/lib/spatialformer/config
2026-03-26T19:16:49,941   copying spatialformer/config/_config_train.json -> build/lib/spatialformer/config
2026-03-26T19:16:49,943   copying spatialformer/config/_config_train_large_pair.json -> build/lib/spatialformer/config
2026-03-26T19:16:49,946   copying spatialformer/config/_config_train_large_single.json -> build/lib/spatialformer/config
2026-03-26T19:16:49,948   copying spatialformer/tokenizer/token.json -> build/lib/spatialformer/tokenizer
2026-03-26T19:16:49,951   copying spatialformer/tokenizer/tokenv2.json -> build/lib/spatialformer/tokenizer
2026-03-26T19:16:49,956   copying spatialformer/tokenizer/tokenv3.json -> build/lib/spatialformer/tokenizer
2026-03-26T19:16:49,959   copying spatialformer/tokenizer/tokenv4.json -> build/lib/spatialformer/tokenizer
2026-03-26T19:16:49,962   copying spatialformer/tokenizer/tokenv5.json -> build/lib/spatialformer/tokenizer
2026-03-26T19:16:49,998   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2026-03-26T19:16:49,998   !!

2026-03-26T19:16:50,000           ********************************************************************************
2026-03-26T19:16:50,000           Please avoid running ``setup.py`` directly.
2026-03-26T19:16:50,001           Instead, use pypa/build, pypa/installer or other
2026-03-26T19:16:50,001           standards-based tools.

2026-03-26T19:16:50,002           This deprecation is overdue, please update your project and remove deprecated
2026-03-26T19:16:50,002           calls to avoid build errors in the future.

2026-03-26T19:16:50,003           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2026-03-26T19:16:50,004           ********************************************************************************

2026-03-26T19:16:50,004   !!
2026-03-26T19:16:50,005     self.initialize_options()
2026-03-26T19:16:50,029   installing to build/bdist.linux-armv7l/wheel
2026-03-26T19:16:50,029   running install
2026-03-26T19:16:50,054   running install_lib
2026-03-26T19:16:50,082   creating build/bdist.linux-armv7l/wheel
2026-03-26T19:16:50,084   creating build/bdist.linux-armv7l/wheel/spatialformer
2026-03-26T19:16:50,086   copying build/lib/spatialformer/data_loader.py -> build/bdist.linux-armv7l/wheel/./spatialformer
2026-03-26T19:16:50,089   copying build/lib/spatialformer/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer
2026-03-26T19:16:50,091   copying build/lib/spatialformer/processor.py -> build/bdist.linux-armv7l/wheel/./spatialformer
2026-03-26T19:16:50,094   creating build/bdist.linux-armv7l/wheel/spatialformer/preprocess
2026-03-26T19:16:50,096   copying build/lib/spatialformer/preprocess/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/preprocess
2026-03-26T19:16:50,098   copying build/lib/spatialformer/preprocess/find_gene_interaction.py -> build/bdist.linux-armv7l/wheel/./spatialformer/preprocess
2026-03-26T19:16:50,101   copying build/lib/spatialformer/graphsage.py -> build/bdist.linux-armv7l/wheel/./spatialformer
2026-03-26T19:16:50,104   creating build/bdist.linux-armv7l/wheel/spatialformer/spatial_embeddings
2026-03-26T19:16:50,105   copying build/lib/spatialformer/spatial_embeddings/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/spatial_embeddings
2026-03-26T19:16:50,107   copying build/lib/spatialformer/spatial_embeddings/xenium_5k_pandavid_gene_embeddings.pkl -> build/bdist.linux-armv7l/wheel/./spatialformer/spatial_embeddings
2026-03-26T19:16:50,288   creating build/bdist.linux-armv7l/wheel/spatialformer/config
2026-03-26T19:16:50,290   copying build/lib/spatialformer/config/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/config
2026-03-26T19:16:50,291   copying build/lib/spatialformer/config/_config_fine_tune_probe.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config
2026-03-26T19:16:50,293   copying build/lib/spatialformer/config/_config_graphsave.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config
2026-03-26T19:16:50,295   copying build/lib/spatialformer/config/_config_train_large_single.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config
2026-03-26T19:16:50,297   copying build/lib/spatialformer/config/_config_train.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config
2026-03-26T19:16:50,299   copying build/lib/spatialformer/config/_config_train_large_pair.json -> build/bdist.linux-armv7l/wheel/./spatialformer/config
2026-03-26T19:16:50,301   creating build/bdist.linux-armv7l/wheel/spatialformer/dataloader
2026-03-26T19:16:50,302   copying build/lib/spatialformer/dataloader/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/dataloader
2026-03-26T19:16:50,304   copying build/lib/spatialformer/dataloader/dataloader_paired.py -> build/bdist.linux-armv7l/wheel/./spatialformer/dataloader
2026-03-26T19:16:50,308   copying build/lib/spatialformer/GraphSAGE.py -> build/bdist.linux-armv7l/wheel/./spatialformer
2026-03-26T19:16:50,311   creating build/bdist.linux-armv7l/wheel/spatialformer/tokenizer
2026-03-26T19:16:50,312   copying build/lib/spatialformer/tokenizer/token.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer
2026-03-26T19:16:50,315   copying build/lib/spatialformer/tokenizer/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer
2026-03-26T19:16:50,316   copying build/lib/spatialformer/tokenizer/tokenv3.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer
2026-03-26T19:16:50,319   copying build/lib/spatialformer/tokenizer/tokenv4.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer
2026-03-26T19:16:50,322   copying build/lib/spatialformer/tokenizer/tokenv5.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer
2026-03-26T19:16:50,326   copying build/lib/spatialformer/tokenizer/tokenv2.json -> build/bdist.linux-armv7l/wheel/./spatialformer/tokenizer
2026-03-26T19:16:50,331   creating build/bdist.linux-armv7l/wheel/spatialformer/model
2026-03-26T19:16:50,332   copying build/lib/spatialformer/model/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model
2026-03-26T19:16:50,333   copying build/lib/spatialformer/model/Spaformer_pair.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model
2026-03-26T19:16:50,337   copying build/lib/spatialformer/model/model.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model
2026-03-26T19:16:50,339   copying build/lib/spatialformer/model/Spaformer.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model
2026-03-26T19:16:50,342   copying build/lib/spatialformer/model/settings.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model
2026-03-26T19:16:50,344   creating build/bdist.linux-armv7l/wheel/spatialformer/model/submodules
2026-03-26T19:16:50,345   copying build/lib/spatialformer/model/submodules/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules
2026-03-26T19:16:50,347   copying build/lib/spatialformer/model/submodules/flash_attention2.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules
2026-03-26T19:16:50,350   copying build/lib/spatialformer/model/submodules/masked_conv.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules
2026-03-26T19:16:50,352   copying build/lib/spatialformer/model/submodules/masked_batchnorm.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules
2026-03-26T19:16:50,355   copying build/lib/spatialformer/model/submodules/modules.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules
2026-03-26T19:16:50,357   copying build/lib/spatialformer/model/submodules/layer_modules.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules
2026-03-26T19:16:50,359   copying build/lib/spatialformer/model/submodules/alibi.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules
2026-03-26T19:16:50,361   copying build/lib/spatialformer/model/submodules/activations.py -> build/bdist.linux-armv7l/wheel/./spatialformer/model/submodules
2026-03-26T19:16:50,364   creating build/bdist.linux-armv7l/wheel/spatialformer/gene_gene_calculation
2026-03-26T19:16:50,365   copying build/lib/spatialformer/gene_gene_calculation/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation
2026-03-26T19:16:50,367   copying build/lib/spatialformer/gene_gene_calculation/process.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation
2026-03-26T19:16:50,369   copying build/lib/spatialformer/gene_gene_calculation/h5toloader.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation
2026-03-26T19:16:50,372   copying build/lib/spatialformer/gene_gene_calculation/find_gene_interaction.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation
2026-03-26T19:16:50,374   copying build/lib/spatialformer/gene_gene_calculation/build_h5ad.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation
2026-03-26T19:16:50,377   copying build/lib/spatialformer/gene_gene_calculation/mask_dataset.py -> build/bdist.linux-armv7l/wheel/./spatialformer/gene_gene_calculation
2026-03-26T19:16:50,380   creating build/bdist.linux-armv7l/wheel/spatialformer/tools
2026-03-26T19:16:50,381   copying build/lib/spatialformer/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./spatialformer/tools
2026-03-26T19:16:50,383   copying build/lib/spatialformer/tools/get_embeddings.py -> build/bdist.linux-armv7l/wheel/./spatialformer/tools
2026-03-26T19:16:50,386   copying build/lib/spatialformer/train.py -> build/bdist.linux-armv7l/wheel/./spatialformer
2026-03-26T19:16:50,388   copying build/lib/spatialformer/utils.py -> build/bdist.linux-armv7l/wheel/./spatialformer
2026-03-26T19:16:50,392   running install_egg_info
2026-03-26T19:16:50,425   Copying spatialformer.egg-info to build/bdist.linux-armv7l/wheel/./spatialformer-0.1.6-py3.11.egg-info
2026-03-26T19:16:50,435   running install_scripts
2026-03-26T19:16:50,446   creating build/bdist.linux-armv7l/wheel/spatialformer-0.1.6.dist-info/WHEEL
2026-03-26T19:16:50,449   creating '/tmp/pip-wheel-891wtgw8/spatialformer-0.1.6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-03-26T19:16:50,453   adding 'spatialformer/GraphSAGE.py'
2026-03-26T19:16:50,454   adding 'spatialformer/__init__.py'
2026-03-26T19:16:50,458   adding 'spatialformer/data_loader.py'
2026-03-26T19:16:50,460   adding 'spatialformer/graphsage.py'
2026-03-26T19:16:50,462   adding 'spatialformer/processor.py'
2026-03-26T19:16:50,464   adding 'spatialformer/train.py'
2026-03-26T19:16:50,472   adding 'spatialformer/utils.py'
2026-03-26T19:16:50,474   adding 'spatialformer/config/__init__.py'
2026-03-26T19:16:50,475   adding 'spatialformer/config/_config_fine_tune_probe.json'
2026-03-26T19:16:50,476   adding 'spatialformer/config/_config_graphsave.json'
2026-03-26T19:16:50,477   adding 'spatialformer/config/_config_train.json'
2026-03-26T19:16:50,479   adding 'spatialformer/config/_config_train_large_pair.json'
2026-03-26T19:16:50,480   adding 'spatialformer/config/_config_train_large_single.json'
2026-03-26T19:16:50,482   adding 'spatialformer/dataloader/__init__.py'
2026-03-26T19:16:50,489   adding 'spatialformer/dataloader/dataloader_paired.py'
2026-03-26T19:16:50,491   adding 'spatialformer/gene_gene_calculation/__init__.py'
2026-03-26T19:16:50,493   adding 'spatialformer/gene_gene_calculation/build_h5ad.py'
2026-03-26T19:16:50,495   adding 'spatialformer/gene_gene_calculation/find_gene_interaction.py'
2026-03-26T19:16:50,498   adding 'spatialformer/gene_gene_calculation/h5toloader.py'
2026-03-26T19:16:50,500   adding 'spatialformer/gene_gene_calculation/mask_dataset.py'
2026-03-26T19:16:50,502   adding 'spatialformer/gene_gene_calculation/process.py'
2026-03-26T19:16:50,506   adding 'spatialformer/model/Spaformer.py'
2026-03-26T19:16:50,512   adding 'spatialformer/model/Spaformer_pair.py'
2026-03-26T19:16:50,513   adding 'spatialformer/model/__init__.py'
2026-03-26T19:16:50,515   adding 'spatialformer/model/model.py'
2026-03-26T19:16:50,516   adding 'spatialformer/model/settings.py'
2026-03-26T19:16:50,518   adding 'spatialformer/model/submodules/__init__.py'
2026-03-26T19:16:50,519   adding 'spatialformer/model/submodules/activations.py'
2026-03-26T19:16:50,521   adding 'spatialformer/model/submodules/alibi.py'
2026-03-26T19:16:50,524   adding 'spatialformer/model/submodules/flash_attention2.py'
2026-03-26T19:16:50,526   adding 'spatialformer/model/submodules/layer_modules.py'
2026-03-26T19:16:50,527   adding 'spatialformer/model/submodules/masked_batchnorm.py'
2026-03-26T19:16:50,529   adding 'spatialformer/model/submodules/masked_conv.py'
2026-03-26T19:16:50,531   adding 'spatialformer/model/submodules/modules.py'
2026-03-26T19:16:50,532   adding 'spatialformer/preprocess/__init__.py'
2026-03-26T19:16:50,534   adding 'spatialformer/preprocess/find_gene_interaction.py'
2026-03-26T19:16:50,536   adding 'spatialformer/spatial_embeddings/__init__.py'
2026-03-26T19:16:52,266   adding 'spatialformer/spatial_embeddings/xenium_5k_pandavid_gene_embeddings.pkl'
2026-03-26T19:16:52,344   adding 'spatialformer/tokenizer/__init__.py'
2026-03-26T19:16:52,346   adding 'spatialformer/tokenizer/token.json'
2026-03-26T19:16:52,370   adding 'spatialformer/tokenizer/tokenv2.json'
2026-03-26T19:16:52,378   adding 'spatialformer/tokenizer/tokenv3.json'
2026-03-26T19:16:52,385   adding 'spatialformer/tokenizer/tokenv4.json'
2026-03-26T19:16:52,409   adding 'spatialformer/tokenizer/tokenv5.json'
2026-03-26T19:16:52,411   adding 'spatialformer/tools/__init__.py'
2026-03-26T19:16:52,417   adding 'spatialformer/tools/get_embeddings.py'
2026-03-26T19:16:52,419   adding 'spatialformer-0.1.6.dist-info/licenses/LICENSE'
2026-03-26T19:16:52,421   adding 'spatialformer-0.1.6.dist-info/METADATA'
2026-03-26T19:16:52,421   adding 'spatialformer-0.1.6.dist-info/WHEEL'
2026-03-26T19:16:52,422   adding 'spatialformer-0.1.6.dist-info/top_level.txt'
2026-03-26T19:16:52,423   adding 'spatialformer-0.1.6.dist-info/RECORD'
2026-03-26T19:16:52,536   removing build/bdist.linux-armv7l/wheel
2026-03-26T19:16:52,663   Building wheel for spatialformer (setup.py): finished with status 'done'
2026-03-26T19:16:52,824   Created wheel for spatialformer: filename=spatialformer-0.1.6-py3-none-any.whl size=10884831 sha256=1221890b54152fe026ba6186c8c5e2d48fd585be186695c11b30b89cc0957602
2026-03-26T19:16:52,825   Stored in directory: /tmp/pip-ephem-wheel-cache-96uvwmqm/wheels/0c/a9/9f/469e5dcde8f6ecd6861133c48ef0c2e819a887e2c73ab62332
2026-03-26T19:16:52,840 Successfully built spatialformer
2026-03-26T19:16:53,235 Removed build tracker: '/tmp/pip-build-tracker-f9l10zup'