vima-spatial 0.2.4__tar.gz → 0.2.5__tar.gz

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Files changed (40) hide show
  1. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/PKG-INFO +3 -2
  2. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/README.md +1 -1
  3. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/setup.cfg +2 -1
  4. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima_spatial.egg-info/PKG-INFO +3 -2
  5. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima_spatial.egg-info/requires.txt +1 -0
  6. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/pyproject.toml +0 -0
  7. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/__init__.py +0 -0
  8. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/_settings.py +0 -0
  9. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/cc.py +0 -0
  10. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/data/__init__.py +0 -0
  11. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/data/download.py +0 -0
  12. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/data/patchcollection.py +0 -0
  13. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/data/samples.py +0 -0
  14. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/fingerprints.py +0 -0
  15. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/ingest/__init__.py +0 -0
  16. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/ingest/dimreduce.py +0 -0
  17. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/ingest/ingest.py +0 -0
  18. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/ingest/nonst.py +0 -0
  19. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/ingest/st.py +0 -0
  20. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/ingest/util.py +0 -0
  21. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/models/__init__.py +0 -0
  22. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/models/resnet_vae.py +0 -0
  23. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/models/resnetlight_decoder.py +0 -0
  24. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/models/resnetlight_encoder.py +0 -0
  25. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/models/simple_vae.py +0 -0
  26. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/models/vae.py +0 -0
  27. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/patchfeatures.py +0 -0
  28. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/train/__init__.py +0 -0
  29. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/train/logging.py +0 -0
  30. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/train/training.py +0 -0
  31. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/vis/__init__.py +0 -0
  32. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/vis/features.py +0 -0
  33. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/vis/patches.py +0 -0
  34. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/vis/patchexamples.py +0 -0
  35. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/vis/spatial.py +0 -0
  36. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima/vis/umaps.py +0 -0
  37. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima_spatial.egg-info/SOURCES.txt +0 -0
  38. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima_spatial.egg-info/dependency_links.txt +0 -0
  39. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima_spatial.egg-info/top_level.txt +0 -0
  40. {vima_spatial-0.2.4 → vima_spatial-0.2.5}/tests/test_ra_regression.py +0 -0
{vima_spatial-0.2.4 → vima_spatial-0.2.5}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: vima-spatial
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- Version: 0.2.4
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+ Version: 0.2.5
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  Summary: variational inference-based microniche analysis
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  Home-page: https://github.com/yakirr/vima
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  Author: Yakir Reshef
@@ -25,6 +25,7 @@ Requires-Dist: netcdf4
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  Requires-Dist: seaborn
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  Requires-Dist: pandas>=2.2.3
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  Requires-Dist: scipy
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+ Requires-Dist: scikit-misc>=0.3.1
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  Requires-Dist: cna>=0.2.4
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  Requires-Dist: tqdm
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  Requires-Dist: pyarrow
@@ -49,4 +50,4 @@ To see how to apply `vima` to a stain-based modality like CODEX, immunohistochem
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  ## citation
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  If you use `vima`, please cite:
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- [Y. Reshef, et al. Powerful and accurate case-control analysis of spatial molecular data. bioRxiv. https://doi.org/10.1101/2025.02.07.637149v1](https://www.biorxiv.org/content/10.1101/2025.02.07.637149v2).
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+ [Y. Reshef, et al. Powerful and accurate case-control analysis of spatial molecular data. bioRxiv (In press at _Nature Methods_). https://doi.org/10.1101/2025.02.07.637149v1](https://www.biorxiv.org/content/10.1101/2025.02.07.637149v2).
{vima_spatial-0.2.4 → vima_spatial-0.2.5}/README.md RENAMED
@@ -16,4 +16,4 @@ To see how to apply `vima` to a stain-based modality like CODEX, immunohistochem
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  ## citation
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  If you use `vima`, please cite:
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- [Y. Reshef, et al. Powerful and accurate case-control analysis of spatial molecular data. bioRxiv. https://doi.org/10.1101/2025.02.07.637149v1](https://www.biorxiv.org/content/10.1101/2025.02.07.637149v2).
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+ [Y. Reshef, et al. Powerful and accurate case-control analysis of spatial molecular data. bioRxiv (In press at _Nature Methods_). https://doi.org/10.1101/2025.02.07.637149v1](https://www.biorxiv.org/content/10.1101/2025.02.07.637149v2).
{vima_spatial-0.2.4 → vima_spatial-0.2.5}/setup.cfg RENAMED
@@ -1,6 +1,6 @@
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  [metadata]
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  name = vima-spatial
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- version = 0.2.4
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+ version = 0.2.5
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  author = Yakir Reshef
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  author_email = yreshef@broadinstitute.org
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  description = variational inference-based microniche analysis
@@ -35,6 +35,7 @@ install_requires =
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  seaborn
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  pandas>=2.2.3
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  scipy
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+ scikit-misc>=0.3.1
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  cna>=0.2.4
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  tqdm
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  pyarrow
{vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima_spatial.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: vima-spatial
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- Version: 0.2.4
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+ Version: 0.2.5
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  Summary: variational inference-based microniche analysis
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  Home-page: https://github.com/yakirr/vima
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  Author: Yakir Reshef
@@ -25,6 +25,7 @@ Requires-Dist: netcdf4
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  Requires-Dist: seaborn
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  Requires-Dist: pandas>=2.2.3
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  Requires-Dist: scipy
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+ Requires-Dist: scikit-misc>=0.3.1
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  Requires-Dist: cna>=0.2.4
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  Requires-Dist: tqdm
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  Requires-Dist: pyarrow
@@ -49,4 +50,4 @@ To see how to apply `vima` to a stain-based modality like CODEX, immunohistochem
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  ## citation
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  If you use `vima`, please cite:
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- [Y. Reshef, et al. Powerful and accurate case-control analysis of spatial molecular data. bioRxiv. https://doi.org/10.1101/2025.02.07.637149v1](https://www.biorxiv.org/content/10.1101/2025.02.07.637149v2).
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+ [Y. Reshef, et al. Powerful and accurate case-control analysis of spatial molecular data. bioRxiv (In press at _Nature Methods_). https://doi.org/10.1101/2025.02.07.637149v1](https://www.biorxiv.org/content/10.1101/2025.02.07.637149v2).
{vima_spatial-0.2.4 → vima_spatial-0.2.5}/src/vima_spatial.egg-info/requires.txt RENAMED
@@ -11,6 +11,7 @@ netcdf4
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  seaborn
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  pandas>=2.2.3
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  scipy
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+ scikit-misc>=0.3.1
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  cna>=0.2.4
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  tqdm
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  pyarrow