SURE-tools 2.4.3__tar.gz → 2.4.4__tar.gz

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Files changed (32) hide show
  1. {sure_tools-2.4.3 → sure_tools-2.4.4}/PKG-INFO +1 -1
  2. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/TranscriptomeDecoder.py +4 -2
  3. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE_tools.egg-info/PKG-INFO +1 -1
  4. {sure_tools-2.4.3 → sure_tools-2.4.4}/setup.py +1 -1
  5. {sure_tools-2.4.3 → sure_tools-2.4.4}/LICENSE +0 -0
  6. {sure_tools-2.4.3 → sure_tools-2.4.4}/README.md +0 -0
  7. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/DensityFlow.py +0 -0
  8. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/PerturbE.py +0 -0
  9. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/SURE.py +0 -0
  10. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/__init__.py +0 -0
  11. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/assembly/__init__.py +0 -0
  12. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/assembly/assembly.py +0 -0
  13. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/assembly/atlas.py +0 -0
  14. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/atac/__init__.py +0 -0
  15. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/atac/utils.py +0 -0
  16. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/codebook/__init__.py +0 -0
  17. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/codebook/codebook.py +0 -0
  18. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/flow/__init__.py +0 -0
  19. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/flow/flow_stats.py +0 -0
  20. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/flow/plot_quiver.py +0 -0
  21. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/perturb/__init__.py +0 -0
  22. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/perturb/perturb.py +0 -0
  23. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/utils/__init__.py +0 -0
  24. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/utils/custom_mlp.py +0 -0
  25. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/utils/queue.py +0 -0
  26. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/utils/utils.py +0 -0
  27. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE_tools.egg-info/SOURCES.txt +0 -0
  28. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE_tools.egg-info/dependency_links.txt +0 -0
  29. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE_tools.egg-info/entry_points.txt +0 -0
  30. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE_tools.egg-info/requires.txt +0 -0
  31. {sure_tools-2.4.3 → sure_tools-2.4.4}/SURE_tools.egg-info/top_level.txt +0 -0
  32. {sure_tools-2.4.3 → sure_tools-2.4.4}/setup.cfg +0 -0
{sure_tools-2.4.3 → sure_tools-2.4.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: SURE-tools
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- Version: 2.4.3
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+ Version: 2.4.4
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  Summary: Succinct Representation of Single Cells
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  Home-page: https://github.com/ZengFLab/SURE
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  Author: Feng Zeng
{sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/TranscriptomeDecoder.py RENAMED
@@ -166,6 +166,8 @@ class TranscriptomeDecoder:
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  self.output_scale = nn.Parameter(torch.ones(1))
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  self.output_bias = nn.Parameter(torch.zeros(1))
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+ self.latent_to_gene = nn.Linear(hidden_dim, gene_dim)
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+
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  self._init_weights()
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  def _init_weights(self):
@@ -185,8 +187,8 @@ class TranscriptomeDecoder:
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  gene_features = self.gene_projection(latent)
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  # 3. Add latent information
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- print(f'{gene_features.shape}; {latent_expanded.unsqueeze(1).shape}')
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- gene_features = gene_features + latent_expanded.unsqueeze(1)
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+ latent_gene_injection = self.latent_to_gene(latent_expanded)
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+ gene_features = gene_features + latent_gene_injection
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  # 4. Chunked processing (memory efficient)
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  gene_features = self.chunked_processor(gene_features)
{sure_tools-2.4.3 → sure_tools-2.4.4}/SURE_tools.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: SURE-tools
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- Version: 2.4.3
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+ Version: 2.4.4
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  Summary: Succinct Representation of Single Cells
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  Home-page: https://github.com/ZengFLab/SURE
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  Author: Feng Zeng
{sure_tools-2.4.3 → sure_tools-2.4.4}/setup.py RENAMED
@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
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  setup(
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  name='SURE-tools',
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- version='2.4.3',
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+ version='2.4.4',
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  description='Succinct Representation of Single Cells',
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  long_description=long_description,
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  long_description_content_type="text/markdown",
{sure_tools-2.4.3 → sure_tools-2.4.4}/LICENSE RENAMED
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{sure_tools-2.4.3 → sure_tools-2.4.4}/README.md RENAMED
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{sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/PerturbE.py RENAMED
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{sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/SURE.py RENAMED
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{sure_tools-2.4.3 → sure_tools-2.4.4}/SURE/__init__.py RENAMED
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{sure_tools-2.4.3 → sure_tools-2.4.4}/setup.cfg RENAMED
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