SURE-tools 2.1.31__tar.gz → 2.1.32__tar.gz

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Files changed (30) hide show
  1. {sure_tools-2.1.31 → sure_tools-2.1.32}/PKG-INFO +1 -1
  2. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/PerturbFlow.py +0 -1
  3. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/SURE.py +22 -9
  4. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE_tools.egg-info/PKG-INFO +1 -1
  5. {sure_tools-2.1.31 → sure_tools-2.1.32}/setup.py +1 -1
  6. {sure_tools-2.1.31 → sure_tools-2.1.32}/LICENSE +0 -0
  7. {sure_tools-2.1.31 → sure_tools-2.1.32}/README.md +0 -0
  8. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/__init__.py +0 -0
  9. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/assembly/__init__.py +0 -0
  10. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/assembly/assembly.py +0 -0
  11. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/assembly/atlas.py +0 -0
  12. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/atac/__init__.py +0 -0
  13. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/atac/utils.py +0 -0
  14. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/codebook/__init__.py +0 -0
  15. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/codebook/codebook.py +0 -0
  16. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/flow/__init__.py +0 -0
  17. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/flow/flow_stats.py +0 -0
  18. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/flow/plot_quiver.py +0 -0
  19. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/perturb/__init__.py +0 -0
  20. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/perturb/perturb.py +0 -0
  21. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/utils/__init__.py +0 -0
  22. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/utils/custom_mlp.py +0 -0
  23. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/utils/queue.py +0 -0
  24. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/utils/utils.py +0 -0
  25. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE_tools.egg-info/SOURCES.txt +0 -0
  26. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE_tools.egg-info/dependency_links.txt +0 -0
  27. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE_tools.egg-info/entry_points.txt +0 -0
  28. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE_tools.egg-info/requires.txt +0 -0
  29. {sure_tools-2.1.31 → sure_tools-2.1.32}/SURE_tools.egg-info/top_level.txt +0 -0
  30. {sure_tools-2.1.31 → sure_tools-2.1.32}/setup.cfg +0 -0
{sure_tools-2.1.31 → sure_tools-2.1.32}/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: 2.1.31
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+ Version: 2.1.32
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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-2.1.31 → sure_tools-2.1.32}/SURE/PerturbFlow.py RENAMED
@@ -207,7 +207,6 @@ class PerturbFlow(nn.Module):
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  post_act_fct=post_act_fct,
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  allow_broadcast=self.allow_broadcast,
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  use_cuda=self.use_cuda,
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- bias=True,
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  )
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  )
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  else:
{sure_tools-2.1.31 → sure_tools-2.1.32}/SURE/SURE.py RENAMED
@@ -111,6 +111,7 @@ class SURE(nn.Module):
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  config_enum: str = 'parallel',
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  use_cuda: bool = False,
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  seed: int = 42,
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+ zero_bias: bool = True,
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  dtype = torch.float32, # type: ignore
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  ):
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  super().__init__()
@@ -134,6 +135,7 @@ class SURE(nn.Module):
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  self.post_layer_fct = post_layer_fct
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  self.post_act_fct = post_act_fct
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  self.hidden_layer_activation = hidden_layer_activation
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+ self.use_bias = not zero_bias
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  self.codebook_weights = None
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@@ -232,15 +234,26 @@ class SURE(nn.Module):
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  )
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  if self.cell_factor_size>0:
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- self.cell_factor_effect = MLP(
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- [self.latent_dim + self.cell_factor_size] + self.decoder_hidden_layers + [self.latent_dim],
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- activation=activate_fct,
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- output_activation=None,
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- post_layer_fct=post_layer_fct,
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- post_act_fct=post_act_fct,
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- allow_broadcast=self.allow_broadcast,
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- use_cuda=self.use_cuda,
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- )
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+ if self.use_bias:
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+ self.cell_factor_effect = MLP(
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+ [self.latent_dim + self.cell_factor_size] + self.decoder_hidden_layers + [self.latent_dim],
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+ activation=activate_fct,
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+ output_activation=None,
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+ post_layer_fct=post_layer_fct,
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+ post_act_fct=post_act_fct,
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+ allow_broadcast=self.allow_broadcast,
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+ use_cuda=self.use_cuda,
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+ )
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+ else:
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+ self.cell_factor_effect = ZeroBiasMLP(
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+ [self.latent_dim + self.cell_factor_size] + self.decoder_hidden_layers + [self.latent_dim],
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+ activation=activate_fct,
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+ output_activation=None,
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+ post_layer_fct=post_layer_fct,
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+ post_act_fct=post_act_fct,
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+ allow_broadcast=self.allow_broadcast,
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+ use_cuda=self.use_cuda,
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+ )
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  self.decoder_concentrate = MLP(
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  [self.latent_dim] + self.decoder_hidden_layers + [self.input_size],
{sure_tools-2.1.31 → sure_tools-2.1.32}/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: 2.1.31
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+ Version: 2.1.32
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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-2.1.31 → sure_tools-2.1.32}/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='2.1.31',
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+ version='2.1.32',
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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-2.1.31 → sure_tools-2.1.32}/LICENSE RENAMED
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{sure_tools-2.1.31 → sure_tools-2.1.32}/README.md RENAMED
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{sure_tools-2.1.31 → sure_tools-2.1.32}/setup.cfg RENAMED
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