SURE-tools 2.1.22__tar.gz → 2.1.24__tar.gz

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Files changed (30) hide show
  1. {sure_tools-2.1.22 → sure_tools-2.1.24}/PKG-INFO +1 -1
  2. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/SURE.py +2 -2
  3. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/utils/custom_mlp.py +1 -1
  4. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE_tools.egg-info/PKG-INFO +1 -1
  5. {sure_tools-2.1.22 → sure_tools-2.1.24}/setup.py +1 -1
  6. {sure_tools-2.1.22 → sure_tools-2.1.24}/LICENSE +0 -0
  7. {sure_tools-2.1.22 → sure_tools-2.1.24}/README.md +0 -0
  8. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/PerturbFlow.py +0 -0
  9. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/__init__.py +0 -0
  10. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/assembly/__init__.py +0 -0
  11. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/assembly/assembly.py +0 -0
  12. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/assembly/atlas.py +0 -0
  13. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/atac/__init__.py +0 -0
  14. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/atac/utils.py +0 -0
  15. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/codebook/__init__.py +0 -0
  16. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/codebook/codebook.py +0 -0
  17. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/flow/__init__.py +0 -0
  18. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/flow/flow_stats.py +0 -0
  19. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/flow/plot_quiver.py +0 -0
  20. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/perturb/__init__.py +0 -0
  21. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/perturb/perturb.py +0 -0
  22. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/utils/__init__.py +0 -0
  23. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/utils/queue.py +0 -0
  24. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/utils/utils.py +0 -0
  25. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE_tools.egg-info/SOURCES.txt +0 -0
  26. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE_tools.egg-info/dependency_links.txt +0 -0
  27. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE_tools.egg-info/entry_points.txt +0 -0
  28. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE_tools.egg-info/requires.txt +0 -0
  29. {sure_tools-2.1.22 → sure_tools-2.1.24}/SURE_tools.egg-info/top_level.txt +0 -0
  30. {sure_tools-2.1.22 → sure_tools-2.1.24}/setup.cfg +0 -0
{sure_tools-2.1.22 → sure_tools-2.1.24}/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: 2.1.22
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+ Version: 2.1.24
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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-2.1.22 → sure_tools-2.1.24}/SURE/SURE.py RENAMED
@@ -10,7 +10,7 @@ from torch.distributions.utils import logits_to_probs, probs_to_logits, clamp_pr
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  from torch.distributions import constraints
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  from torch.distributions.transforms import SoftmaxTransform
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- from .utils.custom_mlp import MLP, Exp
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+ from .utils.custom_mlp import MLP, Exp, ZeroBiasMLP
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  from .utils.utils import CustomDataset, CustomDataset2, CustomDataset4, tensor_to_numpy, convert_to_tensor
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@@ -232,7 +232,7 @@ 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.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,
{sure_tools-2.1.22 → sure_tools-2.1.24}/SURE/utils/custom_mlp.py RENAMED
@@ -239,6 +239,6 @@ class ZeroBiasMLP(nn.Module):
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  def forward(self, x):
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  y = self.mlp(x)
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  mask = torch.zeros_like(y)
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- mask[x[1]>0,:] = 1
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+ mask[x[1][:,0]>0,:] = 1
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  return y*mask
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{sure_tools-2.1.22 → sure_tools-2.1.24}/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: 2.1.22
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+ Version: 2.1.24
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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-2.1.22 → sure_tools-2.1.24}/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='2.1.22',
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+ version='2.1.24',
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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-2.1.22 → sure_tools-2.1.24}/LICENSE RENAMED
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{sure_tools-2.1.22 → sure_tools-2.1.24}/README.md RENAMED
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{sure_tools-2.1.22 → sure_tools-2.1.24}/setup.cfg RENAMED
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