SURE-tools 2.1.90__tar.gz → 2.1.92__tar.gz

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Files changed (30) hide show
  1. {sure_tools-2.1.90 → sure_tools-2.1.92}/PKG-INFO +1 -1
  2. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/PerturbFlow.py +2 -14
  3. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE_tools.egg-info/PKG-INFO +1 -1
  4. {sure_tools-2.1.90 → sure_tools-2.1.92}/setup.py +1 -1
  5. {sure_tools-2.1.90 → sure_tools-2.1.92}/LICENSE +0 -0
  6. {sure_tools-2.1.90 → sure_tools-2.1.92}/README.md +0 -0
  7. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/SURE.py +0 -0
  8. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/__init__.py +0 -0
  9. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/assembly/__init__.py +0 -0
  10. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/assembly/assembly.py +0 -0
  11. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/assembly/atlas.py +0 -0
  12. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/atac/__init__.py +0 -0
  13. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/atac/utils.py +0 -0
  14. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/codebook/__init__.py +0 -0
  15. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/codebook/codebook.py +0 -0
  16. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/flow/__init__.py +0 -0
  17. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/flow/flow_stats.py +0 -0
  18. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/flow/plot_quiver.py +0 -0
  19. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/perturb/__init__.py +0 -0
  20. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/perturb/perturb.py +0 -0
  21. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/utils/__init__.py +0 -0
  22. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/utils/custom_mlp.py +0 -0
  23. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/utils/queue.py +0 -0
  24. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/utils/utils.py +0 -0
  25. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE_tools.egg-info/SOURCES.txt +0 -0
  26. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE_tools.egg-info/dependency_links.txt +0 -0
  27. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE_tools.egg-info/entry_points.txt +0 -0
  28. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE_tools.egg-info/requires.txt +0 -0
  29. {sure_tools-2.1.90 → sure_tools-2.1.92}/SURE_tools.egg-info/top_level.txt +0 -0
  30. {sure_tools-2.1.90 → sure_tools-2.1.92}/setup.cfg +0 -0
{sure_tools-2.1.90 → sure_tools-2.1.92}/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: 2.1.90
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+ Version: 2.1.92
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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-2.1.90 → sure_tools-2.1.92}/SURE/PerturbFlow.py RENAMED
@@ -59,7 +59,6 @@ class PerturbFlow(nn.Module):
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  input_size: int,
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  codebook_size: int = 200,
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  cell_factor_size: int = 0,
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- cell_factor_effect_discrete: bool = False,
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  supervised_mode: bool = False,
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  z_dim: int = 10,
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  z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'gumbel',
@@ -103,7 +102,6 @@ class PerturbFlow(nn.Module):
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  else:
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  self.use_bias = [not zero_bias] * self.cell_factor_size
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  #self.use_bias = not zero_bias
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- self.enumrate = cell_factor_effect_discrete
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  self.codebook_weights = None
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@@ -431,12 +429,7 @@ class PerturbFlow(nn.Module):
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  zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1))
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  if self.cell_factor_size>0:
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- if self.enumrate:
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- _, ind = torch.topk(ns, 1)
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- zn_loc = acs_loc[ind]
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- zus = self._total_effects(zn_loc, us)
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- else:
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- zus = self._total_effects(zns, us)
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+ zus = self._total_effects(zns, us)
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  zs = zns+zus
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  else:
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  zs = zns
@@ -638,12 +631,7 @@ class PerturbFlow(nn.Module):
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  # zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
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  # else:
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  # zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
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- if self.enumrate:
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- _, ind = torch.topk(ns, 1)
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- zn_loc = acs_loc[ind]
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- zus = self._total_effects(zn_loc, us)
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- else:
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- zus = self._total_effects(zns, us)
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+ zus = self._total_effects(zns, us)
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  zs = zns+zus
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  else:
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  zs = zns
{sure_tools-2.1.90 → sure_tools-2.1.92}/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: 2.1.90
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+ Version: 2.1.92
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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-2.1.90 → sure_tools-2.1.92}/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='2.1.90',
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+ version='2.1.92',
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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-2.1.90 → sure_tools-2.1.92}/LICENSE RENAMED
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{sure_tools-2.1.90 → sure_tools-2.1.92}/README.md RENAMED
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{sure_tools-2.1.90 → sure_tools-2.1.92}/SURE/SURE.py RENAMED
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{sure_tools-2.1.90 → sure_tools-2.1.92}/setup.cfg RENAMED
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