SURE-tools 2.1.73__tar.gz → 2.1.74__tar.gz

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  1. {sure_tools-2.1.73 → sure_tools-2.1.74}/PKG-INFO +1 -1
  2. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/PerturbFlow.py +7 -1
  3. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE_tools.egg-info/PKG-INFO +1 -1
  4. {sure_tools-2.1.73 → sure_tools-2.1.74}/setup.py +1 -1
  5. {sure_tools-2.1.73 → sure_tools-2.1.74}/LICENSE +0 -0
  6. {sure_tools-2.1.73 → sure_tools-2.1.74}/README.md +0 -0
  7. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/SURE.py +0 -0
  8. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/__init__.py +0 -0
  9. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/assembly/__init__.py +0 -0
  10. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/assembly/assembly.py +0 -0
  11. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/assembly/atlas.py +0 -0
  12. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/atac/__init__.py +0 -0
  13. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/atac/utils.py +0 -0
  14. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/codebook/__init__.py +0 -0
  15. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/codebook/codebook.py +0 -0
  16. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/flow/__init__.py +0 -0
  17. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/flow/flow_stats.py +0 -0
  18. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/flow/plot_quiver.py +0 -0
  19. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/perturb/__init__.py +0 -0
  20. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/perturb/perturb.py +0 -0
  21. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/utils/__init__.py +0 -0
  22. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/utils/custom_mlp.py +0 -0
  23. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/utils/queue.py +0 -0
  24. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/utils/utils.py +0 -0
  25. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE_tools.egg-info/SOURCES.txt +0 -0
  26. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE_tools.egg-info/dependency_links.txt +0 -0
  27. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE_tools.egg-info/entry_points.txt +0 -0
  28. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE_tools.egg-info/requires.txt +0 -0
  29. {sure_tools-2.1.73 → sure_tools-2.1.74}/SURE_tools.egg-info/top_level.txt +0 -0
  30. {sure_tools-2.1.73 → sure_tools-2.1.74}/setup.cfg +0 -0
{sure_tools-2.1.73 → sure_tools-2.1.74}/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: 2.1.73
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+ Version: 2.1.74
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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-2.1.73 → sure_tools-2.1.74}/SURE/PerturbFlow.py RENAMED
@@ -104,6 +104,7 @@ class PerturbFlow(nn.Module):
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  #self.use_bias = not zero_bias
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  self.codebook_weights = None
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+ self.total_count = None
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  set_random_seed(seed)
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  self.setup_networks()
@@ -317,6 +318,7 @@ class PerturbFlow(nn.Module):
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  if self.loss_func=='negbinomial':
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  total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
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  xs.new_ones(self.input_size), constraint=constraints.positive)
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+ self.total_count = total_count
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  if self.use_zeroinflate:
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  gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -396,6 +398,7 @@ class PerturbFlow(nn.Module):
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  if self.loss_func=='negbinomial':
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  total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
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  xs.new_ones(self.input_size), constraint=constraints.positive)
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+ self.total_count = total_count
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  if self.use_zeroinflate:
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  gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -480,6 +483,7 @@ class PerturbFlow(nn.Module):
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  if self.loss_func=='negbinomial':
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  total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
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  xs.new_ones(self.input_size), constraint=constraints.positive)
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+ self.total_count = total_count
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  if self.use_zeroinflate:
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  gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -576,6 +580,7 @@ class PerturbFlow(nn.Module):
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  if self.loss_func=='negbinomial':
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  total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
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  xs.new_ones(self.input_size), constraint=constraints.positive)
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+ self.total_count = total_count
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  if self.use_zeroinflate:
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  gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -880,7 +885,8 @@ class PerturbFlow(nn.Module):
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  rate = concentrate.exp()
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  theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
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- total_count = pyro.param("inverse_dispersion")
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+ total_count = self.total_count
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+ #total_count = pyro.param("inverse_dispersion")
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  #store = pyro.get_param_store()
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  #total_count = store['inverse_dispersion']
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  counts = dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1).mean
{sure_tools-2.1.73 → sure_tools-2.1.74}/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: 2.1.73
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+ Version: 2.1.74
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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-2.1.73 → sure_tools-2.1.74}/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='2.1.73',
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+ version='2.1.74',
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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-2.1.73 → sure_tools-2.1.74}/LICENSE RENAMED
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{sure_tools-2.1.73 → sure_tools-2.1.74}/README.md RENAMED
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{sure_tools-2.1.73 → sure_tools-2.1.74}/SURE/SURE.py RENAMED
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{sure_tools-2.1.73 → sure_tools-2.1.74}/setup.cfg RENAMED
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