SURE-tools 2.1.55__tar.gz → 2.1.56__tar.gz

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  1. {sure_tools-2.1.55 → sure_tools-2.1.56}/PKG-INFO +1 -1
  2. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/PerturbFlow.py +14 -14
  3. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE_tools.egg-info/PKG-INFO +1 -1
  4. {sure_tools-2.1.55 → sure_tools-2.1.56}/setup.py +1 -1
  5. {sure_tools-2.1.55 → sure_tools-2.1.56}/LICENSE +0 -0
  6. {sure_tools-2.1.55 → sure_tools-2.1.56}/README.md +0 -0
  7. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/SURE.py +0 -0
  8. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/__init__.py +0 -0
  9. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/assembly/__init__.py +0 -0
  10. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/assembly/assembly.py +0 -0
  11. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/assembly/atlas.py +0 -0
  12. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/atac/__init__.py +0 -0
  13. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/atac/utils.py +0 -0
  14. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/codebook/__init__.py +0 -0
  15. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/codebook/codebook.py +0 -0
  16. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/flow/__init__.py +0 -0
  17. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/flow/flow_stats.py +0 -0
  18. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/flow/plot_quiver.py +0 -0
  19. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/perturb/__init__.py +0 -0
  20. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/perturb/perturb.py +0 -0
  21. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/utils/__init__.py +0 -0
  22. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/utils/custom_mlp.py +0 -0
  23. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/utils/queue.py +0 -0
  24. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/utils/utils.py +0 -0
  25. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE_tools.egg-info/SOURCES.txt +0 -0
  26. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE_tools.egg-info/dependency_links.txt +0 -0
  27. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE_tools.egg-info/entry_points.txt +0 -0
  28. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE_tools.egg-info/requires.txt +0 -0
  29. {sure_tools-2.1.55 → sure_tools-2.1.56}/SURE_tools.egg-info/top_level.txt +0 -0
  30. {sure_tools-2.1.55 → sure_tools-2.1.56}/setup.cfg +0 -0
{sure_tools-2.1.55 → sure_tools-2.1.56}/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: 2.1.55
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+ Version: 2.1.56
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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-2.1.55 → sure_tools-2.1.56}/SURE/PerturbFlow.py RENAMED
@@ -244,7 +244,7 @@ class PerturbFlow(nn.Module):
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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.encoder_concentrate = self.decoder_concentrate
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+ #self.encoder_concentrate = self.decoder_concentrate
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  else:
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  self.decoder_concentrate = MLP(
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  [self.latent_dim] + self.decoder_hidden_layers + [self.input_size],
@@ -417,9 +417,9 @@ class PerturbFlow(nn.Module):
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  alpha = self.encoder_n(zns)
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  ns = pyro.sample('n', dist.OneHotCategorical(logits=alpha))
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- if self.loss_func == 'gamma-poisson':
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- con_alpha,con_beta = self.encoder_concentrate(zns)
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- rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
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+ #if self.loss_func == 'gamma-poisson':
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+ # con_alpha,con_beta = self.encoder_concentrate(zns)
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+ # rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
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  def model2(self, xs, us=None):
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  pyro.module('PerturbFlow', self)
@@ -521,9 +521,9 @@ class PerturbFlow(nn.Module):
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  alpha = self.encoder_n(zns)
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  ns = pyro.sample('n', dist.OneHotCategorical(logits=alpha))
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- if self.loss_func == 'gamma-poisson':
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- con_alpha,con_beta = self.encoder_concentrate(zns)
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- rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
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+ #if self.loss_func == 'gamma-poisson':
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+ # con_alpha,con_beta = self.encoder_concentrate(zns)
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+ # rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
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  def model3(self, xs, ys, embeds=None):
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  pyro.module('PerturbFlow', self)
@@ -631,9 +631,9 @@ class PerturbFlow(nn.Module):
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  else:
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  zns = embeds
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- if self.loss_func == 'gamma-poisson':
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- con_alpha,con_beta = self.encoder_concentrate(zns)
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- rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
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+ #if self.loss_func == 'gamma-poisson':
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+ # con_alpha,con_beta = self.encoder_concentrate(zns)
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+ # rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
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  def model4(self, xs, us, ys, embeds=None):
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  pyro.module('PerturbFlow', self)
@@ -751,9 +751,9 @@ class PerturbFlow(nn.Module):
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  else:
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  zns = embeds
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- if self.loss_func == 'gamma-poisson':
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- con_alpha,con_beta = self.encoder_concentrate(zns)
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- rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
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+ #if self.loss_func == 'gamma-poisson':
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+ # con_alpha,con_beta = self.encoder_concentrate(zns)
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+ # rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
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  def _total_effects(self, zns, us):
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  zus = None
@@ -933,7 +933,7 @@ class PerturbFlow(nn.Module):
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  def _get_expression_response(self, delta_zs):
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  if self.loss_func == 'gamma-poisson':
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- alpha,beta = self.encoder_concentrate(delta_zs)
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+ alpha,beta = self.decoder_concentrate(delta_zs)
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  xs = dist.Gamma(alpha,beta).to_event(1).mean
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  else:
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  xs = self.decoder_concentrate(delta_zs)
{sure_tools-2.1.55 → sure_tools-2.1.56}/SURE_tools.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
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  Metadata-Version: 2.4
2
2
  Name: SURE-tools
3
- Version: 2.1.55
3
+ Version: 2.1.56
4
4
  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-2.1.55 → sure_tools-2.1.56}/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='2.1.55',
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+ version='2.1.56',
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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-2.1.55 → sure_tools-2.1.56}/LICENSE RENAMED
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{sure_tools-2.1.55 → sure_tools-2.1.56}/README.md RENAMED
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{sure_tools-2.1.55 → sure_tools-2.1.56}/SURE/SURE.py RENAMED
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{sure_tools-2.1.55 → sure_tools-2.1.56}/setup.cfg RENAMED
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