SURE-tools 2.2.20__tar.gz → 2.2.27__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (30) hide show
  1. {sure_tools-2.2.20 → sure_tools-2.2.27}/PKG-INFO +1 -1
  2. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/DensityFlow.py +2 -2
  3. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/utils/custom_mlp.py +9 -2
  4. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE_tools.egg-info/PKG-INFO +1 -1
  5. {sure_tools-2.2.20 → sure_tools-2.2.27}/setup.py +1 -1
  6. {sure_tools-2.2.20 → sure_tools-2.2.27}/LICENSE +0 -0
  7. {sure_tools-2.2.20 → sure_tools-2.2.27}/README.md +0 -0
  8. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/SURE.py +0 -0
  9. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/__init__.py +0 -0
  10. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/assembly/__init__.py +0 -0
  11. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/assembly/assembly.py +0 -0
  12. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/assembly/atlas.py +0 -0
  13. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/atac/__init__.py +0 -0
  14. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/atac/utils.py +0 -0
  15. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/codebook/__init__.py +0 -0
  16. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/codebook/codebook.py +0 -0
  17. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/flow/__init__.py +0 -0
  18. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/flow/flow_stats.py +0 -0
  19. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/flow/plot_quiver.py +0 -0
  20. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/perturb/__init__.py +0 -0
  21. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/perturb/perturb.py +0 -0
  22. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/utils/__init__.py +0 -0
  23. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/utils/queue.py +0 -0
  24. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/utils/utils.py +0 -0
  25. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE_tools.egg-info/SOURCES.txt +0 -0
  26. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE_tools.egg-info/dependency_links.txt +0 -0
  27. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE_tools.egg-info/entry_points.txt +0 -0
  28. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE_tools.egg-info/requires.txt +0 -0
  29. {sure_tools-2.2.20 → sure_tools-2.2.27}/SURE_tools.egg-info/top_level.txt +0 -0
  30. {sure_tools-2.2.20 → sure_tools-2.2.27}/setup.cfg +0 -0
{sure_tools-2.2.20 → sure_tools-2.2.27}/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: 2.2.20
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+ Version: 2.2.27
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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-2.2.20 → sure_tools-2.2.27}/SURE/DensityFlow.py RENAMED
@@ -854,12 +854,12 @@ class DensityFlow(nn.Module):
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  us_i = us[:,pert_idx].reshape(-1,1)
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  # factor effect of xs
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- dzs0 = self.get_cell_response(zs, factor_idx=pert_idx, perturb=us_i)
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+ dzs0 = self.get_cell_response(zs, perturb_idx=pert_idx, perturb_us=us_i)
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  # perturbation effect
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  ps = np.ones_like(us_i)
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  if np.sum(np.abs(ps-us_i))>=1:
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- dzs = self.get_cell_response(zs, factor_idx=pert_idx, perturb=ps)
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+ dzs = self.get_cell_response(zs, perturb_idx=pert_idx, perturb_us=ps)
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  zs = zs + dzs0 + dzs
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  else:
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  zs = zs + dzs0
{sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/utils/custom_mlp.py RENAMED
@@ -237,12 +237,19 @@ class ZeroBiasMLP(nn.Module):
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  # pass through our sequential for the output!
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  def forward(self, x):
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+ print(f'type: {type(x)}; shape: {x.shape}')
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  y = self.mlp(x)
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  mask = torch.zeros_like(y)
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  if len(y.shape)==2:
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- mask[x[1][:,0]>0,:] = 1
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+ if type(x)==list:
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+ mask[x[1][:,0]>0,:] = 1
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+ else:
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+ mask[x[:,0]>0,:] = 1
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  elif len(y.shape)==3:
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- mask[:,x[1][:,0]>0,:] = 1
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+ if type(x)==list:
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+ mask[:,x[1][:,0]>0,:] = 1
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+ else:
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+ mask[:,x[:,0]>0,:] = 1
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  return y*mask
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{sure_tools-2.2.20 → sure_tools-2.2.27}/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: 2.2.20
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+ Version: 2.2.27
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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-2.2.20 → sure_tools-2.2.27}/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='2.2.20',
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+ version='2.2.27',
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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-2.2.20 → sure_tools-2.2.27}/LICENSE RENAMED
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{sure_tools-2.2.20 → sure_tools-2.2.27}/README.md RENAMED
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{sure_tools-2.2.20 → sure_tools-2.2.27}/SURE/SURE.py RENAMED
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{sure_tools-2.2.20 → sure_tools-2.2.27}/setup.cfg RENAMED
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