SURE-tools 2.1.91__tar.gz → 2.2.0__tar.gz

{sure_tools-2.1.91 → sure_tools-2.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.91
+Version: 2.2.0
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

sure_tools-2.1.91/SURE/PerturbFlow.py → sure_tools-2.2.0/SURE/DensityFlow.py

@@ -54,12 +54,11 @@ def set_random_seed(seed):
     # Set seed for Pyro
     pyro.set_rng_seed(seed)
 
-class PerturbFlow(nn.Module):
+class DensityFlow(nn.Module):
     def __init__(self,
                  input_size: int,
                  codebook_size: int = 200,
                  cell_factor_size: int = 0,
-                 cell_factor_effect_discrete: bool = False,
                  supervised_mode: bool = False,
                  z_dim: int = 10,
                  z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'gumbel',
@@ -103,7 +102,6 @@ class PerturbFlow(nn.Module):
         else:
             self.use_bias = [not zero_bias] * self.cell_factor_size
         #self.use_bias = not zero_bias
-        self.enumrate = cell_factor_effect_discrete
         
         self.codebook_weights = None
 
@@ -310,7 +308,7 @@ class PerturbFlow(nn.Module):
         return xs
 
     def model1(self, xs):
-        pyro.module('PerturbFlow', self)
+        pyro.module('DensityFlow', self)
 
         eps = torch.finfo(xs.dtype).eps
         batch_size = xs.size(0)
@@ -389,7 +387,7 @@ class PerturbFlow(nn.Module):
             ns = pyro.sample('n', dist.OneHotCategorical(logits=alpha))
 
     def model2(self, xs, us=None):
-        pyro.module('PerturbFlow', self)
+        pyro.module('DensityFlow', self)
 
         eps = torch.finfo(xs.dtype).eps
         batch_size = xs.size(0)
@@ -431,10 +429,7 @@ class PerturbFlow(nn.Module):
                 zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1))
 
             if self.cell_factor_size>0:
-                if self.enumrate:
-                    zus = self._total_effects(zn_loc, us)
-                else:
-                    zus = self._total_effects(zns, us)
+                zus = self._total_effects(zns, us)
                 zs = zns+zus
             else:
                 zs = zns
@@ -476,7 +471,7 @@ class PerturbFlow(nn.Module):
             ns = pyro.sample('n', dist.OneHotCategorical(logits=alpha))
 
     def model3(self, xs, ys, embeds=None):
-        pyro.module('PerturbFlow', self)
+        pyro.module('DensityFlow', self)
 
         eps = torch.finfo(xs.dtype).eps
         batch_size = xs.size(0)
@@ -572,7 +567,7 @@ class PerturbFlow(nn.Module):
                 zns = embeds
 
     def model4(self, xs, us, ys, embeds=None):
-        pyro.module('PerturbFlow', self)
+        pyro.module('DensityFlow', self)
 
         eps = torch.finfo(xs.dtype).eps
         batch_size = xs.size(0)
@@ -636,10 +631,7 @@ class PerturbFlow(nn.Module):
                 #        zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
                 #    else:
                 #        zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
-                if self.enumrate:
-                    zus = self._total_effects(zn_loc, us)
-                else:
-                    zus = self._total_effects(zns, us)
+                zus = self._total_effects(zns, us)
                 zs = zns+zus
             else:
                 zs = zns
@@ -989,7 +981,7 @@ class PerturbFlow(nn.Module):
             threshold: int = 0,
             use_jax: bool = True):
         """
-        Train the PerturbFlow model.
+        Train the DensityFlow model.
 
         Parameters
         ----------
@@ -1015,7 +1007,7 @@ class PerturbFlow(nn.Module):
             Parameter for optimization.
         use_jax
             If toggled on, Jax will be used for speeding up. CAUTION: This will raise errors because of unknown reasons when it is called in
-            the Python script or Jupyter notebook. It is OK if it is used when runing PerturbFlow in the shell command.
+            the Python script or Jupyter notebook. It is OK if it is used when runing DensityFlow in the shell command.
         """
         xs = self.preprocess(xs, threshold=threshold)
         xs = convert_to_tensor(xs, dtype=self.dtype, device=self.get_device())
@@ -1133,12 +1125,12 @@ class PerturbFlow(nn.Module):
 
         
 EXAMPLE_RUN = (
-    "example run: PerturbFlow --help"
+    "example run: DensityFlow --help"
 )
 
 def parse_args():
     parser = argparse.ArgumentParser(
-        description="PerturbFlow\n{}".format(EXAMPLE_RUN))
+        description="DensityFlow\n{}".format(EXAMPLE_RUN))
 
     parser.add_argument(
         "--cuda", action="store_true", help="use GPU(s) to speed up training"
@@ -1325,7 +1317,7 @@ def main():
     cell_factor_size = 0 if us is None else us.shape[1]
 
     ###########################################
-    perturbflow = PerturbFlow(
+    DensityFlow = DensityFlow(
         input_size=input_size,
         cell_factor_size=cell_factor_size,
         inverse_dispersion=args.inverse_dispersion,
@@ -1344,7 +1336,7 @@ def main():
         dtype=dtype,
     )
 
-    perturbflow.fit(xs, us=us, 
+    DensityFlow.fit(xs, us=us, 
              num_epochs=args.num_epochs,
              learning_rate=args.learning_rate,
              batch_size=args.batch_size,
@@ -1356,9 +1348,9 @@ def main():
 
     if args.save_model is not None:
         if args.save_model.endswith('gz'):
-            PerturbFlow.save_model(perturbflow, args.save_model, compression=True)
+            DensityFlow.save_model(DensityFlow, args.save_model, compression=True)
         else:
-            PerturbFlow.save_model(perturbflow, args.save_model)
+            DensityFlow.save_model(DensityFlow, args.save_model)
     
 
 

{sure_tools-2.1.91 → sure_tools-2.2.0}/SURE/__init__.py

@@ -1,12 +1,12 @@
 from .SURE import SURE
-from .PerturbFlow import PerturbFlow
+from .DensityFlow import DensityFlow
 
 from . import utils 
 from . import codebook
 from . import SURE
-from . import PerturbFlow
+from . import DensityFlow
 from . import atac
 from . import flow 
 from . import perturb
 
-__all__ = ['SURE', 'PerturbFlow', 'flow', 'perturb', 'atac', 'utils', 'codebook']
+__all__ = ['SURE', 'DensityFlow', 'flow', 'perturb', 'atac', 'utils', 'codebook']

{sure_tools-2.1.91 → sure_tools-2.2.0}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.91
+Version: 2.2.0
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.91 → sure_tools-2.2.0}/SURE_tools.egg-info/SOURCES.txt

@@ -1,7 +1,7 @@
 LICENSE
 README.md
 setup.py
-SURE/PerturbFlow.py
+SURE/DensityFlow.py
 SURE/SURE.py
 SURE/__init__.py
 SURE/assembly/__init__.py

{sure_tools-2.1.91 → sure_tools-2.2.0}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.91',
+    version='2.2.0',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",