SURE-tools 2.2.1__tar.gz → 2.2.3__tar.gz

{sure_tools-2.2.1 → sure_tools-2.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.2.1
+Version: 2.2.3
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.2.1 → sure_tools-2.2.3}/SURE/DensityFlow.py

@@ -64,8 +64,8 @@ class DensityFlow(nn.Module):
                  z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'gumbel',
                  loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'poisson',
                  inverse_dispersion: float = 10.0,
-                 use_zeroinflate: bool = False,
-                 hidden_layers: list = [300],
+                 use_zeroinflate: bool = True,
+                 hidden_layers: list = [500],
                  hidden_layer_activation: Literal['relu','softplus','leakyrelu','linear'] = 'relu',
                  nn_dropout: float = 0.1,
                  post_layer_fct: list = ['layernorm'],
@@ -932,9 +932,9 @@ class DensityFlow(nn.Module):
         zs = convert_to_tensor(zs, device=self.get_device())
         
         if type(library_sizes) == list:
-            library_sizes = np.array(library_sizes).view(-1,1)
+            library_sizes = np.array(library_sizes).reshape(-1,1)
         elif len(library_sizes.shape)==1:
-            library_sizes = library_sizes.view(-1,1)
+            library_sizes = library_sizes.reshape(-1,1)
         ls = convert_to_tensor(library_sizes, device=self.get_device())
             
         dataset = CustomDataset2(zs,ls)

{sure_tools-2.2.1 → sure_tools-2.2.3}/SURE/SURE.py

@@ -99,17 +99,17 @@ class SURE(nn.Module):
                  cell_factor_size: int = 0,
                  supervised_mode: bool = False,
                  z_dim: int = 10,
-                 z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'normal',
-                 loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'negbinomial',
+                 z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'gumbel',
+                 loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'poisson',
                  inverse_dispersion: float = 10.0,
                  use_zeroinflate: bool = True,
-                 hidden_layers: list = [300],
+                 hidden_layers: list = [500],
                  hidden_layer_activation: Literal['relu','softplus','leakyrelu','linear'] = 'relu',
                  nn_dropout: float = 0.1,
                  post_layer_fct: list = ['layernorm'],
                  post_act_fct: list = None,
                  config_enum: str = 'parallel',
-                 use_cuda: bool = False,
+                 use_cuda: bool = True,
                  seed: int = 42,
                  dtype = torch.float32, # type: ignore
                  ):
@@ -817,7 +817,7 @@ class SURE(nn.Module):
             us = None, 
             ys = None,
             zs = None,
-            num_epochs: int = 200, 
+            num_epochs: int = 500, 
             learning_rate: float = 0.0001, 
             batch_size: int = 256, 
             algo: Literal['adam','rmsprop','adamw'] = 'adam', 
@@ -826,7 +826,7 @@ class SURE(nn.Module):
             decay_rate: float = 0.9,
             config_enum: str = 'parallel',
             threshold: int = 0,
-            use_jax: bool = False):
+            use_jax: bool = True):
         """
         Train the SURE model.
 

{sure_tools-2.2.1 → sure_tools-2.2.3}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.2.1
+Version: 2.2.3
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.2.1 → sure_tools-2.2.3}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.2.1',
+    version='2.2.3',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",