SURE-tools 2.2.0__py3-none-any.whl → 2.2.2__py3-none-any.whl

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'],
@@ -970,7 +970,7 @@ class DensityFlow(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', 

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/flow/flow_stats.py

@@ -41,6 +41,18 @@ class VectorFieldEval:
         divergence[np.isnan(divergence)] = 0
         
         return divergence
+    
+    def movement_stats(self,vectors):
+        return calculate_movement_stats(vectors)
+    
+    def direction_stats(self, vectors):
+        return calculate_direction_stats(vectors)
+    
+    def movement_energy(self, vectors, masses=None):
+        return calculate_movement_energy(vectors, masses)
+    
+    def movement_divergence(self, positions, vectors):
+        return calculate_movement_divergence(positions, vectors)
 
         
 def calculate_movement_stats(vectors):

{sure_tools-2.2.0.dist-info → sure_tools-2.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.2.0
+Version: 2.2.2
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.2.0.dist-info → sure_tools-2.2.2.dist-info}/RECORD

@@ -1,6 +1,6 @@
-SURE/DensityFlow.py,sha256=ORpsfsY4TBWZUz0ZIUvmMtEtk_6-e6hUtqRsXkhy5Cw,54677
+SURE/DensityFlow.py,sha256=ACSFkwzlyBqLH39SSOKKepaVFXldpX0Hbu50jd9jjXQ,54676
 SURE/PerturbFlow.py,sha256=kVpEdVgW_AGvvv7d1KnnBydx_hGfpXUXmFg4t4dPlwY,54677
-SURE/SURE.py,sha256=g8EhovBxjfpbVJA0AkmVkQ_ZW_JFc8TtkTCg8FCybV4,47750
+SURE/SURE.py,sha256=MXs7iuvcj-lU4dJ_MwKegpL2Rqk2HB4eFfAgHRA3RtA,47744
 SURE/__init__.py,sha256=NVp22RCHrhSwHNMomABC-eftoCYvt7vV1XOzim-UZHE,293
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
 SURE/assembly/assembly.py,sha256=6IMdelPOiRO4mUb4dC7gVCoF1Uvfw86-Map8P_jnUag,21477
@@ -10,7 +10,7 @@ SURE/atac/utils.py,sha256=m4NYwpy9O5T1pXTzgCOCcmlwrC6GTi-cQ5sm2wZu2O8,4354
 SURE/codebook/__init__.py,sha256=2T5gjp8JIaBayrXAnOJYSebQHsWprOs87difpR1OPNw,243
 SURE/codebook/codebook.py,sha256=ZlN6gRX9Gj2D2u3P5KeOsbZri0MoMAiJo9lNeL-MK-I,17117
 SURE/flow/__init__.py,sha256=rsAjYsh1xVIrxBCuwOE0Q_6N5th1wBgjJceV0ABPG3c,183
-SURE/flow/flow_stats.py,sha256=_pF7m4-87SKlCHVtVmx3LG2bAGVXOnAfEgMzLhLx4Io,10910
+SURE/flow/flow_stats.py,sha256=6SzNMT59WRFRP1nC6bvpBPF7BugWnkIS_DSlr4S-Ez0,11338
 SURE/flow/plot_quiver.py,sha256=UbmuScUcgbQHeMmjKmgqxjrIjHhiHx0VWct16UMMwuE,8110
 SURE/perturb/__init__.py,sha256=8TP1dSUhXiZzKpFebHZmm8XMMGbUz_OfQ10xu-6uPPY,43
 SURE/perturb/perturb.py,sha256=1iSsCePcwkA2CyM1nCdq_G8gogUNjhMH0BfhhvhpJQk,5037
@@ -18,9 +18,9 @@ SURE/utils/__init__.py,sha256=YF5jB-PAHJQ40OlcZ7BCZbsN2q1JKuPT6EppilRXQqM,680
 SURE/utils/custom_mlp.py,sha256=HuNb7f8-6RFjsvfEu1XOuNpLrHZkGYHgf8TpJfPSNO0,9382
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.2.0.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.2.0.dist-info/METADATA,sha256=qN5WqFDldXTOMaQJ0XBCFxOsLTJrsRqnI2GP7T-47v4,2677
-sure_tools-2.2.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.2.0.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.2.0.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.2.0.dist-info/RECORD,,
+sure_tools-2.2.2.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.2.2.dist-info/METADATA,sha256=ptLGAXYWNil97QNNpcCCasW3pWTNe6kMRYm-vTm6TBE,2677
+sure_tools-2.2.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.2.2.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.2.2.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.2.2.dist-info/RECORD,,