SURE-tools 2.1.41__tar.gz → 2.1.43__tar.gz

{sure_tools-2.1.41 → sure_tools-2.1.43}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.41
+Version: 2.1.43
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.41 → sure_tools-2.1.43}/SURE/PerturbFlow.py

@@ -73,7 +73,7 @@ class PerturbFlow(nn.Module):
                  config_enum: str = 'parallel',
                  use_cuda: bool = False,
                  seed: int = 42,
-                 zero_bias: bool = True,
+                 zero_bias: bool|list = True,
                  dtype = torch.float32, # type: ignore
                  ):
         super().__init__()
@@ -97,7 +97,11 @@ class PerturbFlow(nn.Module):
         self.post_layer_fct = post_layer_fct
         self.post_act_fct = post_act_fct
         self.hidden_layer_activation = hidden_layer_activation
-        self.use_bias = not zero_bias
+        if type(zero_bias) == list:
+            self.use_bias = [not x for x in zero_bias]
+        else:
+            self.use_bias = [not zero_bias] * self.cell_factor_size
+        #self.use_bias = not zero_bias
         
         self.codebook_weights = None
 
@@ -198,7 +202,7 @@ class PerturbFlow(nn.Module):
         if self.cell_factor_size>0:
             self.cell_factor_effect = nn.ModuleList()
             for i in np.arange(self.cell_factor_size):
-                if self.use_bias:
+                if self.use_bias[i]:
                     self.cell_factor_effect.append(MLP(
                         [self.latent_dim+1] + self.decoder_hidden_layers + [self.latent_dim],
                         activation=activate_fct,

{sure_tools-2.1.41 → sure_tools-2.1.43}/SURE/perturb/perturb.py

@@ -117,15 +117,14 @@ def matrix_to_labels(matrix, unique_labels):
 def _numba_fill_matrix(dose_matrix, label_indices, label_doses):
     """Numba 加速的矩阵填充函数"""
     for i in range(len(label_indices)):
-        for j, dose in zip(label_indices[i], label_doses[i]):
-            dose_matrix[i, j] = dose
+        dose_matrix[i, label_indices[i]] = label_doses[i]
 
 def dose_to_matrix(labels, label_dose, all_labels=None):
     """
     使用 Numba 的终极加速版本（需预先安装 numba）
     """
     if all_labels is None:
-        all_labels = sorted(set().union(*labels))
+        all_labels = sorted(set().union(labels))
     
     label_to_idx = {label: idx for idx, label in enumerate(all_labels)}
     n_samples = len(labels)
@@ -135,16 +134,10 @@ def dose_to_matrix(labels, label_dose, all_labels=None):
     # 预处理为 Numba 兼容格式
     label_indices = []
     label_doses = []
-    for sample_labels in labels:
-        indices = []
-        doses = []
-        if sample_labels:
-            for label in sample_labels:
-                indices.append(label_to_idx[label])
-                doses.append(label_dose[label])
-        label_indices.append(np.array(indices, dtype=np.int64))
-        label_doses.append(np.array(doses, dtype=np.float64))
+    for i, label in enumerate(labels):
+        label_indices.append(label_to_idx[label])
+        label_doses.append(label_dose[i])
     
     # 调用 Numba 加速函数
     _numba_fill_matrix(dose_matrix, label_indices, label_doses)
-    return dose_matrix,all_labels
+    return dose_matrix,np.array(all_labels)

{sure_tools-2.1.41 → sure_tools-2.1.43}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.41
+Version: 2.1.43
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.41 → sure_tools-2.1.43}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.41',
+    version='2.1.43',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",