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scverse · Feb 24, 2021 · c39c76c · c39c76c
1 parent 2f86a20
commit c39c76c
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Showing 4 changed files with 22 additions and 3 deletions.
diff --git a/mypackage/_mymodel.py b/mypackage/_mymodel.py
@@ -11,7 +11,9 @@
 class MyModel(VAEMixin, UnsupervisedTrainingMixin, BaseModelClass):
     """
     Skeleton for an scvi-tools model.
+
     Please use this skeleton to create new models.
+
     Parameters
     ----------
     adata

diff --git a/mypackage/_mymodule.py b/mypackage/_mymodule.py
@@ -28,8 +28,6 @@ class MyModule(BaseModuleClass):
         Number of input genes
     n_batch
         Number of batches, if 0, no batch correction is performed.
-    n_labels
-        Number of labels
     n_hidden
         Number of nodes per hidden layer
     n_latent

diff --git a/mypackage/_mypyromodel.py b/mypackage/_mypyromodel.py
@@ -146,6 +146,7 @@ def train(
             train_size=train_size,
             validation_size=validation_size,
             batch_size=batch_size,
+            use_gpu=use_gpu,
         )
         training_plan = PyroTrainingPlan(self.module, **plan_kwargs)
         runner = TrainRunner(

diff --git a/mypackage/_mypyromodule.py b/mypackage/_mypyromodule.py
@@ -6,7 +6,25 @@
 
 
 class MyPyroModule(PyroBaseModuleClass):
-    def __init__(self, n_input, n_latent, n_hidden, n_layers):
+    """
+    Skeleton Variational auto-encoder Pyro model.
+
+    Here we implement a basic version of scVI's underlying VAE [Lopez18]_.
+    This implementation is for instructional purposes only.
+
+    Parameters
+    ----------
+    n_input
+        Number of input genes
+    n_latent
+        Dimensionality of the latent space
+    n_hidden
+        Number of nodes per hidden layer
+    n_layers
+        Number of hidden layers used for encoder and decoder NNs
+    """
+
+    def __init__(self, n_input: int, n_latent: int, n_hidden: int, n_layers: int):
 
         super().__init__()
         self.n_input = n_input