Merge pull request #25 from jgu13/master

Fix on line 297 of celltype.py

astir/data/data_readers.py

@@ -22,6 +22,8 @@ def from_csv_yaml(
     create_design_mat: bool = True,
     random_seed: int = 1234,
     dtype: torch.dtype = torch.float64,
+    sep: str = ',',
+    usecols: list = None
 ) -> Any:
     """Create an Astir object from an expression CSV and marker YAML
 
@@ -36,7 +38,7 @@ def from_csv_yaml(
         defaults to 1234
     :param dtype: datatype of the model parameters, defaults to torch.float64
     """
-    df_gex = pd.read_csv(csv_input, index_col=0)
+    df_gex = pd.read_csv(csv_input, sep=sep, usecols=usecols, index_col=0)
 
     design = None
     if design_csv is not None and create_design_mat == True:

astir/models/celltype.py

@@ -294,7 +294,7 @@ def predict(self, new_dset: pd.DataFrame) -> np.array:
         :param new_dset: the dataset to be predicted
         :return: the resulting cell type assignment
         """
-        _, exprs_X, _ = new_dset[:]
+        exprs_X = torch.tensor(new_dset[:].values)
         g = pd.DataFrame(self._recog.forward(exprs_X)[0].detach().cpu().numpy())
         return g
 

requirements.txt

@@ -29,4 +29,4 @@ nbsphinx-link
 tables
 typeguard
 mypy
-
+scanpy