Changes

deepchem/data/data_loader.py

@@ -976,7 +976,8 @@ def create_dataset(self,
     Parameters
     ----------
     inputs: Sequence[Any]
-      List of inputs to process. Entries can be filenames or arbitrary objects.
+      List of inputs to process. Entries can be arbitrary objects so long as
+      they are understood by `self.featurizer`
     data_dir: str, optional
       Directory to store featurized dataset.
     shard_size: int, optional

deepchem/data/datasets.py

@@ -1943,7 +1943,12 @@ def __init__(self,
     self._X_shape = self._find_array_shape(X)
     self._y_shape = self._find_array_shape(y)
     if w is None:
-      if len(self._y_shape) == 1:
+      if len(self._y_shape) == 0:
+        # Case n_samples should be 1
+        if n_samples != 1:
+          raise ValueError("y can only be a scalar if n_samples == 1")
+        w = np.ones_like(y)
+      elif len(self._y_shape) == 1:
         w = np.ones(self._y_shape[0], np.float32)
       else:
         w = np.ones((self._y_shape[0], 1), np.float32)

deepchem/utils/save.py

@@ -11,7 +11,7 @@
 import deepchem
 import warnings
 import logging
-from typing import List, Optional, Iterator
+from typing import List, Optional, Iterator, Any
 from deepchem.utils.genomics import encode_bio_sequence as encode_sequence, encode_fasta_sequence as fasta_sequence, seq_one_hot_encode as seq_one_hotencode
 
 logger = logging.getLogger(__name__)
@@ -45,7 +45,8 @@ def get_input_type(input_file):
     raise ValueError("Unrecognized extension %s" % file_extension)
 
 
-def load_data(input_files, shard_size=None):
+def load_data(input_files: List[str],
+              shard_size: Optional[int] = None) -> Iterator[Any]:
   """Loads data from disk.
 
   For CSV files, supports sharded loading for large files.
@@ -77,7 +78,9 @@ def load_data(input_files, shard_size=None):
       yield load_pickle_from_disk(input_file)
 
 
-def load_sdf_files(input_files, clean_mols, tasks=[]):
+def load_sdf_files(input_files: List[str],
+                   clean_mols: bool = True,
+                   tasks: List[str] = []) -> List[pd.DataFrame]:
   """Load SDF file into dataframe.
 
   Parameters
@@ -99,7 +102,7 @@ def load_sdf_files(input_files, clean_mols, tasks=[]):
   -------
   dataframes: list
     This function returns a list of pandas dataframes. Each dataframe will
-    columns `('mol_id', 'smiles', 'mol')`.
+    contain columns `('mol_id', 'smiles', 'mol')`.
   """
   from rdkit import Chem
   dataframes = []
@@ -130,12 +133,13 @@ def load_sdf_files(input_files, clean_mols, tasks=[]):
   return dataframes
 
 
-def load_csv_files(filenames, shard_size=None):
+def load_csv_files(filenames: List[str],
+                   shard_size: Optional[int] = None) -> Iterator[pd.DataFrame]:
   """Load data as pandas dataframe.
 
   Parameters
   ----------
-  input_files: list[str]
+  filenames: list[str]
     List of filenames
   shard_size: int, optional (default None) 
     The shard size to yield at one time.