Update type annotations (#9917)

Unblocks merging to master.

.github/workflows/linting.yml

@@ -25,7 +25,7 @@ jobs:
       # Skip workflow if only certain files have been changed.
       - name: Get changed files
         id: changed-files-specific
-        uses: tj-actions/changed-files@v41
+        uses: tj-actions/changed-files@v45
         with:
           files: |
             benchmark/**

torch_geometric/datasets/git_mol_dataset.py

@@ -187,7 +187,7 @@ def process(self) -> None:
                 img = self.img_transform(img).unsqueeze(0)
                 # graph
                 atom_features_list = []
-                for atom in mol.GetAtoms():  # type: ignore
+                for atom in mol.GetAtoms():
                     atom_feature = [
                         safe_index(
                             allowable_features['possible_atomic_num_list'],
@@ -219,7 +219,7 @@ def process(self) -> None:
 
                 edges_list = []
                 edge_features_list = []
-                for bond in mol.GetBonds():  # type: ignore
+                for bond in mol.GetBonds():
                     i, j = bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()
                     edge_feature = [
                         safe_index(

torch_geometric/datasets/molecule_gpt_dataset.py

@@ -122,7 +122,10 @@ def clean_up_description(description: str) -> str:
     return first_sentence
 
 
-def extract_name(name_raw: str, description: str) -> Tuple[str, str, str]:
+def extract_name(
+    name_raw: str,
+    description: str,
+) -> Tuple[Optional[str], str, str]:
     first_sentence = clean_up_description(description)
 
     splitter = '  --  --  '
@@ -446,12 +449,12 @@ def extract_one_SDF_file(block_id: int) -> None:
 
                 x: torch.Tensor = torch.tensor([
                     types[atom.GetSymbol()] if atom.GetSymbol() in types else 5
-                    for atom in m.GetAtoms()  # type: ignore
+                    for atom in m.GetAtoms()
                 ])
                 x = one_hot(x, num_classes=len(types), dtype=torch.float)
 
                 rows, cols, edge_types = [], [], []
-                for bond in m.GetBonds():  # type: ignore
+                for bond in m.GetBonds():
                     i, j = bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()
                     edge_types += [bonds[bond.GetBondType()]] * 2
                     rows += [i, j]

torch_geometric/utils/smiles.py

@@ -91,7 +91,7 @@ def from_rdmol(mol: Any) -> 'torch_geometric.data.Data':
     assert isinstance(mol, Chem.Mol)
 
     xs: List[List[int]] = []
-    for atom in mol.GetAtoms():  # type: ignore
+    for atom in mol.GetAtoms():
         row: List[int] = []
         row.append(x_map['atomic_num'].index(atom.GetAtomicNum()))
         row.append(x_map['chirality'].index(str(atom.GetChiralTag())))
@@ -108,7 +108,7 @@ def from_rdmol(mol: Any) -> 'torch_geometric.data.Data':
     x = torch.tensor(xs, dtype=torch.long).view(-1, 9)
 
     edge_indices, edge_attrs = [], []
-    for bond in mol.GetBonds():  # type: ignore
+    for bond in mol.GetBonds():
         i = bond.GetBeginAtomIdx()
         j = bond.GetEndAtomIdx()