chore: ruff

Author: nscorley

docs/examples/dataset_exploration.py

@@ -231,9 +231,7 @@ def simple_loading_fn(raw_data: Any) -> dict:
     data=interfaces_df,
     name="interfaces_dataset",
     # We use a pre-built loader that takes in a list of column names and returns a loader function
-    loader=create_loader_with_query_pn_units(
-        pn_unit_iid_colnames=["pn_unit_1_iid", "pn_unit_2_iid"]
-    ),
+    loader=create_loader_with_query_pn_units(pn_unit_iid_colnames=["pn_unit_1_iid", "pn_unit_2_iid"]),
     transform=pipe,
 )
 

src/atomworks/io/tools/rdkit.py

@@ -4,7 +4,7 @@
 import io
 import logging
 from collections import Counter
-from collections.abc import Callable, Generator
+from collections.abc import Callable
 from functools import cache, wraps
 from os import PathLike
 from pathlib import Path

src/atomworks/io/utils/bonds.py

@@ -337,7 +337,7 @@ def get_struct_conn_bonds(
         `struct_conn.conn_type_id <https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_struct_conn.conn_type_id.html>`_
     """
 
-    def match_or_wildcard(array, value):
+    def match_or_wildcard(array: np.ndarray, value: str) -> np.ndarray:
         if value == "*":
             return np.ones_like(array, dtype=bool)
         return array == value
@@ -424,7 +424,7 @@ def match_or_wildcard(array, value):
         # For non-polymers, we use the auth_seq_id if available and valid (i.e., not "." or "?"); otherwise we use the label_seq_id
         # (Required to avoid ambiguity, since if using `label` only we may have multiple residue within a
         # chain with the same label_seq_id and the same res_name; see: 6MUB)
-        
+
         res_id1 = int(
             row["ptnr1_label_seq_id"]
             if ((chain_id1 in relevant_polymer_chain_identifiers) or ("ptnr1_auth_seq_id" not in row))

tests/io/tools/test_rdkit.py

@@ -13,7 +13,6 @@
     get_morgan_fingerprint_from_rdkit_mol,
     smiles_to_rdkit,
 )
-from atomworks.io.utils.ccd import atom_array_from_ccd_code
 from atomworks.io.utils.io_utils import load_any
 from tests.io.conftest import TEST_DATA_IO
 
@@ -230,7 +229,5 @@ def test_chriality_in_spoofed_rdkit_molecules():
     assert Chem.FindMolChiralCenters(mol_ala_inverted) == [(1, "R")]
 
 
-
-
 if __name__ == "__main__":
     pytest.main(["-v", "-x", __file__])