reformat with ruff

Author: sfluegel05

chebi_utils/dataset_builder.py

@@ -36,6 +36,7 @@ def _count_molecules_per_class(closure: nx.DiGraph, mol_ids: set[str]) -> dict[s
         counts[mid] += 1
     return dict(counts)
 
+
 def build_labeled_dataset(
     chebi_graph: nx.DiGraph,
     molecules: pd.DataFrame,

chebi_utils/obo_extractor.py

@@ -115,6 +115,7 @@ def build_chebi_graph(filepath: str | Path) -> nx.DiGraph:
 
     return graph
 
+
 def get_hierarchy_subgraph(chebi_graph: nx.DiGraph) -> nx.Graph:
     """Subgraph of ChEBI including only edges corresponding to hierarchical relations (is_a). Also removes nodes that are not connected by any is_a edges to other nodes."""
     return chebi_graph.edge_subgraph(

chebi_utils/sdf_extractor.py

@@ -166,6 +166,7 @@ def extract_molecules(filepath: str | Path) -> pd.DataFrame:
 
     return df
 
+
 if __name__ == "__main__":
     df = extract_molecules("data/chebi.sdf.gz")
-    print(df.head())
+    print(df.head())

tests/test_dataset_builder.py

@@ -56,6 +56,7 @@ def simple_molecules() -> pd.DataFrame:
         }
     )
 
+
 class TestBuildLabeledDataset:
     def test_returns_dataframe_with_base_columns(self, simple_graph, simple_molecules):
         df, labels = build_labeled_dataset(simple_graph, simple_molecules, min_molecules=2)

tests/test_obo_extractor.py

@@ -41,7 +41,9 @@ def test_node_name_attribute(self):
 
     def test_smiles_extracted_from_property_value(self):
         g = build_chebi_graph(SAMPLE_OBO)
-        expected = "COc1cc2c3cc1Oc1c(O)c(OC)cc4c1[C@H](Cc1ccc(O)c(c1)Oc1ccc(cc1)C[C@@H]3N(C)CC2)N(C)CC4"
+        expected = (
+            "COc1cc2c3cc1Oc1c(O)c(OC)cc4c1[C@H](Cc1ccc(O)c(c1)Oc1ccc(cc1)C[C@@H]3N(C)CC2)N(C)CC4"
+        )
         assert g.nodes["10"]["smiles"] == expected
 
     def test_smiles_none_when_absent(self):