fix linting

prolif/interactions/base.py

@@ -67,11 +67,9 @@ def metadata(self, lig_res, prot_res, lig_indices, prot_indices, **data):
                 "protein": prot_indices,
             },
             "parent_indices": {
-                "ligand": tuple(
-                    [get_mapindex(lig_res, index) for index in lig_indices],
-                ),
+                "ligand": tuple(get_mapindex(lig_res, index) for index in lig_indices),
                 "protein": tuple(
-                    [get_mapindex(prot_res, index) for index in prot_indices],
+                    get_mapindex(prot_res, index) for index in prot_indices
                 ),
             },
             **data,

pyproject.toml

@@ -105,9 +105,7 @@ exclude = [
     "dist",
     "site-packages",
 ]
-
-[tool.ruff.format]
-exclude = ["*.ipynb"]
+extend-exclude = ["*.ipynb"]
 
 [tool.ruff.lint]
 select = [
@@ -150,7 +148,8 @@ select = [
 ]
 ignore = [
     "PLW1514", "PTH123", "PLR0904", "PLR0911", "PLR0913", "PLR0914", "PLR0915",
-    "PLR0916", "PLR0917", "PLR2004", "PLR6301", "PD901", "PT018", "FURB103", "COM812",
+    "PLR0916", "PLR0917", "PLR2004", "PLR6301", "PD901", "PT001", "PT018", "FURB103",
+    "COM812",
     # typing incompatible with 3.9
     "UP035", "UP006", "UP007",
 ]

tests/test_ifp.py

@@ -14,8 +14,8 @@ def ifp(u, ligand_ag, protein_ag) -> IFP:
 
 def test_ifp_indexing(ifp: IFP) -> None:
     lig_id, prot_id = "LIG1.G", "LEU126.A"
-    metadata1 = ifp[(ResidueId.from_string(lig_id), ResidueId.from_string(prot_id))]
-    metadata2 = ifp[(lig_id, prot_id)]
+    metadata1 = ifp[ResidueId.from_string(lig_id), ResidueId.from_string(prot_id)]
+    metadata2 = ifp[lig_id, prot_id]
     assert metadata1 is metadata2
 
 
@@ -24,7 +24,7 @@ def test_ifp_filtering(ifp: IFP) -> None:
     assert ifp[lig_id] == ifp
     assert (
         next(iter(ifp[prot_id].values()))
-        == ifp[(ResidueId.from_string(lig_id), ResidueId.from_string(prot_id))]
+        == ifp[ResidueId.from_string(lig_id), ResidueId.from_string(prot_id)]
     )
 
 

tests/test_interactions.py

@@ -139,7 +139,7 @@ def detect(self):
         assert old != new
         # fix dummy Hydrophobic class being reused in later unrelated tests
 
-        class Hydrophobic(prolif.interactions.Hydrophobic):  # noqa: F811
+        class Hydrophobic(prolif.interactions.Hydrophobic):
             __doc__ = prolif.interactions.Hydrophobic.__doc__
 
     def test_error_no_detect(self):

tests/test_utils.py

@@ -199,13 +199,13 @@ def test_to_df(ifp):
     assert df.dtypes.iloc[0].type is np.bool_
     assert df.index.name == "Frame"
     assert ("LIG", "ALA1", "A") in df.columns
-    assert df[("LIG", "ALA1", "A")][0] is np.bool_(True)
+    assert df["LIG", "ALA1", "A"][0] is np.bool_(True)
     assert ("LIG", "ALA1", "B") in df.columns
-    assert df[("LIG", "ALA1", "B")][0] is np.bool_(False)
+    assert df["LIG", "ALA1", "B"][0] is np.bool_(False)
     assert ("LIG", "ALA1", "C") not in df.columns
     assert ("LIG", "GLU2", "A") not in df.columns
     assert ("LIG", "ASP3", "B") in df.columns
-    assert df[("LIG", "ASP3", "B")][0] is np.bool_(False)
+    assert df["LIG", "ASP3", "B"][0] is np.bool_(False)
 
 
 @pytest.mark.parametrize(
@@ -219,9 +219,9 @@ def test_to_df(ifp):
 def test_to_df_dtype(dtype, ifp):
     df = to_dataframe(ifp, ["A", "B", "C"], dtype=dtype)
     assert df.dtypes.iloc[0].type is dtype
-    assert df[("LIG", "ALA1", "A")][0] == dtype(True)
-    assert df[("LIG", "ALA1", "B")][0] == dtype(False)
-    assert df[("LIG", "ASP3", "B")][0] == dtype(False)
+    assert df["LIG", "ALA1", "A"][0] == dtype(True)
+    assert df["LIG", "ALA1", "B"][0] == dtype(False)
+    assert df["LIG", "ASP3", "B"][0] == dtype(False)
 
 
 def test_to_df_drop_empty(ifp):
@@ -238,7 +238,7 @@ def test_to_df_no_interaction_in_first_frame(ifp_single):
 def test_to_df_count(ifp_count):
     df = to_dataframe(ifp_count, ["A", "B", "C"], count=True)
     assert df[df > 1].any().any()
-    value = df[("LIG", "ALA1", "A")][0]
+    value = df["LIG", "ALA1", "A"][0]
     assert value.dtype == np.uint8
     assert value == 2