DEV: ruff formatted

src/piqtree2/iqtree/_tree.py

@@ -133,7 +133,7 @@ def _parse_lie_model(
             tree.params[lie_model_name]["model_parameters"] = model_parameters
 
 
-def _tree_equal(node1:PhyloNode, node2:PhyloNode)->bool:
+def _tree_equal(node1: PhyloNode, node2: PhyloNode) -> bool:
     children_group1 = node1.children
     children_group2 = node2.children
 

src/piqtree2/model/_options.py

@@ -43,15 +43,18 @@ def available_models(model_type: str | None = None) -> _Table:
     template = "Available {}substitution models"
     if model_type == "dna":
         table = make_table(
-            data=_make_models(DnaModel), title=template.format("nucleotide "),
+            data=_make_models(DnaModel),
+            title=template.format("nucleotide "),
         )
     elif model_type == "protein":
         table = make_table(
-            data=_make_models(AaModel), title=template.format("protein "),
+            data=_make_models(AaModel),
+            title=template.format("protein "),
         )
     else:
         table = make_table(
-            data=_make_models(SubstitutionModel), title=template.format(""),
+            data=_make_models(SubstitutionModel),
+            title=template.format(""),
         )
 
     return table

tests/test_iqtree/test_tree_yaml.py

@@ -186,19 +186,24 @@ def test_non_lie_dna_model_motif_absent(
     non_lie_dna_with_rate_model: dict[str, Any],
 ) -> None:
     non_lie_dna_with_rate_model["ModelDNA"].pop("state_freq")
-    with pytest.raises(ParseIqTreeError, match=re.escape("IQ-TREE output malformated, motif parameters not found.")):
+    with pytest.raises(
+        ParseIqTreeError,
+        match=re.escape("IQ-TREE output malformated, motif parameters not found."),
+    ):
         _ = _process_tree_yaml(non_lie_dna_with_rate_model, ["a", "b", "c", "d"])
 
 
 def test_non_lie_dna_model_rate_absent(
     non_lie_dna_with_rate_model: dict[str, Any],
 ) -> None:
     non_lie_dna_with_rate_model["ModelDNA"].pop("rates")
-    with pytest.raises(ParseIqTreeError,match=re.escape("IQ-TREE output malformated, rate parameters not found.")):
+    with pytest.raises(
+        ParseIqTreeError,
+        match=re.escape("IQ-TREE output malformated, rate parameters not found."),
+    ):
         _ = _process_tree_yaml(non_lie_dna_with_rate_model, ["a", "b", "c", "d"])
 
 
-
 def test_lie_dna_model(
     lie_dna_model: dict[str, Any],
 ) -> None:
@@ -215,14 +220,22 @@ def test_lie_dna_model_motif_absent(
     lie_dna_model: dict[str, Any],
 ) -> None:
     lie_dna_model["ModelLieMarkovRY2.2b"].pop("state_freq")
-    with pytest.raises(ParseIqTreeError, match=re.escape("IQ-TREE output malformated, motif parameters not found.")):
+    with pytest.raises(
+        ParseIqTreeError,
+        match=re.escape("IQ-TREE output malformated, motif parameters not found."),
+    ):
         _ = _process_tree_yaml(lie_dna_model, ["a", "b", "c", "d"])
 
 
-@pytest.mark.parametrize(("candidate", "expected"), [("((a:1.0,b:0.9),c:0.8);", True),
-                                                 ("((a:0.9,b:0.9),c:0.8);", False),
-                                                 ("((a:1.0,c:0.8),b:0.9);", False)])
-def test_tree_equal(candidate:str, expected:bool) -> None:
+@pytest.mark.parametrize(
+    ("candidate", "expected"),
+    [
+        ("((a:1.0,b:0.9),c:0.8);", True),
+        ("((a:0.9,b:0.9),c:0.8);", False),
+        ("((a:1.0,c:0.8),b:0.9);", False),
+    ],
+)
+def test_tree_equal(candidate: str, expected: bool) -> None:
     tree = make_tree("((a:1.0,b:0.9),c:0.8);")
     candidate = make_tree(candidate)
     assert _tree_equal(tree, candidate) == expected

tests/test_model/test_substitution_model.py

@@ -45,7 +45,8 @@ def test_model_type(
     ],
 )
 def test_get_substitution_model(
-    substitution_model: SubstitutionModel | str, iqtree_str: str,
+    substitution_model: SubstitutionModel | str,
+    iqtree_str: str,
 ) -> None:
     out = get_substitution_model(substitution_model)
     assert isinstance(out, SubstitutionModel)