DEV: resolve ruff issues

pyproject.toml

@@ -48,8 +48,8 @@ piqtree_random_trees = "piqtree2._app:piqtree_random_trees"
 version = {attr = "piqtree2.__version__"}
 
 [tool.ruff]
-# Exclude a variety of commonly ignored directories.
 exclude = [
+    "iqtree2",
     ".bzr",
     ".direnv",
     ".eggs",
@@ -89,7 +89,7 @@ target-version = "py39"
 # Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
 # McCabe complexity (`C901`) by default.
 select = ["ALL"]
-ignore = ["EXE002"]
+ignore = ["EXE002", "FA100", "E501", "D"]
 
 # Allow fix for all enabled rules (when `--fix`) is provided.
 fixable = ["ALL"]
@@ -102,6 +102,16 @@ dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 "tests/**/*.py" = [
     "S101", # asserts allowed in tests...
     "INP001", # __init__.py files are not required...
+    "ANN",
+    "N802",
+    "N803"
+]
+"noxfile.py" = [
+    "S101", # asserts allowed in tests...
+    "INP001", # __init__.py files are not required...
+    "ANN",
+    "N802",
+    "N803"
 ]
 
 [tool.ruff.format]

tests/conftest.py

@@ -8,6 +8,6 @@ def DATA_DIR():
     return pathlib.Path(__file__).parent / "data"
 
 
-@pytest.fixture(scope="function")
+@pytest.fixture()
 def tmp_dir(tmp_path_factory):
     return tmp_path_factory.mktemp("cli")

tests/test_app.py

@@ -2,7 +2,7 @@
 from cogent3 import get_app, load_aligned_seqs, make_tree
 
 
-@pytest.fixture
+@pytest.fixture()
 def three_otu(DATA_DIR):
     aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
     aln = aln.take_seqs(["Human", "Rhesus", "Mouse"])

tests/test_fit_tree.py

@@ -3,7 +3,7 @@
 from cogent3 import get_app, load_aligned_seqs, make_tree
 
 
-@pytest.fixture
+@pytest.fixture()
 def three_otu(DATA_DIR):
     aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
     aln = aln.take_seqs(["Human", "Rhesus", "Mouse"])

tests/test_options.py

@@ -1,10 +1,9 @@
 # testing the display of functions
 import pytest
-
 from piqtree2 import available_models
 
 
-@pytest.mark.parametrize("model_type", (None, "nucleotide", "protein"))
+@pytest.mark.parametrize("model_type", [(None, "nucleotide", "protein")])
 def test_available_models(model_type):
     table = available_models(model_type)
     assert table.shape[0] > 0