unignore ruff FBT001 FBT002 and fix existing errors

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.4
+    rev: v0.4.8
     hooks:
       - id: ruff
         args: [--fix]
@@ -26,7 +26,7 @@ repos:
       - id: mypy
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
@@ -48,6 +48,6 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.362
+    rev: v1.1.366
     hooks:
       - id: pyright

matcalc/elasticity.py

@@ -25,6 +25,7 @@ class ElasticityCalc(PropCalc):
     def __init__(
         self,
         calculator: Calculator,
+        *,
         norm_strains: Sequence[float] | float = (-0.01, -0.005, 0.005, 0.01),
         shear_strains: Sequence[float] | float = (-0.06, -0.03, 0.03, 0.06),
         fmax: float = 0.1,

matcalc/eos.py

@@ -23,6 +23,7 @@ class EOSCalc(PropCalc):
     def __init__(
         self,
         calculator: Calculator,
+        *,
         optimizer: Optimizer | str = "FIRE",
         max_steps: int = 500,
         max_abs_strain: float = 0.1,

matcalc/neb.py

@@ -23,6 +23,7 @@ class NEBCalc(PropCalc):
     def __init__(
         self,
         images: list[Structure],
+        *,
         calculator: str | Calculator = "M3GNet-MP-2021.2.8-DIRECT-PES",
         optimizer: str | Optimizer = "BFGS",
         traj_folder: str | None = None,
@@ -63,6 +64,7 @@ def from_end_images(
         start_struct: Structure,
         end_struct: Structure,
         calculator: str | Calculator = "M3GNet-MP-2021.2.8-DIRECT-PES",
+        *,
         n_images: int = 7,
         interpolate_lattices: bool = False,
         autosort_tol: float = 0.5,

matcalc/phonon.py

@@ -67,7 +67,8 @@ class PhononCalc(PropCalc):
     write_phonon: bool | str | Path = True
 
     def __post_init__(self) -> None:
-        # map True to canonical default path,False to "" and Path to str
+        """Set default paths for where to save output files."""
+        # map True to canonical default path, False to "" and Path to str
         for key, val, default_path in (
             ("write_force_constants", self.write_force_constants, "force_constants"),
             ("write_band_structure", self.write_band_structure, "band_structure.yaml"),

matcalc/relaxation.py

@@ -73,6 +73,7 @@ class RelaxCalc(PropCalc):
     def __init__(
         self,
         calculator: Calculator,
+        *,
         optimizer: Optimizer | str = "FIRE",
         max_steps: int = 500,
         traj_file: str | None = None,

pyproject.toml

@@ -1,7 +1,3 @@
-[build-system]
-requires = ["oldest-supported-numpy", "setuptools>=58.0.3"]
-build-backend = "setuptools.build_meta"
-
 [project]
 name = "matcalc"
 authors = [
@@ -48,6 +44,10 @@ models = ["chgnet", "mace-torch", "matgl>=0.9.0"]
 [tool.setuptools]
 packages = ["matcalc"]
 
+[build-system]
+requires = ["oldest-supported-numpy", "setuptools>=58.0.3"]
+build-backend = "setuptools.build_meta"
+
 [tool.ruff]
 target-version = "py39"
 line-length = 120
@@ -59,15 +59,12 @@ ignore = [
     "ANN101",
     "ANN401",
     "COM812",  # trailing comma missing
-    "D105",    # Missing docstring in magic method
     "D205",    # 1 blank line required between summary line and description
     "D212",    # Multi-line docstring summary should start at the first line
     "EM101",
     "EM102",
-    "FBT001",
-    "FBT002",
     "ISC001",
-    "PLR",     # pylint refactor
+    "PLR0913", # too many arguments
     "PLW0603", # Using the global statement to update variables is discouraged
     "PTH",     # prefer Path to os.path
     "SIM105",  # Use contextlib.suppress(OSError) instead of try-except-pass
@@ -83,7 +80,7 @@ docstring-code-format = true
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]
 "tasks.py" = ["ANN", "D", "T203"]
-"tests/*" = ["D", "INP001", "N802", "N803", "S101"]
+"tests/*" = ["", "D", "INP001", "N802", "N803", "S101"]
 
 [tool.pytest.ini_options]
 addopts = "--durations=30 --quiet -rXs --color=yes -p no:warnings"

tasks.py

@@ -128,7 +128,7 @@ def release_github(ctx):  # noqa: ARG001
 
 
 @task
-def release(ctx, notest: bool = False) -> None:
+def release(ctx, notest: bool = False) -> None:  # noqa: FBT001, FBT002
     ctx.run("rm -r dist build matcalc.egg-info", warn=True)
     if not notest:
         ctx.run("pytest tests")