Auto-update pre-commit hooks

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.15.10
+  rev: v0.16.3
   hooks:
   - id: ruff
     args: [--fix]
@@ -33,15 +33,15 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.20.1
+  rev: v2.3.0
   hooks:
   - id: mypy
     files: ^src/
     additional_dependencies:
     - tokenize-rt==4.1.0
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.4.2
+  rev: v2.4.3
   hooks:
   - id: codespell
     stages: [pre-commit, commit-msg]

pyproject.toml

@@ -215,6 +215,7 @@ ignore = [
     "C408",    # Unnecessary (dict/list/tuple) call - remove call
     "C901",    # function too complex
     "COM812",  # trailing comma missing
+    "CPY001",  # copyright notice at top of file
     "EM",      # exception message must not use f-string literal
     "ERA001",  # found commented out code
     "FBT001",
@@ -229,6 +230,7 @@ ignore = [
     "PLR0912", # too many branches
     "PLR0913", # too many arguments
     "PLR0915", # too many local statements
+    "PLR0917", # too many positional arguments
     "PLR2004",
     "PT006",   # pytest-parametrize-names-wrong-type
     "PT013",   # pytest-incorrect-pytest-import

src/atomate2/abinit/files.py

@@ -28,7 +28,7 @@
 ALL_ABIEXTS = abi_extensions()
 
 
-def fname2ext(filepath: Path | str) -> None | str:
+def fname2ext(filepath: Path | str) -> str | None:
     """Get the abinit extension of a given filename.
 
     This will return None if no extension is found.

src/atomate2/cp2k/sets/base.py

@@ -40,7 +40,7 @@ class Cp2kInputSet(InputSet):
     def __init__(
         self,
         cp2k_input: Cp2kInput,
-        optional_files: dict | None | Literal[False] = None,
+        optional_files: dict | Literal[False] | None = None,
     ) -> None:
         """Initialize the set.
 
@@ -187,7 +187,7 @@ def get_input_set(
         self,
         structure: Structure | Molecule = None,
         prev_dir: str | Path = None,
-        optional_files: dict | None | Literal[False] = None,
+        optional_files: dict | Literal[False] | None = None,
     ) -> Cp2kInputSet:
         """Get a CP2K input set.
 

src/atomate2/jdftx/sets/base.py

@@ -64,7 +64,7 @@ class JdftxInputGenerator(InputGenerator):
     user_settings: dict = field(default_factory=dict)
     coulomb_truncation: bool = False
     auto_kpoint_density: int = 1000
-    potential: None | float = None
+    potential: float | None = None
     calc_type: str = "bulk"
     pseudopotentials: str = "GBRV"
     config_dict: dict = field(default_factory=lambda: _GENERATION_CONFIG)

src/atomate2/openmm/utils.py

@@ -181,9 +181,11 @@ def generate_opls_xml(
 
                 # Run LigParGen via Shifter / Docker / Apptainer
                 lpg_cmd = [
-                    f"ligpargen -n {name} -p {name} "
-                    f"-r {name} -c {charge} -o {checkopt} "
-                    f"-cgen {charge_method} -s '{smiles}'"
+                    (
+                        f"ligpargen -n {name} -p {name} "
+                        f"-r {name} -c {charge} -o {checkopt} "
+                        f"-cgen {charge_method} -s '{smiles}'"
+                    )
                 ]
                 run_container = (
                     f"{os.environ['CONTAINER_SOFTWARE']} "

src/atomate2/vasp/flows/ferroelectric.py

@@ -50,7 +50,7 @@ class FerroelectricMaker(Maker):
 
     name: str = "ferroelectric"
     nimages: int = 8
-    relax_maker: BaseVaspMaker | None | tuple = field(
+    relax_maker: BaseVaspMaker | tuple | None = field(
         default_factory=lambda: DoubleRelaxMaker.from_relax_maker(RelaxMaker())
     )
     lcalcpol_maker: BaseVaspMaker = field(default_factory=PolarizationMaker)

tests/forcefields/conftest.py

@@ -44,7 +44,7 @@ def get_deepmd_pretrained_model_path(test_dir: Path) -> Path:
     file_url = "https://raw.github.com/sliutheorygroup/UniPero/main/model/graph.pb"
     local_path = tempfile.NamedTemporaryFile(suffix=".pb")  # noqa : SIM115
     ref_md5 = "2814ae7f2eb1c605dd78f2964187de40"
-    _, http_message = urllib.request.urlretrieve(file_url, local_path.name)  # noqa: S310
+    _, http_message = urllib.request.urlretrieve(file_url, local_path.name)
     if "Content-Type: text/html" in http_message:
         raise RuntimeError(f"Failed to download from: {file_url}")