Auto-update pre-commit hooks

Author: rdguha1995

.pre-commit-config.yaml

@@ -2,21 +2,21 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.1.13
+  rev: v0.11.12
   hooks:
   - id: ruff
     args: [--fix]
   - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v5.0.0
   hooks:
   - id: check-yaml
   - id: fix-encoding-pragma
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/asottile/blacken-docs
-  rev: 1.16.0
+  rev: 1.19.1
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
@@ -29,17 +29,17 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.8.0
+  rev: v1.16.0
   hooks:
   - id: mypy
     files: ^src/
     additional_dependencies:
     - tokenize-rt==4.1.0
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
+  rev: v2.4.1
   hooks:
   - id: codespell
-    stages: [commit, commit-msg]
+    stages: [pre-commit, commit-msg]
     args: [--ignore-words-list, 'titel,statics,ba,nd,te,atomate']
     types_or: [python, rst, markdown]

src/atomate2/cli/dev.py

@@ -1,6 +1,5 @@
 """Module containing command line scripts for developers."""
 
-
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

src/atomate2/common/schemas/cclib.py

@@ -67,7 +67,7 @@ class TaskDocument(MoleculeMetadata, extra="allow"):  # type: ignore[call-arg]
     @classmethod
     @requires(cclib, "The cclib TaskDocument requires cclib to be installed.")
     def from_logfile(
-        cls: type[_T],
+        cls,
         dir_name: Union[str, Path],
         logfile_extensions: Union[str, list[str]],
         store_trajectory: bool = False,

src/atomate2/common/schemas/elastic.py

@@ -1,4 +1,5 @@
 """Schemas for elastic tensor fitting and related properties."""
+
 from copy import deepcopy
 from typing import Optional
 

src/atomate2/cp2k/schemas/task.py

@@ -1,4 +1,5 @@
 """Core definition of a CP2K task document."""
+
 import logging
 from collections import OrderedDict
 from pathlib import Path
@@ -305,7 +306,7 @@ class TaskDocument(StructureMetadata, MoleculeMetadata):
 
     @classmethod
     def from_directory(
-        cls: type[_T],
+        cls,
         dir_name: Union[Path, str],
         volumetric_files: tuple[str, ...] = _VOLUMETRIC_FILES,
         store_additional_json: bool = SETTINGS.CP2K_STORE_ADDITIONAL_JSON,

src/atomate2/utils/file_client.py

@@ -1,6 +1,5 @@
 """Tools for remote file IO using paramiko."""
 
-
 from __future__ import annotations
 
 import shutil
@@ -403,9 +402,10 @@ def gzip(
                 )
 
         if host is None:
-            with open(path, "rb") as f_in, GzipFile(
-                path_gz, "wb", compresslevel=compresslevel
-            ) as f_out:
+            with (
+                open(path, "rb") as f_in,
+                GzipFile(path_gz, "wb", compresslevel=compresslevel) as f_out,
+            ):
                 shutil.copyfileobj(f_in, f_out)
             shutil.copystat(path, path_gz)
             path.unlink()

src/atomate2/vasp/flows/phonons.py

@@ -203,10 +203,12 @@ def make(
                 "structure"
             )
 
-        if (
-            self.kpath_scheme
-            not in "seekpath hinuma setyawan_curtarolo latimer_munro".split()
-        ):
+        if self.kpath_scheme not in [
+            "seekpath",
+            "hinuma",
+            "setyawan_curtarolo",
+            "latimer_munro",
+        ]:
             raise ValueError("kpath scheme is not implemented")
 
         jobs = []

src/atomate2/vasp/sets/core.py

@@ -597,9 +597,9 @@ def get_kpoints_updates(
             kpoints["zero_weighted_line_density"] = self.line_density
 
         elif self.mode == "uniform_dense":
-            kpoints[
-                "zero_weighted_reciprocal_density"
-            ] = self.zero_weighted_reciprocal_density
+            kpoints["zero_weighted_reciprocal_density"] = (
+                self.zero_weighted_reciprocal_density
+            )
 
         added_kpoints = deepcopy(self.added_kpoints)
         if vasprun is not None and self.mode == "gap":

tests/common/schemas/test_cclib.py

@@ -73,9 +73,10 @@ def test_cclib_taskdoc(test_dir):
     # Let's try a volumetric analysis
     # We'll gunzip the .cube.gz file because cclib can't read cube.gz files yet.
     # Can remove the gzip part when https://github.com/cclib/cclib/issues/108 is closed.
-    with gzip.open(p / "psi_test.cube.gz", "r") as f_in, open(
-        p / "psi_test.cube", "wb"
-    ) as f_out:
+    with (
+        gzip.open(p / "psi_test.cube.gz", "r") as f_in,
+        open(p / "psi_test.cube", "wb") as f_out,
+    ):
         shutil.copyfileobj(f_in, f_out)
     doc = TaskDocument.from_logfile(p, "psi_test.out", analysis=["Bader"]).dict()
     os.remove(p / "psi_test.cube")

tests/conftest.py

@@ -50,7 +50,7 @@ def clean_dir(debug_mode):
         shutil.rmtree(new_path)
 
 
-@pytest.fixture()
+@pytest.fixture
 def tmp_dir():
     """Same as clean_dir but is fresh for every test"""
 
@@ -79,7 +79,7 @@ def lpad(database, debug_mode):
             lpad.db[coll].drop()
 
 
-@pytest.fixture()
+@pytest.fixture
 def memory_jobstore():
     store = JobStore(MemoryStore(), additional_stores={"data": MemoryStore()})
     store.connect()
@@ -92,7 +92,7 @@ def log_to_stdout_auto_use():
     initialize_logger()
 
 
-@pytest.fixture()
+@pytest.fixture
 def si_structure(test_dir):
     return Structure.from_file(test_dir / "structures" / "Si.cif")