Update precommit

.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: v0.4.10
+  rev: v0.5.2
   hooks:
   - id: ruff
     args: [--fix]
@@ -17,7 +17,7 @@ repos:
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/asottile/blacken-docs
-  rev: 1.16.0
+  rev: 1.18.0
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
@@ -30,7 +30,7 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.10.0
+  rev: v1.10.1
   hooks:
   - id: mypy
     files: ^src/

pyproject.toml

@@ -193,6 +193,7 @@ ignore = [
     "PTH",     # prefer Pathlib to os.path
     "RUF013",  # implicit-optional
     "S324",    # use of insecure hash function
+    "S603",    # use of insecure subprocess
     "S507",    # paramiko auto trust
     "TD",      # TODOs
     "TRY003",  # long message outside exception class

src/atomate2/abinit/run.py

@@ -49,7 +49,7 @@ def run_abinit(
     command.append(INPUT_FILE_NAME)
 
     with open(LOG_FILE_NAME, "w") as stdout, open(STDERR_FILE_NAME, "w") as stderr:
-        process = subprocess.Popen(command, stdout=stdout, stderr=stderr)  # noqa: S603
+        process = subprocess.Popen(command, stdout=stdout, stderr=stderr)
 
         if wall_time is not None:
             while True:

src/atomate2/aims/run.py

@@ -40,7 +40,7 @@ def run_aims(
     aims_cmd = expandvars(aims_cmd)
 
     logger.info(f"Running command: {aims_cmd}")
-    return_code = subprocess.call(["/bin/bash", "-c", aims_cmd], env=os.environ)  # noqa: S603
+    return_code = subprocess.call(["/bin/bash", "-c", aims_cmd], env=os.environ)
     logger.info(f"{aims_cmd} finished running with return code: {return_code}")
 
 

src/atomate2/amset/run.py

@@ -17,7 +17,7 @@ def run_amset() -> None:
     # Run AMSET using the command line as calling from python can cause issues
     # with multiprocessing
     with open("std_out.log", "w") as f_std, open("std_err.log", "w") as f_err:
-        subprocess.call(["amset", "run"], stdout=f_std, stderr=f_err)  # noqa: S603, S607
+        subprocess.call(["amset", "run"], stdout=f_std, stderr=f_err)  # noqa: S607
 
 
 def check_converged(

src/atomate2/cli/dev.py

@@ -602,13 +602,13 @@ def save_abinit_maker(maker: Maker) -> None:
     author_mail = None
     if git:
         name = subprocess.run(
-            "git config user.name".split(),  # noqa: S603
+            "git config user.name".split(),
             capture_output=True,
             encoding="utf-8",
             check=True,
         )
         mail = subprocess.run(
-            "git config user.email".split(),  # noqa: S603
+            "git config user.email".split(),
             capture_output=True,
             encoding="utf-8",
             check=True,

src/atomate2/vasp/builders/elastic.py

@@ -148,9 +148,9 @@ def process_item(self, tasks: list[dict]) -> list[ElasticDocument]:
         grouped = _group_deformations(tasks, self.structure_match_tol)
 
         elastic_docs = []
-        for tasks in grouped:
+        for group in grouped:
             elastic_doc = _get_elastic_document(
-                tasks, self.symprec, self.fitting_method
+                group, self.symprec, self.fitting_method
             )
             elastic_docs.append(elastic_doc)
 

tests/forcefields/test_utils.py

@@ -142,7 +142,7 @@ def test_ext_load(force_field: str):
     }[force_field]
     calc_from_decode = ase_calculator(decode_dict)
     calc_from_preset = ase_calculator(str(MLFF(force_field)))
-    assert type(calc_from_decode) == type(calc_from_preset)
+    assert type(calc_from_decode) is type(calc_from_preset)
     assert calc_from_decode.name == calc_from_preset.name
     assert calc_from_decode.parameters == calc_from_preset.parameters == {}