Fix WalltimeHandler crash on incomplete OUTCAR + new test (#412)

* Fix WalltimeHandler crash on incomplete OUTCAR + new test

* fix lints

* update legacy ruff pre-commit hook name

Author: janosh

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.14.7
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
@@ -30,15 +30,15 @@ repos:
     rev: v2.4.1
     hooks:
       - id: codespell
-        stages: [ commit-msg ]
-        exclude_types: [ html ]
-        additional_dependencies: [ tomli ] # needed to read pyproject.toml below py3.11
+        stages: [commit-msg]
+        exclude_types: [html]
+        additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
 
   - repo: https://github.com/MarcoGorelli/cython-lint
     rev: v0.18.1
     hooks:
       - id: cython-lint
-        args: [ --no-pycodestyle ]
+        args: [--no-pycodestyle]
       - id: double-quote-cython-strings
 
   - repo: https://github.com/adamchainz/blacken-docs
@@ -55,13 +55,13 @@ repos:
         # MD033: no inline HTML
         # MD041: first line in a file should be a top-level heading
         # MD025: single title
-        args: [ --disable, MD013, MD024, MD025, MD033, MD041, "--" ]
+        args: [--disable, MD013, MD024, MD025, MD033, MD041, '--']
 
   - repo: https://github.com/kynan/nbstripout
     rev: 0.8.2
     hooks:
       - id: nbstripout
-        args: [ --drop-empty-cells, --keep-output ]
+        args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
     rev: v1.1.407

pyproject.toml

@@ -18,7 +18,15 @@ authors = [
 ]
 maintainers = [{ name = "Shyue Ping Ong" }]
 readme = "README.md"
-keywords = ["jit", "job", "just-in-time", "management", "vasp", "nwchem", "qchem"]
+keywords = [
+    "jit",
+    "job",
+    "just-in-time",
+    "management",
+    "nwchem",
+    "qchem",
+    "vasp",
+]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Science/Research",
@@ -38,8 +46,10 @@ requires-python = ">=3.10"
 dependencies = ["monty>=2.0.6", "psutil", "ruamel.yaml>=0.15.6"]
 
 [project.optional-dependencies]
-matsci = ["pymatgen"]  # Error handlers and jobs for materials simulations, e.g., VASP, Nwchem, qchem, etc.
-gaussian = ["pymatgen", "matplotlib"]
+matsci = [
+    "pymatgen",
+] # Error handlers and jobs for materials simulations, e.g., VASP, Nwchem, qchem, etc.
+gaussian = ["matplotlib", "pymatgen"]
 error-statistics = ["sentry-sdk>=0.8.0"]
 
 [project.scripts]
@@ -63,55 +73,56 @@ line-length = 120
 
 [tool.ruff.lint]
 select = [
-    "B", # flake8-bugbear
-    "C4", # flake8-comprehensions
-    "D", # pydocstyle
-    "E", # pycodestyle error
-    "EXE", # flake8-executable
-    "F", # pyflakes
-    "FA", # flake8-future-annotations
-    "FLY", # flynt
-    "I", # isort
-    "ICN", # flake8-import-conventions
-    "ISC", # flake8-implicit-str-concat
-    "PD", # pandas-vet
+    "B",    # flake8-bugbear
+    "C4",   # flake8-comprehensions
+    "D",    # pydocstyle
+    "E",    # pycodestyle error
+    "EXE",  # flake8-executable
+    "F",    # pyflakes
+    "FA",   # flake8-future-annotations
+    "FLY",  # flynt
+    "I",    # isort
+    "ICN",  # flake8-import-conventions
+    "ISC",  # flake8-implicit-str-concat
+    "PD",   # pandas-vet
     "PERF", # perflint
-    "PIE", # flake8-pie
-    "PL", # pylint
-    "PT", # flake8-pytest-style
-    "PYI", # flakes8-pyi
-    "Q", # flake8-quotes
-    "RET", # flake8-return
-    "RSE", # flake8-raise
-    "RUF", # Ruff-specific rules
-    "SIM", # flake8-simplify
+    "PIE",  # flake8-pie
+    "PL",   # pylint
+    "PT",   # flake8-pytest-style
+    "PYI",  # flakes8-pyi
+    "Q",    # flake8-quotes
+    "RET",  # flake8-return
+    "RSE",  # flake8-raise
+    "RUF",  # Ruff-specific rules
+    "SIM",  # flake8-simplify
     "SLOT", # flake8-slots
-    "TCH", # flake8-type-checking
-    "TID", # tidy imports
-    "TID", # flake8-tidy-imports
-    "UP", # pyupgrade
-    "W", # pycodestyle warning
-    "YTT", # flake8-2020
+    "TCH",  # flake8-type-checking
+    "TID",  # tidy imports
+    "TID",  # flake8-tidy-imports
+    "UP",   # pyupgrade
+    "W",    # pycodestyle warning
+    "YTT",  # flake8-2020
 ]
 ignore = [
-    "B023", # Function definition does not bind loop variable
-    "B028", # No explicit stacklevel keyword argument found
-    "B904", # Within an except clause, raise exceptions with ...
-    "C408", # unnecessary-collection-call
+    "B023",    # Function definition does not bind loop variable
+    "B028",    # No explicit stacklevel keyword argument found
+    "B904",    # Within an except clause, raise exceptions with ...
+    "C408",    # unnecessary-collection-call
     "COM812",
-    "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
+    "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
     "ISC001",
-    "PD011", # pandas-use-of-dot-values
-    "PD901", # pandas-df-variable-name
+    "PD011",   # pandas-use-of-dot-values
+    "PD901",   # pandas-df-variable-name
     "PERF203", # try-except-in-loop
-    "PLR", # pylint refactor
+    "PLC0415", # import-outside-top-level (used for performance/optional deps)
+    "PLR",     # pylint refactor
     "PLW2901", # Outer for loop variable overwritten by inner assignment target
-    "PT013", # pytest-incorrect-pytest-import
+    "PT013",   # pytest-incorrect-pytest-import
     "PTH",
-    "RUF012", # Disable checks for mutable class args
-    "SIM105", # Use contextlib.suppress(OSError) instead of try-except-pass
+    "RUF012",  # Disable checks for mutable class args
+    "SIM105",  # Use contextlib.suppress(OSError) instead of try-except-pass
 ]
 pydocstyle.convention = "google"
 isort.split-on-trailing-comma = false
@@ -163,22 +174,18 @@ exclude = ["**/tests"]
 
 [dependency-groups]
 dev = [
+    "invoke>=2.2.0",
+    "mypy>=1.15.0",
+    "myst-parser>=4.0.1",
     "pre-commit>=4.2.0",
     "pymatgen>=2025.5.16",
-    "pytest>=8.3.5",
     "pytest-cov>=6.0.0",
-    "mypy>=1.15.0",
+    "pytest>=8.3.5",
     "ruff>=0.11.2",
-    "invoke>=2.2.0",
-    "sphinx>=8.1.3",
-    "myst-parser>=4.0.1",
     "sphinx-markdown-builder>=0.6.8",
+    "sphinx>=8.1.3",
 ]
-lint = [
-    "pre-commit>=4.2.0",
-    "mypy>=1.15.0",
-    "ruff>=0.11.2",
-]
+lint = ["mypy>=1.15.0", "pre-commit>=4.2.0", "ruff>=0.11.2"]
 
 [tool.setuptools.package-data]
 custodian = ["py.typed"]

src/custodian/utils.py

@@ -72,7 +72,7 @@ class tracked_lru_cache:
     Allows Custodian to clear the cache after all the checks have been performed.
     """
 
-    cached_functions: ClassVar = set()
+    cached_functions: ClassVar[set] = set()
 
     def __init__(self, func) -> None:
         """

src/custodian/vasp/handlers.py

@@ -1800,7 +1800,10 @@ def check(self, directory="./") -> bool:
         if self.wall_time:
             run_time = datetime.datetime.now() - self.start_time
             total_secs = run_time.total_seconds()
-            outcar = load_outcar(os.path.join(directory, "OUTCAR"))
+            try:
+                outcar = load_outcar(os.path.join(directory, "OUTCAR"))
+            except Exception:  # Can't perform check if Outcar not valid (e.g. file being written)
+                return False
             if not self.electronic_step_stop:
                 # Determine max time per ionic step.
                 outcar.read_pattern({"timings": r"LOOP\+.+real time(.+)"}, postprocess=float)

tests/qchem/test_jobs.py

@@ -778,7 +778,7 @@ def test_OptFF(self) -> None:
             QCInput.from_file(f"{TEST_DIR}/5690_frag18/mol.qin.freq_2").as_dict()
             == QCInput.from_file(os.path.join(SCR_DIR, "mol.qin")).as_dict()
         )
-        with pytest.raises(ValueError, match="ERROR: Can't deal with multiple neg frequencies yet! Exiting..."):
+        with pytest.raises(ValueError, match=r"ERROR: Can't deal with multiple neg frequencies yet! Exiting\.\.\."):
             next(job)
 
 

tests/vasp/test_handlers.py

@@ -1016,6 +1016,24 @@ def test_check_and_correct(self) -> None:
             assert content == "LABORT = .TRUE."
         os.remove("STOPCAR")
 
+    def test_check_with_malformed_outcar(self, tmp_path: Path) -> None:
+        """Test that WalltimeHandler.check() returns False on malformed OUTCAR.
+
+        This can happen when VASP is mid-write and the file contains incomplete
+        data like a standalone '-' instead of a float. See
+        https://github.com/materialsproject/pymatgen/issues/2251
+        """
+        os.chdir(tmp_path)
+
+        # Create a malformed OUTCAR that would cause parsing to fail
+        with open("OUTCAR", "w") as file:
+            file.write("Free energy of the ion-electron system (eV)\n")
+            file.write("  alpha Z        PSCENC =         -\n")  # incomplete value
+
+        handler = WalltimeHandler(wall_time=3600, buffer_time=120)
+        # Should return False (not crash) when OUTCAR parsing fails
+        assert handler.check() is False
+
     @classmethod
     def tearDown(cls) -> None:
         os.environ.pop("CUSTODIAN_WALLTIME_START", None)

tests/vasp/test_io.py

@@ -9,8 +9,6 @@
 @pytest.fixture(autouse=True)
 def _clear_tracked_cache() -> None:
     """Clear the cache of the stored functions between the tests."""
-    from custodian.utils import tracked_lru_cache
-
     tracked_lru_cache.tracked_cache_clear()
 
 

tests/vasp/test_jobs.py

@@ -305,7 +305,7 @@ def test_terminate_exception_during_graceful_termination(self):
         self.mock_process.terminate.side_effect = OSError("Permission denied")
 
         # Act & Assert
-        with pytest.raises(OSError):
+        with pytest.raises(OSError, match="Permission denied"):
             self.vasp_job.terminate()
 
         self.mock_process.terminate.assert_called_once()
@@ -323,7 +323,7 @@ def test_terminate_exception_during_force_kill(self):
         self.mock_process.kill.return_value = None
 
         # Act & Assert
-        with pytest.raises(OSError):
+        with pytest.raises(OSError, match="Process not found"):
             self.vasp_job.terminate()
 
         self.mock_process.terminate.assert_called_once()

tests/vasp/test_validators.py

@@ -3,15 +3,14 @@
 
 import pytest
 
+from custodian.utils import tracked_lru_cache
 from custodian.vasp.validators import VaspAECCARValidator, VaspFilesValidator, VaspNpTMDValidator, VasprunXMLValidator
 from tests.conftest import TEST_FILES
 
 
 @pytest.fixture(autouse=True)
 def _clear_tracked_cache() -> None:
     """Clear the cache of the stored functions between the tests."""
-    from custodian.utils import tracked_lru_cache
-
     tracked_lru_cache.tracked_cache_clear()