Updated pre-commit tools and bracketed reax version

.pre-commit-config.yaml

@@ -1,37 +1,41 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
-      - id: fix-encoding-pragma
-        args: [ --remove ]
       - id: mixed-line-ending
       - id: trailing-whitespace
       - id: check-yaml
 
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.21.0
+    hooks:
+      - id: pyupgrade
+        args: [ --py310-plus ]
+
   - repo: https://github.com/ikamensh/flynt/
-    rev: '1.0.1'
+    rev: '1.0.6'
     hooks:
       - id: flynt
 
   - repo: https://github.com/psf/black
-    rev: 25.1.0
+    rev: 25.9.0
     hooks:
       - id: black
         exclude: (.*)/migrations
 
   - repo: https://github.com/pycqa/flake8
-    rev: 7.2.0
+    rev: 7.3.0
     hooks:
       - id: flake8
 
   - repo: https://github.com/pycqa/isort
-    rev: '6.0.1'
+    rev: '7.0.0'
     hooks:
       - id: isort
 
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.8.3
+    rev: 1.8.6
     hooks:
       - id: bandit
         args: [ "-c", "pyproject.toml" ]
@@ -40,7 +44,7 @@ repos:
   - repo: https://github.com/PyCQA/pylint
     # Configuration help can be found here:
     # https://pylint.pycqa.org/en/latest/user_guide/installation/pre-commit-integration.html
-    rev: v3.3.6
+    rev: v4.0.2
     hooks:
       - id: pylint
         alias: pylint-with-spelling
@@ -55,7 +59,7 @@ repos:
           )$
 
   - repo: https://github.com/commitizen-tools/commitizen
-    rev: v4.6.0
+    rev: v4.9.1
     hooks:
       - id: commitizen
         stages: [ commit-msg ]
@@ -66,6 +70,6 @@ repos:
       - id: nb-clean
 
   - repo: https://github.com/pycqa/doc8
-    rev: v1.1.2
+    rev: v2.0.0
     hooks:
       - id: doc8

pyproject.toml

@@ -32,7 +32,7 @@ dependencies = [
     'orbax-checkpoint',
     'e3nn-jax',
     "equinox",
-    "reax>=0.2.0",
+    "reax>=0.2,<0.6",
     "tensorial>=0.4.2",
     "pymatgen",
 ]

src/e3response/_logging.py

@@ -2,7 +2,7 @@
 import os
 import shutil
 import tempfile
-from typing import TYPE_CHECKING, Union
+from typing import TYPE_CHECKING
 
 from typing_extensions import override
 
@@ -12,7 +12,7 @@
 
 class MlflowHandler(logging.Handler):
     def __init__(
-        self, client: "mlflow.tracking.MlflowClient", run_id: str, level: Union[int, str] = 0
+        self, client: "mlflow.tracking.MlflowClient", run_id: str, level: int | str = 0
     ) -> None:
         super().__init__(level)
         self._tempfile = None

src/e3response/data/barium_titanate.py

@@ -1,9 +1,10 @@
+from collections.abc import Callable, Iterable, Sequence
 import functools
 import logging
 import pathlib
 import re
 import tarfile
-from typing import Any, Callable, Final, Iterable, Optional, Sequence, Union
+from typing import Any, Final
 
 import ase
 import ase.io
@@ -33,13 +34,13 @@ class BtoDataModule(reax.DataModule):
     def __init__(
         self,
         r_max: float,
-        data_dir: Union[str, pathlib.Path] = "data/bto/",
+        data_dir: str | pathlib.Path = "data/bto/",
         archives: Sequence[str] = (
             "BTO_Pm-3m_5atoms_400K_3x3x3_ensemble.tar.gz",
             "BTO_Pm-3m_5atoms_800K_3x3x3.tar.gz",
         ),
         tensors: tuple[str] = ("raman_tensors", "born_charges", "dielectric"),
-        train_val_test_split: Sequence[Union[int, float]] = (0.8, 0.1, 0.1),
+        train_val_test_split: Sequence[int | float] = (0.8, 0.1, 0.1),
         batch_size: int = 64,
     ) -> None:
         """Initialize a `SiliconDataModule`.
@@ -55,14 +56,14 @@ def __init__(
         self._data_dir: Final[str] = str(data_dir)
         self._archives: Final[tuple[str, ...]] = tuple(archives)
         self._tensors = tensors
-        self._train_val_test_split: Final[Sequence[Union[int, float]]] = train_val_test_split
+        self._train_val_test_split: Final[Sequence[int | float]] = train_val_test_split
         self._batch_size: Final[int] = batch_size
 
         # State
         self.batch_size_per_device = batch_size
-        self.data_train: Optional[reax.data.Dataset] = None
-        self.data_val: Optional[reax.data.Dataset] = None
-        self.data_test: Optional[reax.data.Dataset] = None
+        self.data_train: reax.data.Dataset | None = None
+        self.data_val: reax.data.Dataset | None = None
+        self.data_test: reax.data.Dataset | None = None
 
     @override
     def setup(self, stage: "reax.Stage", /) -> None:
@@ -235,7 +236,7 @@ def get_structures(root_dir: pathlib.Path, tensors: Iterable[str]) -> list[ase.A
 
 
 def read_scf(filename) -> ase.Atoms:
-    with open(filename, "r", encoding="utf-8") as fileobj:
+    with open(filename, encoding="utf-8") as fileobj:
         _data, card_lines = espresso.read_fortran_namelist(fileobj)
 
     cell, _ = espresso.get_cell_parameters(card_lines)

src/e3response/data/qm9_nmr.py

@@ -1,21 +1,22 @@
 import collections
+from collections.abc import Callable, Sequence
 import functools
 from functools import lru_cache
 import logging
 import os
 import pathlib
 import re
 import tempfile
-from typing import Any, Callable, Final, Optional, Sequence, Union
+from typing import Any, Final
 import urllib.error
 import urllib.request
 import zipfile
 
 import ase
 import jraph
 import numpy as np
-from pymatgen.io import gaussian  # type: ignore
-import pymatgen.io.ase  # type: ignore
+from pymatgen.io import gaussian
+import pymatgen.io.ase
 import reax
 from tensorial import gcnn
 import tqdm
@@ -58,9 +59,9 @@ def __init__(
         self,
         r_max: float = 5,
         data_dir: str = "data/qm9_nmr/",
-        dataset: Union[str, Sequence[str]] = "gasphase",
-        atom_keys: Optional[Union[str, Sequence[str]]] = None,
-        limit: Optional[int] = None,
+        dataset: str | Sequence[str] = "gasphase",
+        atom_keys: str | Sequence[str] | None = None,
+        limit: int | None = None,
     ) -> None:
         """
         Initialize the QM9-NMR dataset.
@@ -131,7 +132,7 @@ def __init__(
                 try:
                     with zipfile.ZipFile(archive_path, "r") as zip_ref:
                         zip_ref.testzip()
-                except (zipfile.BadZipFile, zipfile.LargeZipFile, IOError) as e:
+                except (zipfile.BadZipFile, zipfile.LargeZipFile, OSError) as e:
                     _LOGGER.warning(
                         "%s is corrupted or unreadable: %s, removing corrupted archive ...",
                         archive_name,
@@ -189,7 +190,7 @@ def reporthook(_block_num, block_size, total_size):
         except OSError as e:
             _LOGGER.error("Filesystem error while writing %s: %s", path, e)
 
-    def _extract_archive_zip(self, zip_path: str, limit: Optional[int] = None) -> list:
+    def _extract_archive_zip(self, zip_path: str, limit: int | None = None) -> list:
 
         structures = []
 
@@ -229,7 +230,7 @@ def _create_molecule_data(log_file):
         structure = gaussian_output.final_structure
 
         # extraction of data from .log file
-        with open(log_file, "r", encoding="utf-8") as file:
+        with open(log_file, encoding="utf-8") as file:
             log_data = file.read()
 
         shielding_pattern = (
@@ -294,12 +295,12 @@ def _create_molecule_data(log_file):
         _LOGGER.error("Error in file %s: %s", log_file, e)
         raise
 
-    except (IOError, OSError) as e:
+    except OSError as e:
         _LOGGER.error("File system error while processing %s: %s", log_file, e)
         raise
 
 
-def get_structure_and_data_from_log(log_path: pathlib.Path) -> Optional[ase.Atoms]:
+def get_structure_and_data_from_log(log_path: pathlib.Path) -> ase.Atoms | None:
     # _LOGGER.info("Parsing Gaussian .log file: %s", log_path)
 
     try:
@@ -333,7 +334,7 @@ def get_structure_and_data_from_log(log_path: pathlib.Path) -> Optional[ase.Atom
 
         return atoms
 
-    except (ValueError, IOError) as e:
+    except (ValueError, OSError) as e:
         _LOGGER.error("Parsing error for %s: %s", log_path, e)
     return None
 
@@ -350,10 +351,10 @@ def __init__(
         self,
         r_max: float = 5,
         data_dir: str = "data/qm9_nmr/",
-        dataset: Union[str, Sequence[str]] = "gasphase",
-        atom_keys: Optional[Sequence[str]] = None,
-        limit: Optional[int] = None,
-        train_val_test_split: Sequence[Union[int, float]] = (0.85, 0.05, 0.1),
+        dataset: str | Sequence[str] = "gasphase",
+        atom_keys: Sequence[str] | None = None,
+        limit: int | None = None,
+        train_val_test_split: Sequence[int | float] = (0.85, 0.05, 0.1),
         batch_size: int = 64,
     ) -> None:
         """Initialize a QM9-NMR data module.
@@ -371,19 +372,19 @@ def __init__(
 
         # Params
         self._data_dir: Final[str] = data_dir
-        self._dataset: Union[str, Sequence[str]] = dataset
-        self.dataset: Optional[Qm9NmrDataset] = None
+        self._dataset: str | Sequence[str] = dataset
+        self.dataset: Qm9NmrDataset | None = None
         self._rmax = r_max
         self._atom_keys = atom_keys
         self._limit = limit
-        self._train_val_test_split: Final[Sequence[Union[int, float]]] = train_val_test_split
+        self._train_val_test_split: Final[Sequence[int | float]] = train_val_test_split
         self._batch_size: Final[int] = batch_size
 
         # State
         self.batch_size_per_device = batch_size
-        self.data_train: Optional[reax.data.Dataset] = None
-        self.data_val: Optional[reax.data.Dataset] = None
-        self.data_test: Optional[reax.data.Dataset] = None
+        self.data_train: reax.data.Dataset | None = None
+        self.data_val: reax.data.Dataset | None = None
+        self.data_test: reax.data.Dataset | None = None
 
     @override
     def setup(self, stage: "reax.Stage", /) -> None:

src/e3response/train.py

@@ -1,6 +1,5 @@
 import logging
 import pathlib
-from typing import Optional
 
 import hydra
 from hydra.core import hydra_config
@@ -102,7 +101,7 @@ def train(cfg: omegaconf.DictConfig):
     return metric_dict, object_dict
 
 
-def main(cfg: omegaconf.DictConfig) -> Optional[float]:
+def main(cfg: omegaconf.DictConfig) -> float | None:
     """Main entry point for training.
 
     :param cfg: DictConfig configuration composed by Hydra.

src/e3response/utils/logging_utils.py

@@ -1,4 +1,4 @@
-from typing import Any, Dict
+from typing import Any
 
 import jax
 from lightning_utilities.core.rank_zero import rank_zero_only
@@ -12,7 +12,7 @@
 
 
 @rank_zero_only
-def log_hyperparameters(object_dict: Dict[str, Any]) -> None:
+def log_hyperparameters(object_dict: dict[str, Any]) -> None:
     """Controls which config parts are saved by Lightning loggers.
 
     Additionally, it saves:

src/e3response/utils/pylogger.py

@@ -1,5 +1,5 @@
+from collections.abc import Mapping
 import logging
-from typing import Mapping, Optional
 
 from lightning_utilities.core import rank_zero
 
@@ -13,7 +13,7 @@ def __init__(
         self,
         name: str = __name__,
         rank_zero_only: bool = False,
-        extra: Optional[Mapping[str, object]] = None,
+        extra: Mapping[str, object] | None = None,
     ) -> None:
         """Initializes a multi-GPU-friendly python command line logger that logs on all processes
         with their rank prefixed in the log message.
@@ -28,7 +28,7 @@ def __init__(
         super().__init__(logger=logger, extra=extra)
         self.rank_zero_only = rank_zero_only
 
-    def log(self, level: int, msg: str, *args, rank: Optional[int] = None, **kwargs) -> None:
+    def log(self, level: int, msg: str, *args, rank: int | None = None, **kwargs) -> None:
         """Delegate a log call to the underlying logger, after prefixing its message with the rank
         of the process it's being logged from. If `'rank'` is provided, then the log will only
         occur on that rank/process.

src/e3response/utils/rich_utils.py

@@ -1,5 +1,5 @@
+from collections.abc import Sequence
 from pathlib import Path
-from typing import Sequence
 
 from hydra.core.hydra_config import HydraConfig
 from lightning_utilities.core.rank_zero import rank_zero_only

src/e3response/utils/utils.py

@@ -1,5 +1,6 @@
+from collections.abc import Callable
 from importlib.util import find_spec
-from typing import Any, Callable, Optional
+from typing import Any
 import warnings
 
 from omegaconf import DictConfig
@@ -99,7 +100,7 @@ def wrap(cfg: DictConfig) -> tuple[dict[str, Any], dict[str, Any]]:
     return wrap
 
 
-def get_metric_value(metric_dict: dict[str, Any], metric_name: Optional[str]) -> Optional[float]:
+def get_metric_value(metric_dict: dict[str, Any], metric_name: str | None) -> float | None:
     """Safely retrieves value of the metric logged in reax.Module.
 
     :param metric_dict: A dict containing metric values.