Update pre-commit and apply tidy fixes

.github/workflows/test.yml

@@ -18,7 +18,6 @@ jobs:
       matrix:
         target:
           - black
-          - dapperdata
           - mypy
           - pytest
           - ruff

.pre-commit-config.yaml

@@ -1,31 +1,4 @@
 repos:
-  - repo: local
-    hooks:
-      - id: pytest
-        name: pytest
-        entry: make test/pytest
-        language: system
-        pass_filenames: false
-      - id: ruff
-        name: ruff
-        entry: make test/ruff
-        language: system
-        pass_filenames: false
-      - id: black
-        name: black
-        entry: make test/black
-        language: system
-        pass_filenames: false
-      - id: mypy
-        name: mypy
-        entry: make test/mypy
-        language: system
-        pass_filenames: false
-      - id: tomlsort
-        name: tomlsort
-        entry: make test/tomlsort
-        language: system
-        pass_filenames: false
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: 3e8a8703264a2f4a69428a0aa4dcb512790b2c8c # v6.0.0 , 9 Aug 2025
     hooks:
@@ -34,14 +7,36 @@ repos:
       - id: check-case-conflict
       - id: check-merge-conflict
       - id: check-shebang-scripts-are-executable
+        exclude: '\.\w+$'
       - id: end-of-file-fixer
-        exclude: '\.(diff|patch)$'
+        exclude: '\.(diff|patch|py)$'
       - id: trailing-whitespace
-        exclude: '\.(diff|patch)$'
+        exclude: '\.(diff|patch|py)$'
       - id: check-json
       - id: check-yaml
 
+  - repo: https://github.com/pappasam/toml-sort
+    rev: 2970ae9bb7124fe5117a27e10c10d2da051ce05a # v0.24.4, 24 Mar 2026
+    hooks:
+      - id: toml-sort-fix
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.13 # 14 May 2026 (immutable)
+    hooks:
+    - id: ruff-check # Linting
+      args: [ --fix ]
+    - id: ruff-format # Formatting
+
 ci:
+  autofix_commit_msg: |
+    Apply fixes from pre-commit hooks: see detailed commit message ↴
+
+    This commit means that you must (please!) install pre-commit
+    on your development machine and run `pre-commit install --install-hooks`.
+    For more information, see
+    https://celeritas-project.github.io/celeritas/user/development/style.html#formatting
+
+    Autogenerated: https://pre-commit.ci
   autoupdate_schedule: quarterly
   autoupdate_commit_msg: "Update pre-commit version"
 

celerpy/cli.py

@@ -1,7 +1,7 @@
 # Copyright 2024 UT-Battelle, LLC, and other Celeritas developers.
 # See the top-level LICENSE file for details.
 # SPDX-License-Identifier: Apache-2.0
-from typing import Annotated, Optional
+from typing import Annotated
 
 import typer
 from pydantic import ValidationError
@@ -31,7 +31,7 @@ def print_version(value: bool):
 @app.command()
 def main(
     version: Annotated[
-        Optional[bool],
+        bool | None,
         typer.Option("--version", callback=print_version, is_eager=True),
     ] = None,
 ):

celerpy/conf/settings.py

@@ -1,7 +1,6 @@
 # Copyright 2024 UT-Battelle, LLC, and other Celeritas developers.
 # See the top-level LICENSE file for details.
 # SPDX-License-Identifier: Apache-2.0
-from typing import Optional
 
 from pydantic import DirectoryPath, FilePath
 from pydantic_settings import BaseSettings, SettingsConfigDict
@@ -24,7 +23,7 @@ class Settings(BaseSettings):
         use_attribute_docstrings=True,
     )
 
-    prefix_path: Optional[DirectoryPath] = None
+    prefix_path: DirectoryPath | None = None
     "Path to the Celeritas build/install directory"
 
     # CELER_ environment variables
@@ -46,7 +45,7 @@ class Settings(BaseSettings):
 
     # Geant4->ORANGE conversion
 
-    g4org_options: Optional[FilePath] = None
+    g4org_options: FilePath | None = None
     "JSON file with conversion options"
 
     # Geant4 configuration

celerpy/model/input.py

@@ -4,7 +4,7 @@
 """Input models for commands and configuration with Celeritas."""
 
 from enum import StrEnum, auto
-from typing import Literal, Optional
+from typing import Literal
 
 from pydantic import FilePath, NonNegativeInt, PositiveFloat, PositiveInt
 from pydantic_core import to_json
@@ -38,7 +38,7 @@ class OrangeGeoFromCsg(_Model):
     unit_length: PositiveFloat = 1.0
     "Scale factor (input unit length), customizable for unit testing"
 
-    tol: Optional[Tolerance] = None
+    tol: Tolerance | None = None
     "Construction and tracking tolerance (native units)"
 
     # Structural conversion
@@ -51,13 +51,13 @@ class OrangeGeoFromCsg(_Model):
 
     # Debug output
 
-    objects_output_file: Optional[str] = None
+    objects_output_file: str | None = None
     "Write converted Geant4 object structure to a JSON file"
 
-    csg_output_file: Optional[str] = None
+    csg_output_file: str | None = None
     "Write constructed CSG surfaces and tree to a JSON file"
 
-    org_output_file: Optional[str] = None
+    org_output_file: str | None = None
     "Write final org.json to a JSON file"
 
 
@@ -95,13 +95,13 @@ class OrangeGeoFromGeant(OrangeGeoFromCsg):
 
 # celer-geo/GeoInput.hh
 class ModelSetup(_Model):
-    cuda_stack_size: Optional[NonNegativeInt] = None
-    cuda_heap_size: Optional[NonNegativeInt] = None
+    cuda_stack_size: NonNegativeInt | None = None
+    cuda_heap_size: NonNegativeInt | None = None
 
     geometry_file: FilePath
     "Path to the GDML input file"
 
-    perfetto_file: Optional[FilePath] = None
+    perfetto_file: FilePath | None = None
     "Path to write Perfetto profiling output"
 
 
@@ -110,10 +110,10 @@ class TraceSetup(_Model):
     _cmd: Literal["trace"] = "trace"
     "Command name in the JSON file"
 
-    geometry: Optional[GeometryEngine] = None
+    geometry: GeometryEngine | None = None
     "Geometry engine with which to perform the trace"
 
-    memspace: Optional[MemSpace] = None
+    memspace: MemSpace | None = None
     "Whether to perform the trace on CPU or GPU"
 
     volumes: bool = True
@@ -137,13 +137,13 @@ class ImageInput(_Model):
     vertical_pixels: NonNegativeInt = 512
     "Number of pixels along the y axis"
 
-    horizontal_divisor: Optional[PositiveInt] = None
+    horizontal_divisor: PositiveInt | None = None
     "Increase the horizontal window to be divisible by this number"
 
 
 # ad hoc: input to a 'trace' command
 class TraceInput(TraceSetup):
-    image: Optional[ImageInput] = None
+    image: ImageInput | None = None
     "Reuse the existing image"
 
 

celerpy/model/output.py

@@ -38,7 +38,7 @@ class ImageParams(_Model):
 class TraceOutput(_Model):
     trace: TraceSetup
     image: ImageParams
-    volumes: Optional[list[str]] = None
+    volumes: list[str] | None = None
     sizeof_int: PositiveInt
 
 
@@ -140,8 +140,8 @@ class ExceptionDump(_Model):
     context: Optional["ExceptionDump"] = None
 
     # corecel/AssertIO.json.cc
-    what: Optional[str]
+    what: str | None
     which: str
-    condition: Optional[str] = None
-    file: Optional[str] = None
-    line: Optional[int] = None
+    condition: str | None = None
+    file: str | None = None
+    line: int | None = None

celerpy/process.py

@@ -7,7 +7,7 @@
 import os
 from signal import SIGINT, SIGKILL, SIGTERM
 from subprocess import PIPE, Popen, TimeoutExpired
-from typing import Optional, TypeVar
+from typing import TypeVar
 
 from pydantic import BaseModel, ValidationError
 
@@ -81,7 +81,7 @@ def close(process: P, *, timeout: float = 0.1):
     return out
 
 
-def communicate(process: P, line: str) -> Optional[str]:
+def communicate(process: P, line: str) -> str | None:
     """Write a line and read a line of response.
 
     For this to work, the child application *must* write a single line of

celerpy/visualize.py

@@ -12,7 +12,7 @@
 from pathlib import Path
 from subprocess import TimeoutExpired
 from tempfile import NamedTemporaryFile
-from typing import Any, NamedTuple, Optional, Union
+from typing import Any, NamedTuple
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -126,7 +126,7 @@ class CelerGeo:
     refactor.
     """
 
-    image: Optional[ImageParams]
+    image: ImageParams | None
     volumes: dict[GeometryEngine, list[str]]
 
     @classmethod
@@ -170,9 +170,9 @@ def reset_id_map(self):
 
     def trace(
         self,
-        image: Optional[ImageInput] = None,
+        image: ImageInput | None = None,
         *,
-        geometry: Optional[GeometryEngine] = None,
+        geometry: GeometryEngine | None = None,
         **kwargs,
     ):
         """Trace with a geometry, memspace, etc."""
@@ -216,7 +216,7 @@ def trace(
 
         return (result, npimg)
 
-    def close(self, *, timeout: float = 0.25) -> Union[dict[str, dict], str]:
+    def close(self, *, timeout: float = 0.25) -> dict[str, dict] | str:
         """Cleanly exit the ray trace loop, returning run statistics if
         possible.
         """
@@ -286,7 +286,7 @@ def calc_axes(length, dir):
 
 
 class Imager:
-    axes: Optional[LabeledAxes] = None
+    axes: LabeledAxes | None = None
 
     def __init__(self, celer_geo: CelerGeo, image: ImageInput):
         self.celer_geo = celer_geo
@@ -296,9 +296,9 @@ def __init__(self, celer_geo: CelerGeo, image: ImageInput):
     def __call__(
         self,
         ax: mpl_Axes,
-        geometry: Optional[GeometryEngine] = None,
-        memspace: Optional[MemSpace] = None,
-        colorbar: Union[bool, None, mpl_Axes] = None,
+        geometry: GeometryEngine | None = None,
+        memspace: MemSpace | None = None,
+        colorbar: bool | None | mpl_Axes = None,
     ) -> dict[str, Any]:
         (trace_output, img) = self.celer_geo.trace(
             self.image, geometry=geometry, memspace=memspace
@@ -354,8 +354,8 @@ def plot_all_geometry(
     trace_image: Imager,
     *,
     colorbar: bool = True,
-    figsize: Optional[tuple] = None,
-    engines: Optional[Iterable] = None,
+    figsize: tuple | None = None,
+    engines: Iterable | None = None,
 ) -> Mapping[GeometryEngine, Any]:
     """Convenience function for plotting all available geometry types."""
     if engines is None:
@@ -376,7 +376,7 @@ def plot_all_geometry(
     if colorbar:
         all_cbar[:0] = [all_ax[-1]]
 
-    for ax, g, cb in zip(all_ax, engines, all_cbar):
+    for ax, g, cb in zip(all_ax, engines, all_cbar, strict=True):
         try:
             result[g] = trace_image(ax, geometry=g, colorbar=cb)
         except Exception as e:
@@ -387,7 +387,7 @@ def plot_all_geometry(
 def centered_image(
     center: ArrayLike = (0, 0, 0),
     *,
-    width: Union[float, tuple, np.ndarray],
+    width: float | tuple | np.ndarray,
     xdir: ArrayLike = (0, 0, 1),
     outdir: ArrayLike = (0, 1, 0),
     **kwargs: Any,

test/mock-prefix/bin/celer-geo

@@ -16,11 +16,17 @@ setup_signals()
 celer_log = environ.get("CELER_LOG")
 assert celer_log == "debug", f"Expected CELER_LOG=debug, got {celer_log}"
 celer_log_local = environ.get("CELER_LOG_LOCAL")
-assert celer_log_local == "warning", f"Expected CELER_LOG_LOCAL=warning, got {celer_log_local}"
+assert celer_log_local == "warning", (
+    f"Expected CELER_LOG_LOCAL=warning, got {celer_log_local}"
+)
 g4org_opts = environ.get("G4ORG_OPTIONS")
-assert g4org_opts and Path(g4org_opts).is_file(), f"Expected G4ORG_OPTIONS=1, got {g4org_opts}"
+assert g4org_opts and Path(g4org_opts).is_file(), (
+    f"Expected G4ORG_OPTIONS=1, got {g4org_opts}"
+)
 profiling = environ.get("CELER_ENABLE_PROFILING")
-assert profiling == "True", f"Expected CELER_ENABLE_PROFILING=1, got {profiling}"
+assert profiling == "True", (
+    f"Expected CELER_ENABLE_PROFILING=1, got {profiling}"
+)
 
 
 # Read the initial command and echo it (with version)
@@ -46,7 +52,7 @@ expect_trace(
 )
 
 cmd = read_input()
-assert cmd == None
+assert cmd is None
 dump(
     {
         "runtime": {"device": None, "kernels": [], "version": "0.7.0-dev"},

test/mock-prefix/bin/mock-process

@@ -2,19 +2,19 @@
 # Copyright 2024 UT-Battelle, LLC, and other Celeritas developers.
 # See the top-level COPYRIGHT file for details.
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-"""Mock a 'JSON lines' style process.
+"""Mock a 'JSON lines' style process."""
 
-"""
-from mockutils import log, dump, read_input, setup_signals
 import sys
 
+from mockutils import dump, log, read_input, setup_signals
+
 setup_signals()
 
 cmd = input()
 log("read command", repr(cmd))
 dump("success")
 log("entering loop")
-while (cmd := read_input()) != None:
+while (cmd := read_input()) is not None:
     log("read command", cmd)
     if cmd == "abort":
         log("Aborting!")