Add pyproject.toml and more pre-commit hooks

and fix all issues

.clang-format

@@ -35,7 +35,7 @@ BreakBeforeTernaryOperators: true
 BreakConstructorInitializers: BeforeColon
 BreakStringLiterals: true
 ColumnLimit: 100
-CommentPragmas: '^ IWYU pragma:'
+CommentPragmas: "^ IWYU pragma:"
 CompactNamespaces: false
 ConstructorInitializerIndentWidth: 4
 ContinuationIndentWidth: 4
@@ -49,20 +49,20 @@ ExperimentalAutoDetectBinPacking: false
 FixNamespaceComments: true
 IncludeBlocks: Regroup
 IncludeCategories:
-  - Regex:           '<[[:alnum:]._/]+>'
-    Priority:        1
-    CaseSensitive:   false
-  - Regex:           '^"(G4|globals\.hh|Randomize\.hh|CLHEP)'
-    Priority:        2
-    CaseSensitive:   false
-  - Regex:           '^"RMG'
-    Priority:        3
-    CaseSensitive:   false
-  - Regex:           '.*'
-    Priority:        4
-    CaseSensitive:   false
-IncludeIsMainRegex: '(Test)?$'
-IncludeIsMainSourceRegex: ''
+  - Regex: "<[[:alnum:]._/]+>"
+    Priority: 1
+    CaseSensitive: false
+  - Regex: '^"(G4|globals\.hh|Randomize\.hh|CLHEP)'
+    Priority: 2
+    CaseSensitive: false
+  - Regex: '^"RMG'
+    Priority: 3
+    CaseSensitive: false
+  - Regex: ".*"
+    Priority: 4
+    CaseSensitive: false
+IncludeIsMainRegex: "(Test)?$"
+IncludeIsMainSourceRegex: ""
 IndentAccessModifiers: true
 IndentCaseLabels: true
 IndentCaseBlocks: false
@@ -75,8 +75,8 @@ IndentWrappedFunctionNames: false
 InsertTrailingCommas: None
 KeepEmptyLinesAtTheStartOfBlocks: true
 LambdaBodyIndentation: Signature
-MacroBlockBegin: ''
-MacroBlockEnd: ''
+MacroBlockBegin: ""
+MacroBlockEnd: ""
 MaxEmptyLinesToKeep: 2
 NamespaceIndentation: All
 PenaltyBreakAssignment: 2

.clang-tidy

@@ -21,8 +21,8 @@ Checks: "-*, \
   -readability-function-cognitive-complexity"
 
 CheckOptions:
-- key: modernize-use-override.IgnoreDestructors
-  value: true
+  - key: modernize-use-override.IgnoreDestructors
+    value: true
 
 FormatStyle: file
 HeaderFilterRegex: 'include/.*\.(hh|icc)'

.github/CONTRIBUTING.md

@@ -14,8 +14,9 @@ Before opening a PR:
 After the CI has run:
 
 - fix all reported problems, if any
-- navigate to the ReadTheDocs documentation build (linked in the GitHub
-  actions report for the PR) and check that the docs are properly rendered
+- navigate to the ReadTheDocs documentation build (linked in the GitHub actions
+  report for the PR) and check that the docs are properly rendered
 - download and check the test outputs from the GitHub actions interface
 
-For more details, refer to the [developer's guide](https://remage.readthedocs.io/en/stable/developer.html).
+For more details, refer to the
+[developer's guide](https://remage.readthedocs.io/en/stable/developer.html).

.github/workflows/main.yml

@@ -4,9 +4,9 @@ on:
   push:
     branches:
       - main
-      - 'releases/**'
+      - "releases/**"
     paths-ignore:
-      - '**.md'
+      - "**.md"
   pull_request:
   release:
 
@@ -15,7 +15,6 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-
   test_on_linux:
     name: Test on remage image
     runs-on: ubuntu-latest
@@ -25,57 +24,57 @@ jobs:
       matrix:
         # guideline: only test on latest patch releases (and maybe previous one)
         container_version:
-        - G4.11.3
-        - G4.11.2
-        - slim
+          - G4.11.3
+          - G4.11.2
+          - slim
 
     container: docker://gipert/remage-base:${{ matrix.container_version }}
 
     steps:
-    - uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-    - name: Build project
-      run: |
-        mkdir build
-        cd build
-        cmake -DRMG_BUILD_EXAMPLES=1 ..
-        make
-        make install
+      - name: Build project
+        run: |
+          mkdir build
+          cd build
+          cmake -DRMG_BUILD_EXAMPLES=1 ..
+          make
+          make install
 
-    - name: Setup and start xvfb (enables Geant4 visualization)
-      run: |
-        Xvfb :99 -screen 0 1920x1080x24 &
+      - name: Setup and start xvfb (enables Geant4 visualization)
+        run: |
+          Xvfb :99 -screen 0 1920x1080x24 &
 
-    - name: Run full test suite
-      if: ${{ matrix.container_version != 'slim' }}
-      env:
-        DISPLAY: :99
-      run: |
-        cd build
-        ctest --output-on-failure
+      - name: Run full test suite
+        if: ${{ matrix.container_version != 'slim' }}
+        env:
+          DISPLAY: :99
+        run: |
+          cd build
+          ctest --output-on-failure
 
-    - name: Upload test suite outputs to GitHub
-      if: ${{ matrix.container_version != 'slim' }}
-      uses: actions/upload-artifact@v4
-      with:
-        name: test-output-${{ matrix.container_version }}
-        # artifacts must have a ".output*" extension
-        path: build/tests/**/*.output*.*
+      - name: Upload test suite outputs to GitHub
+        if: ${{ matrix.container_version != 'slim' }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-output-${{ matrix.container_version }}
+          # artifacts must have a ".output*" extension
+          path: build/tests/**/*.output*.*
 
-    - name: Run minimal test suite
-      if: ${{ matrix.container_version == 'slim' }}
-      env:
-        DISPLAY: :99
-      run: |
-        cd build
-        ctest --output-on-failure --label-exclude 'extra|vis'
+      - name: Run minimal test suite
+        if: ${{ matrix.container_version == 'slim' }}
+        env:
+          DISPLAY: :99
+        run: |
+          cd build
+          ctest --output-on-failure --label-exclude 'extra|vis'
 
-    - name: Compare checked-in doc dump with current result
-      if: ${{ matrix.container_version != 'slim' }}
-      run: |
-        cd build
-        cp ../docs/rmg-commands.md ../docs/rmg-commands.md.bak
-        make remage-doc-dump
-        diff ../docs/rmg-commands.md ../docs/rmg-commands.md.bak
+      - name: Compare checked-in doc dump with current result
+        if: ${{ matrix.container_version != 'slim' }}
+        run: |
+          cd build
+          cp ../docs/rmg-commands.md ../docs/rmg-commands.md.bak
+          make remage-doc-dump
+          diff ../docs/rmg-commands.md ../docs/rmg-commands.md.bak
 
 # vim: expandtab tabstop=2 shiftwidth=2

.pre-commit-config.yaml

@@ -2,48 +2,77 @@ ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autofix_commit_msg: "style: pre-commit fixes"
 
-exclude: ^include/(fmt|magic_enum|CLI11|EcoMug)/
+exclude: ^include/(fmt|magic_enum|CLI11|EcoMug)/|^docs/rmg-commands.md|^docs/extensions/remage/warnings_filter.py
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
-  hooks:
-  - id: check-added-large-files
-    args: ['--maxkb=600']
-  - id: check-case-conflict
-  - id: check-executables-have-shebangs
-  - id: check-merge-conflict
-  - id: check-symlinks
-  - id: check-yaml
-  - id: check-json
-  - id: debug-statements
-  - id: end-of-file-fixer
-  - id: forbid-new-submodules
-  - id: mixed-line-ending
-  - id: trailing-whitespace
-
-- repo: https://github.com/cheshirekow/cmake-format-precommit
-  rev: v0.6.13
-  hooks:
-  - id: cmake-format
-    additional_dependencies: [pyyaml]
-
-- repo: https://github.com/codespell-project/codespell
-  rev: v2.3.0
-  hooks:
-  - id: codespell
-    args: ["-L", "hist,manuel"]
-
-- repo: local
-  hooks:
-   - id: clang-tidy
-     name: clang-tidy
-     entry: bash -c 'command -V run-clang-tidy >&- 2>&-; if [[ $? == 0 && -d build ]]; then run-clang-tidy -fix -quiet -p=build; fi'
-     language: system
-     pass_filenames: false
-     types_or: [c++]
-
-- repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v19.1.5
-  hooks:
-   - id: clang-format
-     types_or: [c++]
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.19.1"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+        args: ["--maxkb=600"]
+      - id: check-case-conflict
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: check-json
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: forbid-new-submodules
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: "v3.3.3"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.7.4"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: v0.6.13
+    hooks:
+      - id: cmake-format
+        additional_dependencies: [pyyaml]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        args: ["-L", "hist,manuel"]
+
+  - repo: local
+    hooks:
+      - id: clang-tidy
+        name: clang-tidy
+        entry:
+          bash -c 'command -V run-clang-tidy >&- 2>&-; if [[ $? == 0 && -d build
+          ]]; then run-clang-tidy -fix -quiet -p=build; fi'
+        language: system
+        pass_filenames: false
+        types_or: [c++]
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v19.1.5
+    hooks:
+      - id: clang-format
+        types_or: [c++]

.readthedocs.yaml

@@ -17,7 +17,8 @@ build:
       - git fetch --unshallow || true
     pre_build: # prepare Doxyfile, run Doxygen, prepare Sphinx
       - export DOXYGEN_DOT_PATH=$(which dot)
-      - sed s/@DOXYGEN_INPUT_DIR@/../g\;s/@DOXYGEN_OUTPUT_DIR@/_doxygen/g docs/Doxyfile.in > docs/Doxyfile
+      - sed s/@DOXYGEN_INPUT_DIR@/../g\;s/@DOXYGEN_OUTPUT_DIR@/_doxygen/g
+        docs/Doxyfile.in > docs/Doxyfile
       - cat docs/Doxyfile
       - cd docs && doxygen
       - mkdir -p docs/extra/doxygen

README.md

@@ -16,37 +16,37 @@ Simulation framework for germanium detector experiments
 
 <br/>
 
-The *remage* project aims to deliver a modern Geant4-based C++ library designed
+The _remage_ project aims to deliver a modern Geant4-based C++ library designed
 for efficient simulation of particle physics processes in typical germanium
 detector experiments. The library is setup-agnostic, requiring users only to
 define the experimental setup's geometry. Supported specification languages
-include C++, GDML, and others. Once the geometry is provided, users can access
-a comprehensive suite of tools for common tasks, such as physics generation and
+include C++, GDML, and others. Once the geometry is provided, users can access a
+comprehensive suite of tools for common tasks, such as physics generation and
 standard output handling.
 
 Get started with our [documentation pages](https://remage.readthedocs.io)!
 
 ### Main features
 
-* Low entry barrier: Most simulations can be executed directly using the
-  `remage` executable and a macro file, eliminating the need to write or
-  compile C++ code.
-* Various pre-compiled *remage* versions available on
+- Low entry barrier: Most simulations can be executed directly using the
+  `remage` executable and a macro file, eliminating the need to write or compile
+  C++ code.
+- Various pre-compiled _remage_ versions available on
   [Docker Hub](https://hub.docker.com/repository/docker/legendexp/remage)
-* Support for modern [Geant4](https://geant4.web.cern.ch), including:
-  * Multithreading
-  * [GDML](https://gdml.web.cern.ch/GDML) support
-  * Multiple output file formats ([ROOT](https://root.cern.ch),
+- Support for modern [Geant4](https://geant4.web.cern.ch), including:
+  - Multithreading
+  - [GDML](https://gdml.web.cern.ch/GDML) support
+  - Multiple output file formats ([ROOT](https://root.cern.ch),
     [HDF5](https://www.hdfgroup.org/solutions/hdf5)...)
-* [LEGEND HDF5 (LH5)](https://legend-exp.github.io/legend-data-format-specs/dev/hdf5/)
+- [LEGEND HDF5 (LH5)](https://legend-exp.github.io/legend-data-format-specs/dev/hdf5/)
   output format
-* Fast third-party cosmic muon generator (through
+- Fast third-party cosmic muon generator (through
   [EcoMug](https://doi.org/10.1016/j.nima.2021.165732))
-* Support for external generators:
-  * [MUSUN](https://doi.org/10.1016/j.cpc.2008.10.013)
-  * [MAURINA](https://doi.org/10.1140/epja/s10050-024-01336-0)
-* Third-party double-beta decay generator (through
+- Support for external generators:
+  - [MUSUN](https://doi.org/10.1016/j.cpc.2008.10.013)
+  - [MAURINA](https://doi.org/10.1140/epja/s10050-024-01336-0)
+- Third-party double-beta decay generator (through
   [bxdecay0](https://github.com/BxCppDev/bxdecay0))
-* Advanced vertex confinement on physical volumes, geometrical solids, surfaces
+- Advanced vertex confinement on physical volumes, geometrical solids, surfaces
   and intersections
-* Sensible output schemes for HPGe and optical detectors
+- Sensible output schemes for HPGe and optical detectors