CMake, C++, Python pre-commit

.clang-format

@@ -102,7 +102,7 @@ IncludeCategories:
     Priority:       14
   # all standard <...> headers
   - Regex:    '<[-\w\/-_]+[\.\/]*[-\w\/-_]+>>'
-    Priority:       99       
+    Priority:       99
   # all local "..." headers
   - Regex:    '"[-\w\/-_]+[\.\/]*[-\w\/-_]+"'
     Priority:       999
@@ -164,4 +164,4 @@ Standard: c++20
 
 TabWidth: 2
 
-UseTab: Never
+UseTab: Never

.codespellrc

@@ -0,0 +1,2 @@
+[codespell]
+ignore-words-list = Mater,nd,multline

.gersemirc

@@ -0,0 +1,4 @@
+definitions: [./cmake/macros,]
+line_length: 90
+indent: 2
+list_expansion: favour-expansion

.github/workflows/clang-format.yml

@@ -1,13 +1,10 @@
 name: Clang-Format Check
 
-on: 
+on:
   push:
     branches:
       - master
   pull_request:
-    branches:
-      - master
-      - devel
     paths-ignore:
       - 'doc/**'
       - 'contrib/**'

.github/workflows/compile_applications.yml

@@ -1,6 +1,6 @@
 name: compile-applications
 
-on: 
+on:
   push:
     branches:
       - master
@@ -52,4 +52,3 @@ jobs:
           export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
           ninja -j $(nproc) install
-

.github/workflows/github-pages.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - master
-    
+
 permissions:
   contents: write
 
@@ -33,7 +33,7 @@ jobs:
         cd doc/doxygen
         cmake .
         make
-      
+
     - name: Update version selector
       run: |
         ./contrib/utilities/update_doc_version_selector.sh doc/doxygen/docs/
@@ -56,4 +56,3 @@ jobs:
         folder: doc/doxygen/docs/
         target-folder: doxygen/
         clean: false # This must be false to keep prior versions of the docs
-

.github/workflows/linux.yml

@@ -1,6 +1,6 @@
 name: linux
 
-on: 
+on:
   push:
     branches:
       - master

.pre-commit-config.yaml

@@ -0,0 +1,58 @@
+fail_fast: true
+
+repos:
+# General purpose hooks
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: check-added-large-files
+    args: [--maxkb=8192]
+  - id: check-merge-conflict
+  - id: end-of-file-fixer
+    exclude: ^contrib/catch/
+  - id: no-commit-to-branch
+    args: [--branch,master]
+  - id: trailing-whitespace
+    exclude: ^contrib/catch/
+- repo: https://github.com/gitleaks/gitleaks
+  rev: v8.24.2
+  hooks:
+  - id: gitleaks
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.4.1
+  hooks:
+  - id: codespell
+    args: [--config=.codespellrc]
+    exclude: ^contrib/catch/
+# Python formatting and linting tools
+- repo: https://github.com/psf/black
+  rev: 25.9.0
+  hooks:
+    - id: black
+      language_version: python3
+      exclude: contrib/utilities/prm_tools.py
+- repo: https://github.com/pycqa/isort
+  rev: 6.0.1
+  hooks:
+    - id: isort
+      args: ["--profile", "black"]
+      exclude: contrib/utilities/prm_tools.py
+# TODO: Enable flake8 after addressing existing linting issues
+# - repo: https://github.com/pycqa/flake8
+#   rev: 7.3.0
+#   hooks:
+#     - id: flake8
+#       args: [--max-line-length=80]
+#       exclude: contrib/utilities/prm_tools.py
+# CMake formatting
+- repo: https://github.com/BlankSpruce/gersemi
+  rev: 0.25.0
+  hooks:
+  - id: gersemi
+# c++ formatting
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev:  v18.1.8
+  hooks:
+  - id: clang-format
+    types_or: [c++, c, cuda]
+    exclude: ^contrib/catch/