ci: Lint updates (#3958)

1. Remove redundant extra CI jobs that are covered by the pre-commit job
2. Make codespell write changes (more convenient to use from pre-commit)

.github/workflows/checks.yml

@@ -38,51 +38,6 @@ jobs:
       - name: Run pre-commit
         run: pre-commit run --all-files --show-diff-on-failure
 
-  license:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-      - name: Check
-        run: >
-          sudo apt-get install -y git
-          && CI/check_license.py . --exclude "*thirdparty/*"
-  include_guards:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-      - name: Check
-        run: >
-          CI/check_include_guards.py . --fail-global --exclude "*thirdparty/*"
-  pragma_once:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Check
-        run: >
-          CI/check_pragma_once.sh
-  type_t:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-      - name: Check
-        run: >
-          CI/check_type_t.py . --exclude "thirdparty/*"
-  boost_test_macro:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Check
-        run: >
-          CI/check_boost_test_macro.sh
   smearing_config:
     runs-on: ubuntu-latest
     steps:
@@ -93,39 +48,7 @@ jobs:
       - name: Check
         run: >
           CI/check_smearing_config.py .
-  cmake_options:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-      - name: Check
-        run: >
-          docs/parse_cmake_options.py CMakeLists.txt --write docs/getting_started.md --verify
-  spelling:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-      - name: Install codespell
-        run: >
-          pip install codespell==2.2.5
-      - name: Check
-        run: >
-          CI/check_spelling
-  math_macros:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-      - name: Check
-        run: >
-          CI/check_math_macros.py . --exclude "thirdparty/*"
+
   missing_includes:
     runs-on: ubuntu-latest
     steps:
@@ -136,6 +59,7 @@ jobs:
       - name: Check
         run: >
           CI/missing_include_check.sh
+
   fpe_masks:
     runs-on: ubuntu-latest
     steps:
@@ -149,6 +73,7 @@ jobs:
       - name: Check
         run: >
           CI/check_fpe_masks.py --token ${{ secrets.GITHUB_TOKEN }}
+
   unused_files:
     runs-on: ubuntu-latest
     steps:

.pre-commit-config.yaml

@@ -35,7 +35,8 @@ repos:
     - id: codespell
       args: [
         "-S", "*.ipynb,*.onnx,_build,*.svg",
-        "-I", "./CI/codespell_ignore.txt"
+        "-I", "./CI/codespell_ignore.txt",
+        "-w"
       ]
       exclude: ^CI/.*$