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Goal

Integrate codee with GitHub to automatically run static analysis over your source code.

Prerequisites​

Ensure you have:

  • codee installed and accessible in your GitHub runners.

Create a GitHub Actions workflow​

GitHub Actions can be used to run codee checks automatically on pull requests and ensure that all contributions do not include bugs in their Fortran code.

In your repository, create the following directory structure if it does not exist:

mkdir
mkdir -p .github/workflows/

Then, create a new workflow file:

touch
touch .github/workflows/codee-checks.yml

Define the GitHub actions workflow​

GitHub action to stop the pipeline if Codee triggers critical checkers​

Warning

A Fatal/Error checker is a user-defined analysis rule that flags high-severity issues in the code. These checkers are explicitly defined by the user using the --check-id flag when running Codee.

GitHub Actions can be used to run codee checks automatically on pull requests and ensure that all contributions do not include bugs in their Fortran code.

This example is done using the MATMUL Fortran code of the codee-demos repository. In this case, the pipeline will be stopped if Codee triggers PWR072 or PWR079.

Add the following content to .github/workflows/codee-checks.yml:

name: Codee Checks

on:
  pull_request:

jobs:
  static-analysis:
    name: Run Codee checks
    runs-on: self-hosted

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Get modified Fortran files
        id: modified-files
        run: |
          MODIFIED_FILES=$(git diff --name-only --diff-filter=d origin/${{ github.base_ref }}...HEAD -- '*.f90' '*.F90' '*.f' '*.F')
          echo "MODIFIED_FILES=$MODIFIED_FILES" >> $GITHUB_ENV

      - name: Run Codee checks
        if: env.MODIFIED_FILES != ''
        run: |
          echo "Generate compile_commands.json"
          cd Fortran/MATMUL && cmake . -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_BUILD_TYPE=Release -DCMAKE_EXPORT_COMPILE_COMMANDS=1 -G "Ninja" -B build
          echo "Running Codee checks on modified files: $MODIFIED_FILES"
          codee checks \
            --check-id PWR072,PWR079 \
            --verbose \
            -p build/compile_commands.json \
            $MODIFIED_FILES --json > codee_output.json

      - name: Fail if critical checkers were found
        if: env.MODIFIED_FILES != ''
        run: |
          ISSUE_COUNT=$(jq '.Checks | length' Fortran/MATMUL/codee_output.json)
          if [ "$ISSUE_COUNT" -gt 0 ]; then
            echo "Codee detected $ISSUE_COUNT critical issues."
            exit 1
          else
            echo "No critical issues found by Codee."
          fi

How it works​

  • The workflow runs whenever a pull request is opened or updated.
  • It runs codee checks if there are modified Fortran source files in the current branch.
  • If codee triggers a PWR072 or a PWR079 checker, the GitHub action will fail.

GitHub action to apply Codee Autofixes​

Warning

Be cautious when using Codee Autofixes to apply automatic changes to your codebase. Always review the proposed modifications before merging, as they might introduce unintended side effects.

GitHub actions can also be used to automatically apply codee rewrite to fix Fortran code if there are Autofixes available for certain checkers.

Add the following content to .github/workflows/codee-rewrite.yml:

name: Codee autofixes

on:
  pull_request:

permissions:
  contents: write
  pull-requests: write

jobs:
  autofix:
    name: Apply autofix if possible
    runs-on: self-hosted

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
          ref: ${{ github.head_ref }}

      - name: Get modified Fortran files
        id: modified-files
        run: |
          MODIFIED_FILES=$(git diff --name-only --diff-filter=d origin/${{ github.base_ref }}...HEAD -- '*.f90' '*.F90' '*.f' '*.F')
          echo "MODIFIED_FILES=$MODIFIED_FILES" >> $GITHUB_ENV

      - name: Run `codee checks` and export JSON
        if: env.MODIFIED_FILES != ''
        run: |
          echo "Generate compile_commands.json"
          cd Fortran/MATMUL && cmake . -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_BUILD_TYPE=Release -DCMAKE_EXPORT_COMPILE_COMMANDS=1 -G "Ninja" -B build
          codee checks \
            --check-id PWR007,PWR008,PWR068,PWR003 \
            --verbose \
            -p build/compile_commands.json \
            $MODIFIED_FILES --json > codee_output.json

      - name: Apply autofixes if available
        if: env.MODIFIED_FILES != ''
        run: |
          echo "Checking for autofixes..."
          cd Fortran/MATMUL
          jq -r '.Checks[] | select(."Auto-fix" != null) | ."Auto-fix"[]' codee_output.json > autofix_commands.txt
          if [ ! -s autofix_commands.txt ]; then
            echo "No autofixes found."
            exit 0
          fi
          applied=0
          while IFS= read -r fix_cmd; do
            echo "Applying: $fix_cmd"
            eval "$fix_cmd"
            applied=$((applied + 1))
            done < autofix_commands.txt
          echo "Total autofixes applied: $applied"

      - name: Commit changes if autofixes were applied
        if: env.MODIFIED_FILES != ''
        run: |
          if ! git diff --quiet; then
            # Push with the github-actions user. More information at:
            # https://github.com/actions/checkout?tab=readme-ov-file#push-a-commit-using-the-built-in-token
            git commit -c user.name="github-actions[bot]" -c user.email="41898282+github-actions[bot]@users.noreply.github.com" -am "Apply Codee autofixes"
            git push --set-upstream origin ${{ github.head_ref }}
          else
            echo "No changes from autofixes."
          fi

How it works​

  • The workflow runs whenever a pull request is opened or updated.
  • It runs codee checks to check if the checkers appear in the code; in this case it is configure to trigger PWR007, PWR008, PWR068 and PWR003.
  • If there is an Autofix available it will automatically apply it and commit the changes.
  • It won't block branch merges.

Troubleshooting​

  • If the action does not trigger, verify the on: section.
  • If formatting does not apply, check if your files match the specified glob patterns (*.f90, *.F90, etc.).
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