[CI/CD] Add Pre-commit Validation as First Step of Testing Pipeline

[Sinitca-Aleksandr]

Issue: [CI/CD] Add Pre-commit Validation as First Step of Testing Pipeline

Summary

Implement GitHub Actions workflow to run pre-commit validation as the first gate in the CI/CD pipeline, preventing style/lint issues from entering the codebase and ensuring consistency across contributions.

Related: Pre-commit configuration already exists in repository (.pre-commit-config.yaml)
Reference Implementation: FluctuationAnalysisTools repository CI/CD pipeline

---

Motivation

• Catch code style, formatting, and linting issues before running expensive tests
• Ensure all contributions follow project standards (black, isort, YAML/JSON validation, etc.)
• Reduce PR review time by automating mechanical checks
• Align with sister project FluctuationAnalysisTools CI/CD patterns for maintainability

---

🔧 Technical Requirements

1. Create Reusable Pre-commit Validation Workflow

Create .github/workflows/reusable_pre-commit-validation.yml based on the reference implementation:

# .github/workflows/reusable_pre-commit-validation.yml
name: Reusable - Pre-commit Validation

on:
  workflow_call:
    outputs:
      cache-key:
        description: 'The cache key used for pip dependencies'
        value: ${{ jobs.pre-commit-validation.outputs.cache-key }}

permissions:
  contents: read

jobs:
  pre-commit-validation:
    runs-on: ubuntu-latest
    outputs:
      cache-key: ${{ steps.cache-pip.outputs.key || 'pip-precommit-' }}

    steps:
      - name: Checkout repository
        uses: actions/checkout@v3

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.11"  # Match pyproject.toml requirement

      - name: Cache pip dependencies
        id: cache-pip
        uses: actions/cache@v3
        with:
          path: ~/.cache/pip
          key: pip-precommit-${{ hashFiles('**/pyproject.toml', '**/.pre-commit-config.yaml') }}
          restore-keys: |
            pip-precommit-

      - name: Install pre-commit
        shell: bash
        run: |
          python -m pip install --upgrade pip
          pip install pre-commit

      - name: Run pre-commit validation
        shell: bash
        run: |
          pre-commit run --all-files

2. Update/Create Main CI Workflow

Create or update .github/workflows/test-and-release.yml to use the reusable workflow:

# .github/workflows/test-and-release.yml (skeleton)
name: Test and Release

on:
  push:
    branches: [master, main]
    tags:
      - 'release/*'
  pull_request:
    branches: [master, main]
  workflow_dispatch:  # Allow manual triggering

permissions:
  contents: read

jobs:
  #  FIRST STEP: Pre-commit validation
  pre-commit-validation:
    uses: ./.github/workflows/reusable_pre-commit-validation.yml

  # Subsequent jobs depend on pre-commit passing
  test:
    needs: pre-commit-validation
    # ... existing test configuration ...

  build:
    needs: pre-commit-validation
    # ... existing build configuration ...

3. Verify Pre-commit Configuration Compatibility

Current .pre-commit-config.yaml uses [[10]]:

repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v3.2.0  #  Consider updating to v6.0.0 (as in FluctuationAnalysisTools)
  - repo: https://github.com/pycqa/isort
    rev: 6.0.0
  - repo: https://github.com/psf/black-pre-commit-mirror
    rev: 25.1.0

Recommended updates:

• Upgrade pre-commit-hooks to v6.0.0 for latest security patches [[1]]
• Ensure black language_version matches project Python requirement (currently python3.10 in bayes_model vs python3 in reference)

---

✅ Acceptance Criteria

• Pre-commit validation runs automatically on:
  • pull_request events (all branches)
  • push to master/main
  • Manual trigger via workflow_dispatch
• Workflow fails fast if pre-commit checks fail (no downstream jobs execute)
• Pip dependencies are cached to reduce CI runtime
• Workflow uses same Python version as defined in pyproject.toml
• Documentation updated in CONTRIBUTION.md to mention CI pre-commit requirement
• Local developers can run same checks via pre-commit run --all-files

---

Implementation Steps

1. Create reusable workflow file:

   mkdir -p .github/workflows
   touch .github/workflows/reusable_pre-commit-validation.yml

2. Copy/adapt workflow content from FluctuationAnalysisTools reference [[1]]

3. Update main CI workflow to call reusable workflow with needs: dependency

4. Test locally:

   # Install pre-commit hooks for local development
   pre-commit install
   # Run validation manually
   pre-commit run --all-files

5. Validate in PR: Create draft PR to trigger GitHub Actions and verify workflow behavior

---

Testing Strategy

Local Testing

# Install pre-commit
pip install pre-commit

# Install git hooks
pre-commit install

# Test all files
pre-commit run --all-files

# Test specific hook
pre-commit run black --all-files

CI Validation Checklist

• Workflow triggers on PR creation
• Pre-commit job appears first in Actions tab
• Cache hit/miss behavior works correctly
• Failure in pre-commit blocks downstream jobs
• Success allows test/build jobs to proceed

---

References

• Reference CI pipeline: FluctuationAnalysisTools/.github/workflows/test-and-release.yml
• Reference reusable workflow: FluctuationAnalysisTools/.github/workflows/reusable_pre-commit-validation.yml
• Pre-commit documentation: https://pre-commit.com
• GitHub Actions caching: https://docs.github.com/en/actions/using-workflows/caching-dependencies-to-speed-up-workflows

---

ℹ️ Note for Contributors:

1. This workflow should be non-breaking for existing PRs — consider adding continue-on-error: true temporarily during rollout if needed.
2. Ensure all existing code passes pre-commit hooks before merging this CI change (run pre-commit run --all-files locally first).
3. Coordinate with maintainers before updating hook versions in .pre-commit-config.yaml to avoid disrupting active development.
4. Follow existing repository conventions: ruff, black, isort configuration in pyproject.toml.