Skip to content

CI/CD

Continuous Integration and Deployment pipeline for Mole.

GitHub Actions Workflows

CI Workflow (.github/workflows/ci.yml)

Runs on pushes and PRs to main:

  1. Setup Environment
  2. Python 3.12, 3.13 and 3.14, as a matrix, so every backend step runs three times

  3. Node.js 22, matching frontend/Dockerfile and e2e.yml. Cypress 16 requires Node 22 or newer.

  4. Backend Testing

  5. Install dependencies from backend/requirements.txt
  6. Run unit tests, tests/test_molecule_generation.py

  7. Run e2e tests, tests/e2e/

  8. Frontend Testing

  9. Install dependencies with npm ci
  10. There is no frontend unit-test step. The repository has no JavaScript unit tests; frontend/cypress/e2e/ is the frontend test suite and runs in the separate e2e workflow described below.

There is no separate lint step in any workflow. The pre-commit hook runs across the repository and is what enforces formatting.

  1. Build Check
  2. docker-compose build

Docker Workflow (.github/workflows/docker.yml)

Builds and pushes Docker images to GitHub Container Registry:

  • Triggered on pushes and PRs
  • Builds backend and frontend images
  • Pushes to ghcr.io

Docs Workflow (.github/workflows/docs.yml)

Builds the documentation site and publishes it to GitHub Pages.

  • Triggered on pushes and pull requests
  • Concurrency group pages, with cancel-in-progress: false, so a queued publish is never cancelled halfway

Release Workflow (.github/workflows/release.yml)

Triggered by a tag matching v*. Builds a single-file CLI binary and attaches it to a GitHub release.

  • pip install pyinstaller, then pyinstaller --onefile src/cli.py --name mole-${{ matrix.target }}
  • Runs on a per-OS matrix. Assets are named per target, so they do not collide:
Runner Asset
ubuntu-latest mole-linux
macos-latest mole-macos
windows-latest mole-windows.exe
  • Attached via softprops/action-gh-release, with generated release notes

This is the fastest way to get the CLI, since it skips building a wheel and needs no Python environment:

curl -LO https://github.com/coccinella-labs/mole/releases/download/v1.1.0/mole-linux
chmod +x mole-linux
./mole-linux --api-key your-key --health

Asset names are per-target. Every release from v1.1.0 onwards publishes mole-linux, mole-macos and mole-windows.exe. Earlier releases used different names, and those assets keep them: a URL pinned to any tag keeps resolving to the file that tag actually published. releases/latest/download/mole-* resolves to the newest release, so it changes target whenever a new release lands; pin the tag for a build that does not move.

E2E Workflow (.github/workflows/e2e.yml)

Full end-to-end testing:

  • Builds Docker containers
  • Starts services
  • Runs Cypress e2e tests
  • Manual trigger available

Pre-commit Hooks

Local quality checks using pre-commit:

  • Ruff linting and formatting
  • Commit message validation

Install:

pip install pre-commit
pre-commit install

Quality Gates

Code Quality

  • Linting: Ruff (Python)
  • Formatting: Ruff format
  • Type checking: Basic validation

Testing

  • Unit tests: pytest
  • E2E tests: Cypress
  • Coverage: Not enforced but monitored

Security

  • Dependencies: Automated scanning
  • Vulnerabilities: npm audit, pip security

Deployment

Manual Deployment

# Build images
docker-compose build

# Deploy
docker-compose up -d

Automated Deployment

Configure your platform (Heroku, AWS, etc.) to: 1. Pull images from GitHub Container Registry 2. Use docker-compose.yml for orchestration 3. Set environment variables from secrets

Monitoring

  • Health check endpoint: GET /health
  • Application logs in Docker
  • GitHub Actions run history