plotlyMol/.github/workflows/security.yml at main · The-Schultz-Lab/plotlyMol · GitHub

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name: Security

on:
  push:
    branches: [main, develop]
  pull_request:
    branches: [main, develop]
  schedule:
    # Run weekly on Monday at 08:00 UTC to catch newly disclosed CVEs
    - cron: "0 8 * * 1"

defaults:
  run:
    shell: bash -el {0}

jobs:
  dependency-audit:
    name: Dependency Audit (pip-audit)
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4

      - name: Set up conda environment
        uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: "3.11"
          environment-file: environment.yml
          activate-environment: plotlymol
          auto-activate: false
          miniforge-version: latest
          conda-solver: libmamba

      - name: Audit dependencies for known CVEs
        run: pip-audit --format=markdown --output=pip-audit-report.md || true

      - name: Upload audit report
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: pip-audit-report
          path: pip-audit-report.md
          retention-days: 30

      - name: Fail on known vulnerabilities
        # --strict would also fail on conda packages not found on PyPI (e.g. rdkit); omit it
        run: pip-audit

  codeql:
    name: CodeQL Static Analysis
    runs-on: ubuntu-latest
    permissions:
      security-events: write
      actions: read
      contents: read

    steps:
      - uses: actions/checkout@v4

      - name: Initialize CodeQL
        uses: github/codeql-action/init@v3
        with:
          languages: python
          # Detects: injection, path-traversal, XSS, unsafe deserialization, etc.
          queries: security-and-quality

      - name: Set up conda environment
        uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: "3.11"
          environment-file: environment.yml
          activate-environment: plotlymol
          auto-activate: false
          miniforge-version: latest
          conda-solver: libmamba

      - name: Install package
        run: pip install -e .

      - name: Perform CodeQL Analysis
        uses: github/codeql-action/analyze@v3
        with:
          category: "/language:python"