BioStructBenchmark/.github/workflows/run_tests.yml at main · DeltaDesign/BioStructBenchmark · GitHub

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# This workflow runs linting, type checking, tests, and security scans

name: CI

on:
  push:
    branches: [main]
    paths-ignore:
      - README.md
      - "*.md"
  pull_request:
    branches: [main]
    paths-ignore:
      - README.md
      - "*.md"

# Cancel in-progress runs for the same branch/PR
concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

permissions:
  contents: read

jobs:
  lint:
    name: Lint and format check
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
        with:
          persist-credentials: false
      - name: Install uv
        uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7.1.4
        with:
          enable-cache: true
          cache-dependency-glob: "uv.lock"
      - name: Set up Python
        run: uv python install 3.13
      - name: Install dependencies
        run: uv sync --frozen --group dev
      - name: Check formatting
        run: uv run ruff format --check biostructbenchmark/ tests/
      - name: Lint
        run: uv run ruff check biostructbenchmark/ tests/

  typecheck:
    name: Type check
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
        with:
          persist-credentials: false
      - name: Install uv
        uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7.1.4
        with:
          enable-cache: true
          cache-dependency-glob: "uv.lock"
      - name: Set up Python
        run: uv python install 3.13
      - name: Install dependencies
        run: uv sync --frozen --group dev
      - name: Type check
        run: uv run mypy biostructbenchmark/

  test:
    name: Test with coverage
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
        with:
          persist-credentials: false
      - name: Install uv
        uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7.1.4
        with:
          enable-cache: true
          cache-dependency-glob: "uv.lock"
      - name: Set up Python
        run: uv python install 3.13
      - name: Install dependencies
        run: uv sync --frozen --group dev
      - name: Run tests with coverage
        run: uv run pytest -v --cov=biostructbenchmark --cov-report=term-missing --cov-fail-under=80

  security:
    name: Security scan
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
        with:
          persist-credentials: false
      - name: Install uv
        uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7.1.4
        with:
          enable-cache: true
          cache-dependency-glob: "uv.lock"
      - name: Set up Python
        run: uv python install 3.13
      - name: Install dependencies
        run: uv sync --frozen --group dev
      - name: Run Bandit
        run: uv run bandit -c pyproject.toml -r biostructbenchmark/
      - name: Run pip-audit
        # PYSEC-2022-42969: ReDoS in py library's SVN path parsing - dev dependency of interrogate, not exploitable
        run: uv run pip-audit --ignore-vuln PYSEC-2022-42969

  zizmor:
    name: GitHub Actions security scan
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
        with:
          persist-credentials: false
      - name: Run zizmor
        uses: zizmorcore/zizmor-action@e639db99335bc9038abc0e066dfcd72e23d26fb4 # v0.3.0