name: CI
on:
push:
branches: [ main, develop ]
pull_request:
branches: [ main, develop ]
jobs:
test:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest, macos-latest, windows-latest]
python-version: ["3.10", "3.11", "3.12"]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache pip packages
uses: actions/cache@v4
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -e ".[dev]"
- name: Run pre-commit hooks
run: |
pre-commit run --all-files
continue-on-error: true
- name: Run tests with pytest
run: |
pytest --cov=biopython_mcp --cov-report=xml --cov-report=term-missing
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v4
with:
file: ./coverage.xml
flags: unittests
name: codecov-umbrella
fail_ci_if_error: false
verbose: true
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
lint:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.11"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -e ".[dev]"
- name: Run Black
run: |
black --check biopython_mcp/ tests/
- name: Run Ruff
run: |
ruff check biopython_mcp/ tests/
- name: Run mypy
run: |
mypy biopython_mcp/
security:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.11"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install bandit safety
- name: Run Bandit security scan
run: |
bandit -r biopython_mcp/ -f json -o bandit-report.json
continue-on-error: true
- name: Run Safety check
run: |
safety check --json
continue-on-error: true
