diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml new file mode 100644 index 0000000..28120d9 --- /dev/null +++ b/.github/workflows/pytest.yml @@ -0,0 +1,41 @@ +name: Tests + +on: + push: + branches: [ master ] + pull_request: + branches: [ master ] + +jobs: + test: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.13"] + + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + run: uv sync --all-extras --dev + + - name: Run linting (ruff check) + run: uv run ruff check . + shell: bash + + - name: Run type checking (mypy) + run: uv run mypy . + shell: bash + continue-on-error: true + + - name: Run tests with pytest + run: uv run pytest + shell: bash diff --git a/README.md b/README.md index 30c91d9..b02bc54 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ CyteOnto helps researchers benchmark cell type annotation algorithms by measurin ### Install ```bash # Clone the repository -git clone +git clone https://github.com/NygenAnalytics/CyteOnto.git cd CyteOnto # Setup environment @@ -149,7 +149,7 @@ We welcome contributions! Please see our contribution guidelines for details. ### Development Setup ```bash -git clone +git clone https://github.com/NygenAnalytics/CyteOnto.git cd CyteOnto uv sync --dev ```