ci.yml

# Continuous integration
name: CI

on:
  pull_request:
    types: [opened, reopened, synchronize]
    paths:
      - "sleap_nn/**"
      - "tests/**"
      - ".github/workflows/ci.yml"
      - "environment_cpu.yml"
      - "environment_mac.yml"
      - "pyproject.toml"

defaults:
  # This is needed for running steps within conda environments.
  run:
    shell: bash -l {0}

jobs:
  # Lint with black, docstring check with pydocstyle, static type checking with mypy
  lint:
    # This job runs:
    #
    # 1. Linting with black
    #
    # 2. Docstring style checking with pydocstyle 
    # Note: This uses Google-style docstring convention
    # Ref: https://google.github.io/styleguide/pyguide.html
    name: Lint
    runs-on: "ubuntu-latest"
    steps:

    - name: Checkout repo
      uses: actions/checkout@v3

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: 3.9

    - name: Install dependencies
      run: |
        pip install --editable .[dev]

    - name: Run Black
      run: |
        black --check sleap_nn tests

    - name: Run ruff
      run: |
        ruff check sleap_nn/

  # Tests with pytest
  tests:
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest", "windows-latest", "macos-14"]
        python: [3.9]
        include:
          # Default values
          - env_file: environment_cpu.yml
          # Mac specific values
          - os: macos-14
            env_file: environment_mac.yml

    name: Tests (${{ matrix.os }}, Python ${{ matrix.python }})
    runs-on: ${{ matrix.os }}

    steps:
      - name: Checkout repo
        uses: actions/checkout@v3

      - name: Setup Conda
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-version: latest
          conda-solver: "libmamba"
          environment-file: ${{ matrix.env_file }}
          activate-environment: sleap-nn
          python-version: ${{ matrix.python }}

      - name: Print environment info
        shell: bash -l {0}
        run: |
          which python
          conda info
          conda list
          pip freeze

      - name: Test with pytest (with coverage)
        shell: bash -l {0}
        run: |
          pytest --cov=sleap_nn --cov-report=xml --durations=-1 tests/

      - name: Upload coverage
        uses: codecov/codecov-action@v4
        with:
          fail_ci_if_error: true
          verbose: false
          token: ${{ secrets.CODECOV_TOKEN }}