ci.yml

# Continuous integration
name: CI

on:
  pull_request:
    types: [opened, reopened, synchronize]
    paths:
      - "sleap_roots/**"
      - "tests/**"
      - ".github/workflows/ci.yml"
      - "environment.yml"
  push:
    branches:
      - main
    paths:
      - "sleap_roots/**"
      - "tests/**"
      - ".github/workflows/ci.yml"
      - "environment.yml"

jobs:
  # Lint with black and docstring check with pydocstyle
  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-22.04"
    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_roots tests
    
    - name: Run pydocstyle
      run: |
        pydocstyle --convention=google sleap_roots/

  # Tests with pytest
  tests:
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-22.04", "windows-2022"]
        python: [3.9]

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

    steps:
      - name: Checkout repo
        uses: actions/checkout@v3
        with:
          lfs: true # Fetch large files with Git LFS

      - name: Setup Micromamba
        # https://github.com/mamba-org/setup-micromamba
        # Note: Set channel-priority in .condarc if needed
        uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: environment.yml
          cache-environment: true
          cache-environment-key: environment-${{ hashFiles('environment.yml') }}-${{ hashFiles('pyproject.toml') }}
          init-shell: >-
            bash
            powershell
          post-cleanup: all

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

      - name: Test with pytest
        if: ${{ !(startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9) }}
        shell: bash -l {0}
        run: |
          pytest

      - name: Test with pytest (with coverage)
        if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9 }}
        shell: bash -l {0}
        run: |
          pytest --cov=sleap_roots --cov-report=xml tests/

      - name: Upload coverage
        uses: codecov/codecov-action@v4
        if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9 }}
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          fail_ci_if_error: true
          verbose: false