ci.yml

# Continuous integration using conda installation
name: CI

on:
  pull_request:
    types: [opened, reopened, synchronize]
    paths:
      - "sleap/**"
      - "tests/**"
      - ".github/workflows/ci.yml"
      - "environment_no_cuda.yml"
      - "requirements.txt"
      - "dev_requirements.txt"
  push:
    branches:
      - master
      - develop
    paths:
      - "sleap/**"
      - "tests/**"
      - ".github/workflows/ci.yml"
      - "environment_no_cuda.yml"
      - "requirements.txt"
      - "dev_requirements.txt"

jobs:
  type_check:
    name: Type Check
    runs-on: "ubuntu-22.04"
    steps:
      - name: Checkout repo
        uses: actions/checkout@v3
      - name: Set up Python 3.7
        uses: actions/setup-python@v4
        with:
          python-version: 3.7
      - name: Install Dependencies
        run: |
          pip install mypy
      - name: Run MyPy
        # TODO: remove this once all MyPy errors get fixed
        continue-on-error: true
        run: |
          mypy --follow-imports=skip --ignore-missing-imports sleap tests
  lint:
    name: Lint
    runs-on: "ubuntu-22.04"
    steps:
      - name: Checkout repo
        uses: actions/checkout@v3
      - name: Set up Python 3.7
        uses: actions/setup-python@v4
        with:
          python-version: 3.7
      - name: Install Dependencies
        run: |
          pip install click==8.0.4
          pip install black==21.6b0
      - name: Run Black
        run: |
          black --check sleap tests
  tests:
    name: Tests (${{ matrix.os }})
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-22.04", "windows-2022", "macos-latest"]
        include:
          # Default values
          - env_file: environment_no_cuda.yml
          - test_args: --durations=-1 tests/
          # Mac specific values
          - os: macos-latest
            env_file: environment_mac.yml
          # Ubuntu specific values
          - os: ubuntu-22.04
            test_args: --cov=sleap --cov-report=xml --durations=-1 tests/
    steps:
      - name: Checkout repo
        uses: actions/checkout@v3

      - name: Setup Micromamba
        # https://github.com/mamba-org/setup-micromamba
        uses: mamba-org/setup-micromamba@v1
        with:
          micromamba-version: '1.4.6-0'
          environment-file: ${{ matrix.env_file }}
          environment-name: sleap_ci
          init-shell: >-
            bash
            powershell
          post-cleanup: all
      
      # Print environment info
      - name: Print environment info
        shell: bash -l {0}
        run: |
          which python
          micromamba info
          micromamba list
          pip freeze
      
      # Test environment
      - name: Test with pytest
        shell: bash -l {0}
        run: |
          pytest ${{ matrix.test_args }}

      # Upload coverage
      - name: Upload coverage
        uses: codecov/codecov-action@v1
        if: matrix.os == 'ubuntu-22.04'
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          fail_ci_if_error: true
          verbose: false