CI_build.yml

name: CI Build

on:
  push:
  pull_request:
    types: [opened, reopened]

jobs:

  thorough_check:
    name: Thorough code check / python-3.9 / ubuntu-latest
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: 3.9
      - name: Python info
        run: |
          which python
          python --version
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e .[dev]
      - name: Show pip list
        run: |
          pip list
      - name: Run test with coverage
        run: pytest --cov --cov-report term --cov-report xml -m "not integration"
      - name: Check style against standards using prospector
        run: prospector -o grouped -o pylint:pylint-report.txt --ignore-paths notebooks
      - name: Check whether import statements are used consistently
        run: isort --check-only --diff .
      - name: SonarCloud Scan
        uses: sonarsource/sonarcloud-github-action@master
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

  basic_checks:
    name: Basic code checks / python-${{ matrix.python-version }} / ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
        python-version: ['3.9', '3.10']
        exclude:
          # already tested in first_check job
          - python-version: 3.9
            os: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
      - name: Python info
        run: |
          which python
          python --version
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e .[dev]
      - name: Show pip list
        run: |
          pip list
      - name: Run tests
        run: |
          pytest -m "not integration"

  integration_checks:
    name: Integration code checks / python-${{ matrix.python-version }} / ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: ['ubuntu-latest']
        python-version: ['3.9']
    steps:
      - uses: actions/checkout@v2
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
      - name: Python info
        run: |
          which python
          python --version
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e .[dev]
      - name: Show pip list
        run: |
          pip list
      - name: Run tests
        run: |
          pytest -m "integration"
  yml_checks:
    name: envionment.yml checks / python-${{ matrix.python-version }} / ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0}
    runs-on: 'ubuntu-latest'
    steps:
      - uses: actions/checkout@v2
      - name: Set up Miniconda
        uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: ms2query
          environment-file: ./environment.yml
          python-version: 3.9
      - name: activate conda environment
        run: |
          conda activate ms2query
      - name: Show conda list
        run: |
          conda info
          conda list
      - name: Run tests
        run: |
          pytest -m "not integration"