ci_macos.yaml

name: CI MacOS

on: 
  pull_request:
    branch:
      - master
  schedule:
    - cron: 0 7 * * 1

jobs:
  run:
    name: Run pipeline
    timeout-minutes: 10
    runs-on: macos-latest
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - uses: actions/checkout@v2
      - uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: testenv
          auto-update-conda: false
          environment-file: environment.osx-64.lock
      - name: Install and check env
        run: |
          conda activate testenv
          pip install .[dev]
          conda info
          conda list
          dbspro --version
      - name: Run flake8
        run: |
          conda activate testenv
          flake8 src/ tests/
          flake8 --select=W292 --filename '*.yaml,*.yml'
      - name: Download test dataset
        env:
          testdata_version: "0.4"
        run: |
          wget -nv https://export.uppmax.uu.se/uppstore2018173/DBS-Pro-testdata-${testdata_version}.tar.gz
          tar xf DBS-Pro-testdata-${testdata_version}.tar.gz
          ln -s DBS-Pro-testdata-${testdata_version} testdata
      - name: Run tests
        run: |
          conda activate testenv
          # Required to make umi-tools output consistent. 
          export PYTHONHASHSEED=1 
          pytest -v tests/