run_tox.yml

name: run_tox
on:
  workflow_dispatch:
  push:
    paths-ignore:
    - README.md
    - .gitignore
  pull_request:
  # schedule:
  #   - cron: "0 8 * * *"

concurrency:
  group: runtests-${{ github.ref }}
  cancel-in-progress: true

jobs:
  test:
    name: test with ${{ matrix.py }} on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        py:
          # - "3.12"
          # - "3.11"
          - "3.10"
          # - "3.9"
          - "3.8"
          # - "3.7" # end-of-life reached
        os:
          - ubuntu-latest
          # - macos-latest
          # - windows-latest
    steps:
      - uses: actions/checkout@v3
        with:
          fetch-depth: 0
          token: ${{ secrets.PAT }} # the special secrets.GITHUB_TOKEN only allows access to the current repository, so we added a personal access token with scope "repo" as a secret to this repo
          submodules: true
      - name: Setup python for test ${{ matrix.py }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.py }}
      - name: Install minimap2
        run: curl -L https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2 | tar -jxvf -
      - name: Fix pyproject for tox
        run: |
          sed -i'.backup' "s@{root:uri}@file://$(pwd)@g" pyproject.toml

          # does not work
          # replace {root:uri} by "file:." in pyproject.toml since tox does not understand it
          # sed -i 's/{root:uri}/file:./g' pyproject.toml
          # remove line that contains {root:uri}
          # sed -i '/{root:uri}/d' pyproject.toml
      - name: Install tox
        run: python -m pip install tox-gh>=1.2
      - name: Setup test suite
        run: tox -vv --notest
      - name: Run test suite
        run: PATH="$(pwd)/minimap2-2.26_x64-linux:$PATH" tox --skip-pkg-install
        # run: PATH="$(pwd)/minimap2-2.26_x64-linux:$PATH" tox --skip-pkg-install -- tests/usecase_helpers/test_run_simulator_with_readfish.py
      - name: archive if failure
        if: ${{ failure() }}
        uses: actions/upload-artifact@v3
        with:
          name: ${{ matrix.os }}-${{ matrix.py }}-${{ github.sha }}
          retention-days: 1
          path: /tmp/pytest-of-runner/
          # path: /tmp/pytest-of-runner/pytest-0/test_simulator_with_readfish0/data/run_dir/simulator_run/reads