adding cli, other fixes #3
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| 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 |