fix: job status method #101
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| env: | |
| PYTHON_VERSION: 3.11 | |
| jobs: | |
| formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out the code | |
| uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| - name: Install poetry | |
| run: pip install poetry | |
| - name: Determine dependencies | |
| run: poetry lock | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| cache: poetry | |
| - name: Install Dependencies using Poetry | |
| run: poetry install | |
| - name: Check formatting | |
| run: poetry run black --check . | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out the code | |
| uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| - name: Install poetry | |
| run: pip install poetry | |
| - name: Determine dependencies | |
| run: poetry lock | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| cache: poetry | |
| - name: Install Dependencies using Poetry | |
| run: poetry install | |
| - name: Check code | |
| run: poetry run flake8 | |
| testing: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: htcondor/mini | |
| env: | |
| PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/submituser/.local/bin | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Python and more yum | |
| run: | | |
| yum install -y python${{ env.PYTHON_VERSION }} | |
| yum install -y python${{ env.PYTHON_VERSION }}-pip | |
| yum install -y python${{ env.PYTHON_VERSION }}-devel | |
| yum install -y gcc | |
| - name: HTCondor master | |
| run: condor_master | |
| - name: Test submit to HTCondor | |
| run: su -c "condor_submit tests/sleep.sub" submituser | |
| - name: Install poetry | |
| run: su -c "pip${{ env.PYTHON_VERSION }} install poetry" submituser | |
| - name: Determine dependencies | |
| run: su -c "poetry lock" submituser | |
| - name: Install dependencies | |
| run: su -c "poetry install" submituser | |
| - name: Run pytest | |
| run: su -c "poetry run coverage run -m pytest tests/tests.py -vvv" submituser | |
| - name: Check HTCondor logs | |
| run: | | |
| ls /tmp/pytest-of-submituser/pytest-0/test_simple_workflow0/simple/.snakemake/htcondor | |
| for file in /tmp/pytest-of-submituser/pytest-0/test_simple_workflow0/simple/.snakemake/htcondor/*.log; do cat "$file"; done | |
| - name: Check HTCondor errors | |
| run: | | |
| ls /tmp/pytest-of-submituser/pytest-0/test_simple_workflow0/simple/.snakemake/htcondor | |
| for file in /tmp/pytest-of-submituser/pytest-0/test_simple_workflow0/simple/.snakemake/htcondor/*.err; do cat "$file"; done | |
| - name: Run Coverage | |
| run: su -c "poetry run coverage report -m --omit=Snakefile" submituser |