fix: update plugin to include docs and fix docker build #26
Workflow file for this run
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| name: CI | |
| on: | |
| pull_request: [] | |
| jobs: | |
| formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out the code | |
| uses: actions/checkout@v4 | |
| - name: Install poetry | |
| run: pipx install poetry | |
| - name: Determine dependencies | |
| run: poetry lock | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| 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 | |
| - name: Install poetry | |
| run: pipx install poetry | |
| - name: Determine dependencies | |
| run: poetry lock | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| cache: poetry | |
| - name: Install Dependencies using Poetry | |
| run: poetry install | |
| - name: Check code | |
| run: poetry run flake8 | |
| # testing: | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - name: Check out the code | |
| # uses: actions/checkout@v3 | |
| # - name: Install poetry | |
| # run: pipx install poetry | |
| # - name: Determine dependencies | |
| # run: poetry lock | |
| # - uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: "3.9" | |
| # cache: poetry | |
| # - name: Install Dependencies using Poetry | |
| # run: poetry install | |
| # - name: Run pytest | |
| # run: poetry run coverage run -m pytest tests/tests.py | |
| # - name: Run Coverage | |
| # run: poetry run coverage report -m | |
| testing: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| packages: read | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| container: ["fluxrm/flux-sched:jammy"] | |
| container: | |
| image: ${{ matrix.container }} | |
| options: "--platform=linux/amd64 --user root -it" | |
| name: ${{ matrix.container }} | |
| steps: | |
| - name: Update environment for Flux | |
| run: | | |
| echo "/opt/conda/bin" >> $GITHUB_PATH | |
| echo "/root/.local/bin" >> $GITHUB_PATH | |
| echo "FLUX_MODULE_PATH=${FLUX_MODULE_PATH}:/usr/lib/x86_64-linux-gnu/flux/modules" >> ${GITHUB_ENV} | |
| - name: Make Space | |
| run: | | |
| rm -rf /usr/share/dotnet | |
| rm -rf /opt/ghc | |
| - uses: actions/checkout@v4 | |
| - name: Install poetry | |
| run: | | |
| sudo apt-get install -y python3-pip | |
| ln -s $(which python3) /bin/python | |
| - name: Install dependencies | |
| run: | | |
| python3 -m pip install git+https://github.com/vsoch/snakemake@update-lazy-property-import | |
| python3 -m pip install . | |
| - name: Start Flux and Test Workflow | |
| run: | | |
| # We must have python3->python accessible for this to work | |
| su fluxuser | |
| echo "ROOT=$PWD" >> $GITHUB_ENV | |
| cd example | |
| which snakemake | |
| python3 -m pip freeze | grep snakemake | |
| pip freeze | grep snakemake | |
| flux start snakemake --show-failed-logs --verbose --executor flux --jobs=1 --no-shared-fs | |
| - name: Test Flux with Conda | |
| run: | | |
| # conda python needs to be after system python | |
| wget https://repo.anaconda.com/archive/Anaconda3-2023.09-0-Linux-x86_64.sh | |
| sudo bash Anaconda3-2023.09-0-Linux-x86_64.sh -p /opt/conda -b | |
| export PATH=$PATH:/opt/conda/bin | |
| # Now install again | |
| python3 -m pip install git+https://github.com/vsoch/snakemake@update-lazy-property-import | |
| cd $ROOT | |
| python3 -m pip install . | |
| which python | |
| which conda | |
| cd $ROOT/example/conda | |
| flux start snakemake --show-failed-logs --verbose --executor flux --jobs=1 --use-conda --conda-frontend=conda |