Merge branch 'main' into pr/vsoch/2305 #39
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| name: Test Flux Executor | |
| # TODO temporarily disable flux executor tests as the test container is based on Python 3.8 but Snakemake now requires Python 3.9 | |
| # on: | |
| # pull_request: [] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| packages: read | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| container: ["fluxrm/flux-sched:focal"] | |
| container: | |
| image: ${{ matrix.container }} | |
| options: "--platform=linux/amd64 --user root -it" | |
| name: ${{ matrix.container }} | |
| steps: | |
| - name: Make Space | |
| run: | | |
| rm -rf /usr/share/dotnet | |
| rm -rf /opt/ghc | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: snakemake | |
| channels: "conda-forge, bioconda" | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| - name: Install Snakemake | |
| shell: bash -el {0} | |
| run: | | |
| conda config --set channel_priority strict | |
| mamba install python>=3.9 pip | |
| # TODO remove and add as regular dependency once released | |
| pip install git+https://github.com/snakemake/snakemake-interface-executor-plugins.git | |
| pip install . | |
| - name: Start Flux and Test Workflow | |
| shell: bash -el {0} | |
| run: | | |
| # We must have python3->python accessible for this to work | |
| ln -s /bin/python3 /usr/local/bin/python | |
| su fluxuser | |
| cd examples/flux | |
| # This run does not use conda | |
| which snakemake | |
| flux start snakemake --show-failed-logs --verbose --flux --jobs=1 --no-shared-fs | |
| - name: Test Flux with Conda | |
| shell: bash -el {0} | |
| run: | | |
| which python | |
| which conda | |
| cp -R ./tests/test_conda /tmp/test_conda | |
| cd /tmp/test_conda | |
| flux start snakemake --show-failed-logs --verbose --flux --jobs=1 --use-conda --conda-frontend=conda |