Add an installation shell script for Linux/MacOS #57
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| name: ⏬ Install Script | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| paths: | |
| - '.github/workflows/install-script.yml' | |
| - 'install.sh' | |
| push: | |
| branches: [main] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| installation-from-script: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| flags: | |
| - --force --verbose | |
| - --force --dryrun | |
| include: | |
| - flags: --force --verbose | |
| to_cache: true | |
| name: Install RTMet from shell script | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -li {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/cache@v3 | |
| name: Cache Workflow installation | |
| id: cache-rtmet | |
| if: ${{ matrix.to_cache }} | |
| with: | |
| key: rtmet-${{ runner.os }}-envs-${{ hashFiles('cylc-src/bioreactor-workflow/envs/*') }}-script-${{ hashFiles('install.sh') }} | |
| path: | | |
| /home/runner/miniforge3/ | |
| /home/runner/.bashrc | |
| /usr/local/bin/cylc | |
| /usr/local/bin/rose | |
| - name: run install.sh script | |
| if: ${{ steps.cache-rtmet.outputs.cache-hit != 'true' || !matrix.to_cache }} | |
| run: | | |
| bash install.sh ${{ matrix.flags }} | |
| - name: install binneR | |
| if: ${{ matrix.to_cache }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| conda run -p /home/runner/miniforge3/envs/wf-binner \ | |
| Rscript -e "remotes::install_github('aberHRML/binneR', upgrade='never')" | |
| - name: force conda path | |
| run: | | |
| echo "export PATH=/home/runner/miniforge3/condabin:$PATH" >> $HOME/.bashrc | |
| validate-installation: | |
| needs: installation-from-script | |
| name: Validate RTMet installation | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -li {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/cache@v3 | |
| with: | |
| key: rtmet-${{ runner.os }}-envs-${{ hashFiles('cylc-src/bioreactor-workflow/envs/*') }}-script-${{ hashFiles('install.sh') }} | |
| fail-on-cache-miss: true | |
| path: | | |
| /home/runner/miniforge3/ | |
| /home/runner/.bashrc | |
| /usr/local/bin/cylc | |
| /usr/local/bin/rose | |
| - name: Copy bioreactor-workflow to sources | |
| run: | | |
| mkdir -p $HOME/cylc-src | |
| cp -r cylc-src/bioreactor-workflow/ $HOME/cylc-src/ | |
| - name: validate RTMet | |
| run: | | |
| cylc --help | |
| rose --help | |
| conda run -p /home/runner/miniforge3/envs/wf-datamunging \ | |
| frictionless --help | |
| conda activate wf-datamunging | |
| frictionless --help | |
| conda deactivate | |
| cylc install bioreactor-workflow \ | |
| --run-name=test-run | |
| cylc validate bioreactor-workflow/test-run | |
| mkdir -p $HOME/cylc-run/bioreactor-workflow/test-run/raws/ | |
| cp $GITHUB_WORKSPACE/test/tutorial_raws/* \ | |
| $HOME/cylc-run/bioreactor-workflow/test-run/raws/ | |
| cylc play bioreactor-workflow/test-run \ | |
| --no-detach \ | |
| --abort-if-any-task-fails \ | |
| --final-cycle-point=3 | |