Merge pull request #230 from BAMresearch/AidaZt-patch-1 #2663
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| name: lebedigital | |
| on: | |
| push: | |
| branches-ignore: | |
| pull_request: | |
| branches: [ main ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| env: | |
| CACHE_NUMBER: 2 # increase to reset cache manually | |
| jobs: | |
| tests: | |
| runs-on: ubuntu-latest | |
| env: | |
| OPENBIS_STATE_DIR: openbis/openbis_state | |
| steps: | |
| - name: build docker | |
| run: | | |
| mkdir -p $OPENBIS_STATE_DIR | |
| docker run -d --name=openbis -e SERVER_HOST_PORT="localhost:443" -e GROUP_ID=12940 -e GROUP_NAME="docker-host-folder-group" -e CORE_PLUGINS='enabled-modules = dropbox-monitor, dataset-uploader, dataset-file-search, xls-import, openbis-sync, eln-lims, openbis-ng-ui, search-store' -v /home/$OPENBIS_STATE_DIR:/home/openbis/openbis_state -p 8443:443 --restart=always openbis/debian-openbis:20.10.4 | |
| - name: checkout repo content | |
| uses: actions/checkout@v2 | |
| - name: Setup Mambaforge | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: lebedigital | |
| use-mamba: true | |
| - name: Set cache date | |
| run: echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV | |
| - uses: actions/cache@v2 | |
| with: | |
| path: "/usr/share/miniconda3/envs/lebedigital" | |
| key: conda-${{ hashFiles('environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }} | |
| id: cache | |
| - name: Update environment | |
| run: mamba env update -n lebedigital -f environment.yml | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - name: set default docker settings | |
| shell: bash -l {0} | |
| run: | | |
| cd $GITHUB_WORKSPACE/usecases/openbis_docker_setup/ | |
| python3 -m init_settings_docker --login admin --password changeit --url https://localhost:8443/openbis/ | |
| - name: pytest | |
| id: pytest | |
| shell: bash -l {0} | |
| run: | | |
| cd $GITHUB_WORKSPACE/tests/ | |
| pytest -s --login admin --password changeit | |
| - name: run-minimum-working-example | |
| shell: bash -l {0} | |
| run: | | |
| cd $GITHUB_WORKSPACE/usecases/MinimumWorkingExample/ | |
| doit runson=docker dataset_upload=no | |
| - name: run-optimization-workflow | |
| shell: bash -l {0} | |
| run: | | |
| cd $GITHUB_WORKSPACE/usecases/optimization_paper/optimization_workflow/ | |
| snakemake -c 1 | |
| - name: run-optimization-paper | |
| shell: bash -l {0} | |
| run: | | |
| cd $GITHUB_WORKSPACE/usecases/optimization_paper/ | |
| doit | |
| - name: Archive results of minimum working example | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: minimum_working_example_results | |
| path: | | |
| usecases/MinimumWorkingExample/emodul/ | |
| usecases/MinimumWorkingExample/mixture/ | |
| - name: Archive optimization paper pdf | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: optimization_paper | |
| path: | | |
| usecases/optimization_paper/tex/optimization_paper.pdf | |
| usecases/optimization_paper/figures/ | |
| usecases/optimization_paper/optimization_workflow/Results | |