Update main branch #122
Workflow file for this run
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| name: Run tests | |
| on: | |
| push: | |
| branches: [main, dev] | |
| pull_request: | |
| branches: [main, dev] | |
| jobs: | |
| run-tests: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest", "windows-latest"] | |
| python-version: ["3.8"] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: check files | |
| run: | | |
| ls ${{ github.workspace }} | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| # miniforge-version: latest | |
| use-mamba: true | |
| channel-priority: strict | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: environment.yml | |
| activate-environment: vaep | |
| auto-activate-base: true | |
| # auto-update-conda: true | |
| - name: inspect-conda-environment | |
| run: | | |
| conda info | |
| conda list | |
| conda info -e | |
| - name: test-r-kernel-imports | |
| run: | | |
| Rscript -e "library(stringi)" | |
| Rscript -e "library(stringr)" | |
| Rscript -e "library(reshape2)" | |
| # # currently part of environment | |
| # - name: Install package and install library | |
| # run: | | |
| # pip install pytest | |
| - name: Run Tests on installed package | |
| run: pytest . | |
| - name: View papermill help message for notebooks (as scripts) | |
| run: | | |
| cd project | |
| papermill 01_0_split_data.ipynb --help-notebook | |
| papermill 01_1_train_VAE.ipynb --help-notebook | |
| papermill 01_1_train_DAE.ipynb --help-notebook | |
| papermill 01_1_train_CF.ipynb --help-notebook | |
| - name: Run demo workflow | |
| run: | | |
| cd project | |
| snakemake -p -c1 -n | |
| snakemake -p -c1 | |
| - name: Archive results | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: example-workflow-results-${{ matrix.os }} | |
| path: project/runs/example/01_2_performance_plots.html |