feat: visjs #124
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| name: Test SPRAS | |
| on: | |
| pull_request: | |
| branches: [main] | |
| push: | |
| branches: [main] | |
| # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages | |
| permissions: | |
| contents: read | |
| pages: write | |
| id-token: write | |
| jobs: | |
| pre-commit: | |
| name: Run pre-commit checks | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - name: Run pre-commit checks | |
| uses: pre-commit/[email protected] | |
| checks: | |
| name: Run workflow | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Install uv for scripting | |
| uses: astral-sh/[email protected] | |
| with: | |
| version: "0.7.13" | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: spras | |
| environment-file: spras/environment.yml | |
| auto-activate-base: false | |
| miniconda-version: 'latest' | |
| # Install spras in the environment using pip | |
| - name: Install spras in conda env | |
| shell: bash --login {0} | |
| run: pip install ./spras | |
| # Log conda environment contents | |
| - name: Log conda environment | |
| shell: bash --login {0} | |
| run: conda list | |
| - name: Process raw data through Snakemake | |
| run: sh run_snakemake.sh | |
| - name: Run Snakemake workflow for DMMMs | |
| shell: bash --login {0} | |
| run: snakemake --cores 4 --configfile configs/dmmm.yaml --show-failed-logs -s spras/Snakefile | |
| - name: Run Snakemake workflow for PRAs | |
| shell: bash --login {0} | |
| run: snakemake --cores 4 --configfile configs/pra.yaml --show-failed-logs -s spras/Snakefile | |
| - name: Setup PNPM | |
| uses: pnpm/action-setup@v4 | |
| with: | |
| version: 10 | |
| - name: Install web dependencies | |
| working-directory: ./web | |
| run: pnpm install | |
| - name: Run web builder | |
| working-directory: ./web | |
| run: pnpm build | |
| - name: Upload built website distribution folder | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build | |
| path: web/dist | |
| pages: | |
| needs: checks | |
| if: github.event_name != 'pull_request' | |
| runs-on: ubuntu-latest | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| concurrency: | |
| group: 'pages' | |
| cancel-in-progress: true | |
| steps: | |
| - name: Download Artifacts | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build | |
| path: dist | |
| - name: Setup Pages | |
| uses: actions/configure-pages@v2 | |
| - name: Upload artifact | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: dist | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 |