Create new modeling round #67
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| name: Create new modeling round | |
| on: | |
| schedule: | |
| - cron: "0 03 * * 1" # every Monday at 3 AM UTC | |
| workflow_dispatch: | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| jobs: | |
| create-clade-modeling-round: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout 🛎️ | |
| uses: actions/checkout@v4 | |
| with: | |
| # don't check out repo folders with large amounts of data | |
| # (e.g., model-output, target-data) | |
| sparse-checkout: | | |
| auxiliary-data/ | |
| hub-config/ | |
| src/ | |
| - name: Install uv 🐍 | |
| uses: astral-sh/setup-uv@v2 | |
| with: | |
| version: "0.4.9" | |
| - name: Set up R 📊 | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 4.4.1 | |
| install-r: true | |
| use-public-rspm: true | |
| extra-repositories: 'https://hubverse-org.r-universe.dev' | |
| - name: Set up renv 📦 | |
| uses: r-lib/actions/setup-renv@v2 | |
| with: | |
| working-directory: src | |
| - name: Create clade list and update tasks.json 🦠 | |
| run: | | |
| uv run get_clades_to_model.py | |
| Rscript make_round_config.R | |
| working-directory: src | |
| - name: Get current date and time 🕰️ | |
| run: | | |
| PR_DATETIME=$(date +'%Y-%m-%d_%H-%M-%S') | |
| echo "PR_DATETIME=$PR_DATETIME" >> $GITHUB_ENV | |
| - name: Create PR for new modeling round 🚀 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| git config user.name "github-actions[bot]" | |
| git config user.email "41898282+github-actions[bot]@users.noreply.github.com" | |
| git checkout -b new_round_"$PR_DATETIME" | |
| git add auxiliary-data/modeled-clades/ | |
| git add hub-config/ | |
| git commit -m "Add new round $PR_DATETIME" | |
| git push -u origin new_round_"$PR_DATETIME" | |
| gh pr create \ | |
| --base main \ | |
| --title "Add new round $PR_DATETIME" \ | |
| --body "This PR was created via GitHub Actions: generate clade list and add new round to tasks.json." |