Run USA models #40
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| name: Run USA models | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| # Run every Wednesday at 10am PT which is 5pm (17:00) UTC. | |
| - cron: '0 17 * * 3' | |
| jobs: | |
| run_models: | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| runtime: docker | |
| run: | | |
| nextstrain build \ | |
| --image nextstrain/base \ | |
| --env AWS_DEFAULT_REGION \ | |
| --env GITHUB_RUN_ID \ | |
| . \ | |
| prepare_all_hub_submissions \ | |
| --configfile config/config.yaml config/variant_hub.yaml | |
| env: | | |
| GITHUB_RUN_ID: ${{ github.run_id }} | |
| artifact-name: model-outputs | |
| artifact-paths: | | |
| hub/submissions.txt | |
| hub/model-output/ | |
| !results/ | |
| upload_models: | |
| needs: [run_models] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Extract model outputs | |
| uses: actions/download-artifact@v6 | |
| with: | |
| name: model-outputs | |
| - name: Clone fork of variant nowcast hub | |
| uses: actions/checkout@v6 | |
| with: | |
| repository: nextstrain/variant-nowcast-hub | |
| path: variant-nowcast-hub | |
| token: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_REPO }} | |
| - name: Upload model outputs to hub fork | |
| run: | | |
| rsync -arvz --files-from=hub/submissions.txt hub/ variant-nowcast-hub/ | |
| cd variant-nowcast-hub | |
| export DATE="$(date "+%Y-%m-%d")" | |
| git switch -c blab-${DATE} | |
| git add --pathspec-from-file=../hub/submissions.txt | |
| git commit -m "Add blab models for ${DATE}" | |
| git push origin blab-${DATE} | |
| gh api \ | |
| --method POST \ | |
| -H "Accept: application/vnd.github+json" \ | |
| -H "X-GitHub-Api-Version: 2022-11-28" \ | |
| /repos/${HUB_OWNER}/${HUB_REPO}/pulls \ | |
| -f title="Add blab models for ${DATE}" \ | |
| -f body="" \ | |
| -f head="nextstrain:blab-${DATE}" \ | |
| -f base=main | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_REPO }} | |
| GIT_AUTHOR_EMAIL: ${{ vars.GIT_USER_EMAIL_NEXTSTRAIN_BOT }} | |
| GIT_AUTHOR_NAME: ${{ vars.GIT_USER_NAME_NEXTSTRAIN_BOT }} | |
| GIT_COMMITTER_EMAIL: ${{ vars.GIT_USER_EMAIL_NEXTSTRAIN_BOT }} | |
| GIT_COMMITTER_NAME: ${{ vars.GIT_USER_NAME_NEXTSTRAIN_BOT }} | |
| HUB_OWNER: reichlab | |
| HUB_REPO: variant-nowcast-hub |