Check for new pangolin Release #1263
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Check for new pangolin Release | |
| on: | |
| schedule: | |
| # At the end of every day | |
| - cron: "0 0 * * *" | |
| jobs: | |
| Create-PR-for-new-Pangolin-release: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install mamba | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| mamba-version: "*" | |
| channels: bioconda,conda-forge,defaults | |
| channel-priority: true | |
| - name: Get latest Pangolin release | |
| shell: bash -l {0} | |
| run: | | |
| echo "LATEST_PANGOLIN=$(mamba search -f pangolin -c bioconda | tail -n1 | awk '{print $2}')" >> $GITHUB_ENV | |
| echo "Latest Pangolin release: $(mamba search -f pangolin -c bioconda | tail -n1 | awk '{print $2}')" | |
| - name: Get Pangolin release used in UnCoVar | |
| run: | | |
| echo "CURRENT_PANGOLIN=$(cat workflow/envs/pangolin.yaml | grep pangolin | awk -F "=" '{print $2}')" >> $GITHUB_ENV | |
| echo "Current Pangolin release: $(cat workflow/envs/pangolin.yaml | grep pangolin | awk -F "=" '{print $2}')" | |
| - name: Update Pangolin release used in UnCoVar | |
| if: ${{ env.LATEST_PANGOLIN != env.CURRENT_PANGOLIN }} | |
| run: | | |
| sed -i 's/${{ env.CURRENT_PANGOLIN }}/${{ env.LATEST_PANGOLIN }}/' workflow/envs/pangolin.yaml | |
| - name: Create Pull Request | |
| if: ${{ env.LATEST_PANGOLIN != env.CURRENT_PANGOLIN }} | |
| id: cpr | |
| uses: peter-evans/create-pull-request@v7 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| committer: GitHub <[email protected]> | |
| commit-message: Update pangolin to ${{ env.LATEST_PANGOLIN }} | |
| author: ${{ github.actor }} <${{ github.actor }}@users.noreply.github.com> | |
| branch: pangolin-update-to-${{ env.LATEST_PANGOLIN }} | |
| delete-branch: true | |
| title: "build: update Pangolin to ${{ env.LATEST_PANGOLIN }}" | |
| body: | | |
| Hey there, a new release of Pangolin is available: [${{ env.LATEST_PANGOLIN }}](https://github.com/cov-lineages/pangolin/releases/tag/v${{ env.LATEST_PANGOLIN }}) | |
| Auto-generated by [create-pull-request][1] | |
| [1]: https://github.com/peter-evans/create-pull-request | |
| labels: | | |
| automated pr | |
| - name: Check outputs | |
| run: | | |
| echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}" | |
| echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}" |