Check for new pangolin Release #1244
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| 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 }}" |