lineage_update.yml

name: Get new lineages from pango

on:
   schedule:
     - cron: '0 0,6,12,18 * * *'

jobs:
    scheduled_check:
       runs-on: ubuntu-20.04
       defaults:
           run:
             shell: bash
             working-directory: curated_reports_prep

       steps:
         - name: Checkout
           uses: actions/checkout@main
           with:
              repo-token: ${{ secrets.GITHUB_TOKEN }}
  
         - name: Install python dependencies
           run: python -m pip install --upgrade pip pandas

         - name: process data
           run: |
             echo "starting update"
             python lineages_hierarchy.py
             python generate_curated_lineages_json.py
             echo "removing log file"
             rm curated_lineages_json.log
         - name: commit if output is different 
           run: |
               echo "running git diff, committing if different"
               if [[($(git status ../web/src/assets/genomics/curated_lineages.json --porcelain | wc -c) -ne 0)]]; then
                  echo "changes were made, adding new lineage info"
                  git config --local user.name "$GITHUB_ACTOR"
                  git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
                  git add ../web/src/assets/genomics/curated_lineages.json
                  git add lineages.yml
                  git commit -m "updating lineage metadata"
                  git push origin master
               else
                  echo "no changes were made, doing nothing."
               fi;