scheduled_citedin_update.yml

name: Weekly fetch of WPID citations

on:
  workflow_dispatch:
  schedule:
  - cron: "0 0 * * 0"

concurrency:
  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
  cancel-in-progress: true

jobs:      
  fetch-pmc:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          submodules: true
          fetch-depth: 0
          ref: main

      - name: Setup R
        uses: r-lib/actions/setup-r@v2

      - name: Install packages
        run: |
          sudo apt-get update
          sudo apt-get install libcurl4-openssl-dev
          Rscript -e 'install.packages(c("utils","httr","xml2","dplyr","magrittr","RJSONIO","yaml","rvest"))'

      - name: Run citedin_lookup.R
        run: |
          Rscript -e "source('scripts/citedin_lookup.R')"

      - name: Commit to inbox
        uses: stefanzweifel/git-auto-commit-action@v5
        with:
          commit_message: new content from pmc