update.yml

name: Update
on:
  schedule:
    - cron: "0 5 * * 1"
  push:
    branches: [main]
jobs:
  run_script_and_update:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}
    permissions:
      contents: write

    steps:
      - name: Checkout Repository
        uses: actions/checkout@v4
        with:
          persist-credentials: true
          fetch-depth: 0
          clean: true

      - name: setup miniconda
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-variant: Mambaforge
          miniforge-version: latest
          use-mamba: true
          auto-activate-base: false
          activate-environment: test
          auto-update-conda: true
          python-version: "3.11"
          environment-file: etc/example-environment.yml

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: "4.2.3"
          use-public-rspm: true
      - run: Rscript -e 'install.packages(c("stringr", "tibble","data.table","stringr", "purrr", "usethis"))'

      - name: Run bash scripts1
        run: |
          git submodule update --init --recursive
          ls -al ./metadata/journals

      - name: Run bash scripts2
        run: |
          ls -al
          bash ./main.sh