notebook_check_r.yml

name: Execute R notebooks

on:
  pull_request:
  workflow_dispatch:
  # run once a week
  schedule:
    - cron: "0 0 * * 0"

jobs:
  build:
    runs-on: ubuntu-latest

    steps:
    - id: checkout
      uses: actions/checkout@v3

    - id: python-setup
      name: Set up Python
      uses: actions/setup-python@v2
      with:
        python-version: '3.11'

    - id: install-juptyer
      name: Install Juptyer
      run: |
        python -m pip install --upgrade pip
        pip install jupyter

    - id: r-setup
      name: Set up R
      uses: r-lib/actions/setup-r@v2

    - id: r-dependencies
      name: Install r dependencies
      run: |
        R -e 'install.packages("renv")'
        R -e 'renv::restore()'
        R -e 'install.packages("IRkernel")'
        R -e 'IRkernel::installspec()'

    - id: execute-bioscales
      name: Execute bioscales notebook
      run: |
        jupyter nbconvert --execute --to notebook --inplace bioscales_biogeochemical_metadata/R/bioscales_metadata.ipynb

    - id: execute-neon
      name: Execute NEON metadata notebook
      run: |
        jupyter nbconvert --execute --to notebook --inplace NEON_soil_metadata/R/NEON_data_exploration.ipynb

    - id: execute-taxonomic
      name: Execute taxonomic metadata notebook
      run: |
        jupyter nbconvert --execute --to notebook --inplace taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb