notebook_check_python.yml

name: Execute python 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: python-dependencies
      name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install -r requirements_dev.txt
        pip install jupyter

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

    - id: execute-neon
      name: Execute neon notebook
      run: |
        jupyter nbconvert --execute --to notebook --inplace NEON_soil_metadata/python/neon_soil_metadata_visual_exploration.ipynb

    - id: execute-taxonomic
      name: Execute taxonomic notebook
      run: |
        jupyter nbconvert --execute --to notebook --inplace taxonomic_dist_by_soil_layer/python/taxonomic_dist_soil_layer.ipynb

    - id: execute-NOM
      name: Execute NOM notebook
      run: |
        jupyter nbconvert --execute --to notebook --inplace NOM_visualizations/python/nom_data.ipynb