data-tests.yaml

# This file determines when GitHub Actions (GA) is triggered and if so what
# sequence of steps continous integration takes.
#
# For a video tutorial explaining these steps click: https://youtu.be/JKF6aXtdLHs

# When any of these files are modified trigger GAs (except for the ones with a '!'):
on:
  push:
    paths:
      - 'raw_data/Field_Maps**'
      - '!raw_data/README.md'
      - 'R_scripts/CI_1_Generate_reports.R'
      - 'R_scripts/GitHubAction_checks.csv'
  pull_request:
    paths:
      - 'raw_data/Field_Maps**'
      - '!raw_data/README.md'
      - 'R_scripts/CI_1_Generate_reports.R'
      - 'R_scripts/GitHubAction_checks.csv'

# Name the workflow as it will appear on GA status page
# https://github.com/SCBI-ForestGEO/SCBImortality/actions
name: data-tests

# Here are all the steps GA takes when triggered:
jobs:
  data-tests:
    # Set the operating system GA assumes:
    runs-on: windows-latest
    
    # Allow only authorized collaborators to trigger GA:
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      
    # All steps in workflow: 
    steps:
      # Housekeeping - Import various actions to make process work:
      - uses: actions/checkout@v3
        # Use this action: https://github.com/actions/checkout#checkout-v3
      - uses: r-lib/actions/setup-r@v2
        # Use this action: https://github.com/r-lib/actions/tree/v2/setup-r
      - uses: r-lib/actions/setup-r-dependencies@v2
        
      # Housekeeping - Run package check (may not be needed):
      # - name: Check
      # run: |
      #   options(crayon.enabled = TRUE)
      #    rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
      #  shell: Rscript {0}
        
      # Run R script to generate error reports:
      - name: Generate reports
        id: Generate_reports
        run: |
          source("R_scripts/CI_1_Generate_reports.R")
        shell: Rscript {0}
        
      # Run R script to update progress map:
      - name: Update Progress Map                
        id: update_progress_map                   
        run: |
          source("R_scripts/CI_2_progress_map.R")      
        shell: Rscript {0}

        
        
      # Commit and push all new files, where commits are assigned to GA bot:
      - name: Commit new files
        run: |
          git config --local user.email "actions@github.com"
          git config --local user.name "GitHub Actions"
          git pull
          git add --all
          git commit -am "add data"
          git push