QA_QC_checks.yaml

# Set the list of files that when modified will trigger GitHub Actions
# (GA) continuous integration (CI) to run

# For a video tutorial explaining these steps for the similarly structured
# SCBI mortality census (https://github.com/SCBI-ForestGEO/SCBImortality),
# click this link to YouTube: https://youtu.be/JKF6aXtdLHs

on:
  push:
    paths:
      - 'resources/raw_data/**'
      - 'Rscripts/survey_forms/create_master_csv_2021_and_after.R'
      - 'Rscripts/Generate_reports.R'
      - 'Rscripts/Generate_warnings.R'
      - 'README.Rmd'
  pull_request:
    paths:
      - 'resources/raw_data/**'
      - 'Rscripts/survey_forms/create_master_csv_2021_and_after.R'
      - 'Rscripts/Generate_reports.R'
      - 'Rscripts/Generate_warnings.R'
      - 'README.Rmd'

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

jobs:
  QA_QC_checks:
    # Set the operating system CI assumes:
    runs-on: macOS-latest
    
    # Allow only authorized collaborators to trigger GA:
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      
    # All steps in workflow:
    steps:
      # Housekeeping: Use various GA tools, install R, install pandoc
      # (to be able to use RMarkdown)
      - uses: actions/checkout@v3
      - uses: r-lib/actions/setup-r@v2
      - uses: r-lib/actions/setup-pandoc@v2
           
      
      # Housekeeping: Install all packages listed in DESCRIPTION file
      - name: Install dependencies
        run: |
          install.packages(c("remotes", "rcmdcheck", "rmarkdown"))
          remotes::install_deps(dependencies = TRUE)
        shell: Rscript {0}
      
      # 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}
      
      # Create data/scbi.dendroAll_YEAR.csv from resources/raw_data/YEAR/
      # csv's
      - name: Create current year's master data csv
        id: create_master_csv
        run: |
          source("Rscripts/survey_forms/create_master_csv_2021_and_after.R")
        shell: Rscript {0}     
        
      # Test for data collection errors that require field fixes, outputs
      # saved in testthat/reports/
      - name: Generate error reports
        id: generate_error_reports
        run: |
          source("Rscripts/Generate_reports.R")
        shell: Rscript {0}
      
      # Test for warnings, outputs saved in testthat/reports/
      - name: Generate warning reports
        id: generate_warning_reports
        run: |
          source("Rscripts/Generate_warnings.R")
        shell: Rscript {0}
      
      # Recompute annual summaries in results/dendro_trees_dbhcount/
      - name: Recompute annual summaries
        run: |
          source("Rscripts/analysis/dendrotrees_by_sp-survey-dbh.R")
        shell: Rscript {0}
      
      # Update dashboard: repository README.md front page  
      - name: Update README
        run: |
          Rscript -e 'rmarkdown::render("README.Rmd")'
          rm README.html

      # Commit and push all new files, assigned to GA bot
      - name: Commit and push all new files
        run: |
          git config --local user.email "actions@github.com"
          git config --local user.name "GitHub Actions"
          git add --all || echo "No changes to commit"
          git commit -m "Added/modified files and updated README" || echo "No changes to commit"
          git push origin
      
      # Use testthat package to issue notifications of any data collection errors
      - name: Are there any data collection?
        run: Rscript testthat.R