compile_main_fredi_data.yml

### https://github.com/actions/upload-artifact
### https://github.blog/changelog/2021-11-10-github-actions-input-types-for-manual-workflows/
### https://docs.github.com/en/actions/using-workflows/caching-dependencies-to-speed-up-workflows
### https://github.com/r-lib/actions/tree/v2/setup-r-dependencies
### https://docs.github.com/en/actions/using-jobs/using-conditions-to-control-job-execution
### For uploading artifacts:
###     "path:" is the output path where Pandoc will write the compiled PDF. 
###      Note, this should be the same directory as the input paper.md
name: Compile FrEDI Data

on: 
  workflow_dispatch:
    inputs:
      branch_name:
        type: string
        description: Which FrEDI Package branch do you want to use?
      reshape_test:
        description: Do you want to run the reshape data test?
        type: boolean
        required: false
        default: true
jobs:
  compile_data:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    
    name: Process Data
    steps:
      - name: Checkout
        uses: actions/checkout@v3
        
      - name: Setup R
        uses: r-lib/actions/setup-r@v2
      
      - name: Setup R package dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache: true
          cache-version: 1
          packages: |
            any::tidyverse
            any::ggpubr
            any::openxlsx
            any::devtools
            any::admisc


      - name: Install FrEDI
        run: |
          Rscript -e '
            devtools::install_github( 
              repo    = "https://github.com/USEPA/FrEDI", 
              ref     = "${{ github.event.inputs.branch_name }}", 
              subdir  = "FrEDI", 
              dependencies = FALSE,
              upgrade = "never", 
              force   = TRUE,
              type    = "source" 
            )'
          
      - name: Run createsystemData
        run: |
          Rscript -e '
          projectDir <- "."
          scriptDir  <- projectDir |> file.path("scripts")
          scriptDir |> file.path("configureFrediData.R") |> source()
          test0      <- projectDir |> configureFrediData(save=T, reshape = ifelse("${{ github.event.inputs.reshape_test }}" == "true",TRUE,FALSE))
          "./data_tests/" |> list.files() |> print()
          "./data/" |> list.files() |> print()
          '

      - name: Upload Tests
        uses: actions/upload-artifact@v3
        with:
          name: Data
          path: |
            ./data_tests/*
            ./data/tmp_sysdata.rda
      

      - name: Commit results
        run: |
          git config --local core.autocrlf false
          git config --local user.email "${{ github.actor }}@users.noreply.github.com"
          git config --local user.name  "${{ github.actor }}"
          git add data/tmp_sysdata.rda
          git add data_tests/**.xlsx
          git pull origin ${{ github.head_ref }} --autostash --rebase -X ours
          git commit -a -m "Updated temporary system data and tests"
          git push