update-ss3-models.yml

name: update-ss3-test-models
on: 
  workflow_dispatch:

jobs:
  update-ss3-test-models:
    runs-on: ubuntu-latest
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    steps:

      - name: Checkout repo
        uses: actions/checkout@v4
      
      - name: install libcurl
        run: |
          sudo apt-get update
          sudo apt-get install -y libcurl4-openssl-dev
          sudo add-apt-repository ppa:ubuntu-toolchain-r/test
          sudo apt-get install --only-upgrade libstdc++6

      - name: setup R  
        uses: r-lib/actions/setup-r@v2
      
      - name: install remotes
        run: Rscript -e 'install.packages("remotes")'

      - name: install r4ss
        run: Rscript -e 'remotes::install_github("r4ss/r4ss")'

      - name: install purrr
        run: Rscript -e 'install.packages("purrr")'
        
      # - name: Get the latest SS3 executable
      #   run: |
      #     wget -O ss3 https://github.com/nmfs-ost/ss3-source-code/releases/latest/download/ss3_linux
      #     sudo chmod a+x ss3
      #     mv ss3 /usr/local/bin/ss3
      #     mv models/ss3
      #     export PATH=/usr/local/bin/ss3:$PATH
      #     echo "/usr/local/bin/ss3" >> $GITHUB_PATH
     
      - name: run models
        run: |
          dirs_test <- list.dirs(recursive = FALSE)
          mod_dir_name <- dirs_test[grepl("model", dirs_test)]
          mod_dir_name <- gsub(".*\\./", "", mod_dir_name)

          update_ref_files <- function(new_mod_path, mod_dir_name) {
                  ss_examples_folder <- file.path(getwd(), mod_dir_name)
                  mod_name <- basename(new_mod_path)
                  git_mod_path <- file.path(ss_examples_folder, mod_name)
                  # list model files that need to be moved
                  files_to_move <- c("ss.par", "ss3.par", "ss_summary.sso", "warning.sso")
                  # copy model files from new_mod_path folder to the git_mod_path folder,
                  results_of_move <- lapply(files_to_move,
                                            function(x, new_mod_path, git_mod_path) {
                      # file.remove(file.path(git_mod_path, x))
                      file.copy(from = file.path(new_mod_path, x),
                                to = file.path(git_mod_path, x), 
                                overwrite = TRUE) 
                      #to make sure worked:
                        worked <- file.exists(file.path(git_mod_path, x))
                      }, new_mod_path = new_mod_path, git_mod_path = git_mod_path)
                      if(all(unlist(results_of_move) == TRUE)) {
                          files_replaced <- TRUE
                      } else {
                          files_replaced <- FALSE
                      }
                  files_replaced
                  }
                    
          new_mod_dir_name <- "new_models"

          r4ss::populate_multiple_folders(outerdir.old = mod_dir_name, 
                                outerdir.new = new_mod_dir_name,
                                exe.file = NULL, verbose = FALSE)
          
          run_ssnew <- function(dir) {
            wd <- getwd()
            print(wd)
            on.exit(system(paste0("cd ", wd)))
            system(paste0("cd ", dir, " && ../ss3"))
            model_ran <- file.exists(file.path(dir, "control.ss_new"))
            return(model_ran)
          }
          
          r4ss::get_ss3_exe(dir = file.path(getwd(), new_mod_dir_name))
          
          new_mod_runs_folder <- file.path(new_mod_dir_name)
          new_mod_path_list <- list.dirs(new_mod_runs_folder, recursive = FALSE,
                                        full.names = TRUE)
                                        
          # Run models in parallel using .ss_new files and print out error messages
          purrr::map(
            .x = new_mod_path_list,
            .f = run_ssnew)

            # purrr::map(
            #   .x = file.path(new_mod_dir_name, list.files(new_mod_dir_name)),
            #   .f = r4ss::run,
            #   exe = "ss3", 
            #   verbose = TRUE)
                      
          run_result <- purrr::map(
            .x = new_mod_path_list,
            .f = update_ref_files,
            mod_dir_name = mod_dir_name)

          run_result

          r4ss::populate_multiple_folders(outerdir.old = new_mod_dir_name, 
                                outerdir.new = mod_dir_name,
                                exe.file = NULL, verbose = FALSE, 
                                use_ss_new = TRUE, overwrite = TRUE)

          unlink(new_mod_dir_name, recursive = TRUE)
        shell: Rscript {0}

      - name: Setup git user
        uses: fregante/setup-git-user@v1
      
      - name: Commit
        run: |
          git add .
          git commit -m "update test model files for new ss3 release"
        
      - name: Create Pull Request 
        uses: peter-evans/create-pull-request@v3
        with:
          commit_message: Update model files for new ss3 release
          branch: update-test-models
          title: 'Update test model files for new ss3 release'