run-ss3-bootstrap.yml

# Build SS3 and run Simple_with_DM_sizefreq model from test models 
# repo to make sure that ss3 makes bootstrap files and that all 
# .ss_new files were produced.
# Only runs on a pull request and a push to main if the tpl files have changed.
name: run-ss3-bootstrap-files
on:
  workflow_dispatch:
  push:
    paths:
      - '**.tpl'
    branches:
      - main
  pull_request:
    types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review']
    paths:
      - '**.tpl'
    branches:
      - main

concurrency:
    group: ${{ github.workflow}}-${{ github.ref }}
    cancel-in-progress: true
    
jobs:
  run-ss3-bootstrap-files:
    if: github.event.pull_request.draft == false
    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 ss3 repo
        uses: actions/checkout@v6

      - name: Checkout test models repo
        uses: actions/checkout@v6
        with:
          repository: 'nmfs-ost/ss3-test-models'
          path: test-models-repo

      - name: Install libcurl & other necessary packages
        run: |
          sudo add-apt-repository ppa:ubuntu-toolchain-r/test
          sudo apt-get update
          sudo apt-get install --only-upgrade libstdc++6
          sudo apt-get install -y libcurl4-openssl-dev
          sudo apt-get install -y libfontconfig1-dev
          sudo apt-get install -y libharfbuzz-dev libfribidi-dev

      - name: Setup R
        uses: r-lib/actions/setup-r@v2

      # - name: Get admb and put in path, linux
      #   run: |
      #     wget https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1-linux.zip
      #     sudo unzip admb-13.1-linux.zip -d /usr/local/bin
      #     sudo chmod 755 /usr/local/bin/admb-13.1/bin/admb
      #     echo "/usr/local/bin/admb-13.1/bin" >> $GITHUB_PATH

      # - name: Build stock synthesis
      #   run: |
      #     rm -rf SS330
      #     mkdir SS330
      #     /bin/bash ./Make_SS_330_new.sh -b SS330

      - name: Build stock synthesis with admb docker image
        run: |
          rm -rf SS330
          rm -rf ss3_osx.tar
          mkdir SS330
          chmod 777 SS330
          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330

      - name: Move exes, scripts to needed locations
        run: |
          mv test-models-repo/models test-models-repo/model_runs
          mv SS330/ss3 test-models-repo/model_runs/Simple_with_DM_sizefreq/ss3

      - name: Change permissions on ss3 exes
        run: sudo chmod a+x test-models-repo/model_runs/Simple_with_DM_sizefreq/ss3
      
      - name: Download R packages
        run: Rscript -e 'install.packages(c("remotes", "purrr", "arsenal", "utils"))'

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

      - name: Ensure that ss3 produces bootstrap files
        run: |
          # Use Simple_with_DM_sizefreq model to test bootstrap files
          boot_mod_dir <- grep("Simple_with_DM_sizefreq", list.dirs(file.path("test-models-repo", "model_runs"), full.names = TRUE, recursive = FALSE), value = TRUE)

          # Change to have model output 8 bootstrap files and run model
          boot_files <- r4ss::SS_read(dir = boot_mod_dir)
          boot_files$start$N_bootstraps <- 10
          r4ss::SS_write(boot_files, dir = boot_mod_dir, overwrite = TRUE)
          r4ss::run(dir = boot_mod_dir, exe = file.path(getwd(), "test-models-repo", "model_runs", "Simple_with_DM_sizefreq", "ss3"))

          bootstrap_length <- length(list.files(boot_mod_dir, pattern = "data_boot"))

          if(bootstrap_length != (boot_files$start$N_bootstraps - 2)){
              stop("Did not produce the amount of bootstrap files specified.")
          } else {
              message("All bootstrap files produced.")
              }
          
          # Make sure values in echo and bootstrap files are different
          dat <-  r4ss::SS_readdat(file = file.path(boot_mod_dir,"data_echo.ss_new"))
          boot1 <- r4ss::SS_readdat(file = file.path(boot_mod_dir,"data_boot_001.ss"))
          boot2 <- r4ss::SS_readdat(file = file.path(boot_mod_dir,"data_boot_002.ss"))
          
          # Unlist sizefreq data
          dat_sizefreq <- purrr::map_df(dat$sizefreq_data_list, ~.x)
          boot1_sizefreq <- purrr::map_df(boot1$sizefreq_data_list, ~.x)
          boot2_sizefreq <- purrr::map_df(boot2$sizefreq_data_list, ~.x)

          # Compare data and bootstrap files
          df <- data.frame(
              var = c("lencomp", "lencomp","catch","catch","CPUE","CPUE", "agecomp","agecomp","sizefreq","sizefreq"),
              data_compare = rep(c("dat_boot1", "boot1_boot2"), 5),
              n_diff = c(
                  sum(summary(arsenal::comparedf(dat$lencomp, boot1$lencomp))$diffs.byvar.table$n),
                  sum(summary(arsenal::comparedf(boot1$lencomp, boot2$lencomp))$diffs.byvar.table$n),
                  length(summary(arsenal::comparedf(dat$catch, boot1$catch, int.as.num = TRUE))$diffs.table$row.x),
                  length(summary(arsenal::comparedf(dat$catch, boot1$catch, int.as.num = TRUE))$diffs.table$row.x),
                  length(summary(arsenal::comparedf(dat$CPUE, boot1$CPUE, int.as.num = TRUE))$diffs.table$row.x),
                  length(summary(arsenal::comparedf(boot1$CPUE, boot2$CPUE, int.as.num = TRUE))$diffs.table$row.x),
                  sum(summary(arsenal::comparedf(dat$agecomp, boot1$agecomp))$diffs.byvar.table$n),
                  sum(summary(arsenal::comparedf(boot1$agecomp, boot2$agecomp))$diffs.byvar.table$n),
                  sum(summary(arsenal::comparedf(dat_sizefreq, boot1_sizefreq))$diffs.byvar.table$n),
                  sum(summary(arsenal::comparedf(boot1_sizefreq, boot2_sizefreq))$diffs.byvar.table$n)
              )
          )

          df_error <- df |>
              dplyr::filter(dplyr::if_any(dplyr::where(is.numeric), ~ .x < 20))

          print_and_capture <- function(x){
              paste(utils::capture.output(print(x)), collapse = "\n")
          }

          # Error if not enough changes made in bootstrap files
          if(length(df_error > 0)){
              stop("Bootstrap data produced less than 20 changes in a data type, see printed table below.\n", print_and_capture(df_error))
          } else {
              message("Bootstrap data types all have > 20 changes")
              }
          
          # Check that the model produced all .ss_new files and that they have correct content in them
          ss_new_files <- list.files(boot_mod_dir, pattern = ".ss_new")
          ss_new_validate <- c("control.ss_new", "data_echo.ss_new", "forecast.ss_new", "starter.ss_new", "wtatage.ss_new")

          new_dif <- setdiff(ss_new_files, ss_new_validate)
          if(length(new_dif) > 0){
              stop("Not all .ss_new files were produced")
          } else {
              message("All .ss_new files produced")
              }

          ss_new_length <- purrr::map(ss_new_files, ~length(readLines(file.path(boot_mod_dir, .x))))
          ss_new_too_short <- any(ss_new_length |> purrr::map_lgl(~.x < 10))
          if(ss_new_too_short == TRUE){
            stop("Error producing all lines in one or more .ss_new files")
          } else {
              message("All .ss_new files seem to be appropriate length")
              }
        shell: Rscript {0}