run-ss3-mcmc.yml

# Check that MCMC using the NUTS algorithim in ADMB is reproducible with SS3 using the simple model.
# Developed with Cole Monnahan.
# Only runs on a pull request and a push to main if the tpl files have changed.
name: run-ss3-mcmc
on:
  workflow_dispatch:
  push:
    paths:
      - '**.tpl'
    branches:
      - main
  pull_request:
    types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review']
    paths:
      - '**.tpl'
    branches:
      - main
      
# Check MCMC works
jobs:
  run-ss3-no-est:
    if: github.event.pull_request.draft == false
    runs-on: ubuntu-latest
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"

    steps:
      - name: Checkout ss3 repo
        uses: actions/checkout@v4

      - name: Checkout models repo
        uses: actions/checkout@v4
        with:
          repository: 'nmfs-ost/ss3-test-models'
          path: test-models-repo

      - name: Update Ubuntu packages
        run: |
          sudo add-apt-repository ppa:ubuntu-toolchain-r/test
          sudo apt-get update
          sudo apt-get install --only-upgrade libstdc++6
        
      - 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/Simple/starter.ss starter.ss
          mv test-models-repo/models/Simple/forecast.ss forecast.ss
          mv test-models-repo/models/Simple/control.ss control.ss
          mv test-models-repo/models/Simple/data.ss data.ss
          mv SS330/ss3 ss3
          ls

      - name: Change permissions on ss3 exe
        run: sudo chmod a+x ss3

      - name: Run models without estimation
        run: |
          # Run NUTS algorithim in ADMB to make sure still works with stock synthesis
          # run the simple model with -hbf option to get the necessary files
          system("./ss3 -hbf")
          # run the simple model 30 times using the NUTS algorithim
          niters <- 100
          for (i in 1:niters) {
            message("Running iteration ", i)
            # run simple model
            system("./ss3  -maxfn 0 -phase 40 -nohess -mcmc 10 -nuts -mcseed 1 -max_treedepth 3")
            # read in adaption.csv
            adapt_df <- read.csv("adaptation.csv")
            if(i == 1) {
              compare_val <- adapt_df[nrow(adapt_df), "stepsize__"]
              message("Getting ref value from iteration ", i, ". Ref value is " ,
                      compare_val)
            } else {
              message("Checking iteration ", i)
              val_to_check <- adapt_df[nrow(adapt_df), "stepsize__"]
            	if(!identical(val_to_check, compare_val)) {
                stop("First step size for iteration ", i ," (step size =",
                     val_to_check,
                     ")", " was not equal to values in the first iteration (",
                     compare_val, ").")
            	}
            }
          }
          message("No differences in step size among stock synthesis runs.")
        shell: Rscript {0}