separate annual timeseries from spr series; improve mean_age reporting #306
Workflow file for this run
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| # 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} |