PR_for_spawn_recr_with_timevary_biology_also_SRR_AB #422
Workflow file for this run
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| # Build SS3 and run test models without estimation (from .par) and no hessian | |
| # Runs on every push and PR (even draft PRs) ONLY if tpl files have changed. | |
| name: run-ss3-no-est | |
| on: | |
| workflow_dispatch: | |
| push: | |
| paths: | |
| - '**.tpl' | |
| # branches: | |
| # - main | |
| pull_request: | |
| paths: | |
| - '**.tpl' | |
| branches: | |
| - main | |
| # Run models without estimation, then try to run again with .ss_new | |
| jobs: | |
| run-ss3-no-est: | |
| 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: Get last compiled version of SS; alternative to compiling in same wkflow | |
| # uses: dawidd6/action-download-artifact@v2 | |
| # with: | |
| # workflow: build-centos.yml | |
| # workflow_conclusion: success | |
| # name: ss_linux | |
| # path: ss_linux | |
| - 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 ss3 | |
| # 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 and R scripts to needed locations | |
| run: | | |
| mv test-models-repo/models test-models-repo/model_runs | |
| mv SS330/ss3 test-models-repo/model_runs/ss3 | |
| mv test-models-repo/.github/r_scripts/run_from_par.R test-models-repo/run_from_par.R | |
| mv test-models-repo/.github/r_scripts/run_compare_noest.R test-models-repo/run_compare_noest.R | |
| - name: Change permissions on ss3 exes | |
| run: sudo chmod a+x test-models-repo/model_runs/ss3 | |
| - name: Run test models without estimation | |
| run: | | |
| cd test-models-repo && Rscript run_from_par.R | |
| - name: Download R packages to run models in parallel | |
| run: Rscript -e 'install.packages(c("parallely", "furrr", "future"))' | |
| - name: Run comparison using run_compare_noest.R file in test models repo | |
| run: | | |
| mkdir test-models-repo/run_R | |
| cd test-models-repo && Rscript run_compare_noest.R | |
| - name: Determine results of test using check_failed.R file in test models repo | |
| run: cd test-models-repo && Rscript .github/r_scripts/check_failed.R | |
| - name: Run models using the .ss_new files | |
| run: | | |
| # Get model names and file paths | |
| mod_names <- list.dirs("test-models-repo/model_runs", | |
| full.names = FALSE, recursive = FALSE) | |
| mod_paths <- list.dirs("test-models-repo/model_runs", | |
| full.names = TRUE, recursive = FALSE) | |
| print(mod_names) | |
| # Create function to run models using .ss_new files | |
| run_ssnew <- function(dir) { | |
| wd <- getwd() | |
| print(wd) | |
| on.exit(system(paste0("cd ", wd))) | |
| # delete old starter files, rename forecast.ss_new and starter.ss_new files | |
| file.remove(file.path(dir, "starter.ss")) | |
| file.remove(file.path("forecast.ss")) | |
| file.rename(file.path(dir, "starter.ss_new"), file.path(dir,"starter.ss")) | |
| file.rename(file.path(dir, "forecast.ss_new"), file.path(dir,"forecast.ss")) | |
| # rename control and data files to standardized names (from the starter files) | |
| start <- readLines(file.path(dir, "starter.ss")) | |
| first_val_line <- grep("0=use init values in control file", start, fixed = TRUE) | |
| datname <- start[first_val_line-2] | |
| ctlname <- start[first_val_line-1] | |
| print(datname) | |
| print(ctlname) | |
| file.remove(file.path(dir, datname)) | |
| file.remove(file.path(dir, ctlname)) | |
| file.rename(file.path(dir,"data_echo.ss_new"), file.path(dir, datname)) | |
| file.rename(file.path(dir, "control.ss_new"), file.path(dir, ctlname)) | |
| # run the models without estimation | |
| file.remove(file.path(dir, "Report.sso")) | |
| # see if model finishes without error | |
| system(paste0("cd ", dir, " && ../ss3 -stopph 0 -nohess")) | |
| model_ran <- file.exists(file.path(dir, "control.ss_new")) | |
| return(model_ran) | |
| } | |
| # Setup parallel | |
| ncores <- parallelly::availableCores(omit = 1) | |
| future::plan(future::multisession, workers = ncores) | |
| # Run models in parallel using .ss_new files and print out error messages | |
| mod_ran <- furrr::future_map(mod_paths, function(x) {tryCatch(run_ssnew(x), | |
| error = function(e) print(e) | |
| )} | |
| ) | |
| mod_errors <- mod_names[unlist(lapply(mod_ran, function(x) "simpleError" %in% class(x)))] | |
| success <- TRUE | |
| # Print list of models with errors if there are any | |
| if(length(mod_errors) > 0) { | |
| message("Model code with errors were: ", paste0(mod_errors, collapse = ", "), | |
| ". See error list above for more details.") | |
| success <- FALSE | |
| } else { | |
| message("All code ran without error, but model runs may still have failed.") | |
| } | |
| # Print list of models that didn't run if there are any | |
| mod_no_run <- mod_names[unlist(lapply(mod_ran, function(x) isFALSE(x)))] # false means model didn't run | |
| if(length(mod_no_run) > 0) { | |
| message("Models that didn't run are ", paste0(mod_no_run, collapse = ", ")) | |
| success <- FALSE | |
| } else { | |
| message("All models ran without error.") | |
| } | |
| # Determine if job fails or passes | |
| if(success == FALSE) { | |
| stop("Job failed due to code with errors or models that didn't run.") | |
| } else { | |
| message("Job passed! All models successfully ran.") | |
| } | |
| shell: Rscript {0} | |
| - name: Archive results | |
| uses: actions/upload-artifact@main | |
| if: always() | |
| with: | |
| name: 'result_textfiles' | |
| path: test-models-repo/run_R/ |