add offset option for ENV Q #274
Workflow file for this run
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| # Build SS3 and run models with estimation and hessian | |
| name: run-ss3-with-est | |
| on: | |
| workflow_dispatch: | |
| push: | |
| paths: | |
| - '**.tpl' | |
| branches: | |
| - main | |
| pull_request: | |
| types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review'] | |
| paths: | |
| - '**.tpl' | |
| branches: | |
| - main | |
| # run fast running SS3 models with estimation | |
| jobs: | |
| run-ss3-with-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: 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/ss3 | |
| - name: change permissions on ss3 exes | |
| run: sudo chmod a+x test-models-repo/model_runs/ss3 | |
| - name: download R packages for parallel | |
| run: Rscript -e 'install.packages(c("parallely", "furrr", "future"))' | |
| - name: run models | |
| run: | | |
| ncores <- parallelly::availableCores(omit = 1) | |
| future::plan(future::multisession, workers = ncores) | |
| mod_names <- list.dirs(file.path("test-models-repo", "model_runs"), full.names = FALSE, recursive = FALSE) | |
| mod_paths <- list.dirs(file.path("test-models-repo", "model_runs"), full.names = TRUE, recursive = FALSE) | |
| print(mod_names) | |
| run_ss <- function(dir) { | |
| wd <- getwd() | |
| print(wd) | |
| on.exit(system(paste0("cd ", wd))) | |
| # rename the reference files | |
| file.rename(file.path(dir, "ss_summary.sso"), | |
| file.path(dir, "ss_summary_ref.sso")) | |
| file.rename(file.path(dir, "warning.sso"), | |
| file.path(dir, "warning_ref.sso")) | |
| file.copy(file.path(dir, "ss3.par"), file.path(dir, "ss3_ref.par")) | |
| # run the models with estimation and see if model finishes without error | |
| message("running ss on ", basename(dir)) | |
| system(paste0("cd ", dir, " && ../ss3 -nox")) | |
| model_ran <- file.exists(file.path(dir, "control.ss_new")) | |
| return(model_ran) | |
| } | |
| mod_ran <- furrr::future_map(mod_paths, function(x){tryCatch(run_ss(x), | |
| error = function(e) print(e))}) | |
| mod_errors <- mod_names[unlist(lapply(mod_ran, function(x) "simpleError" %in% class(x)))] | |
| success <- TRUE | |
| 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.") | |
| } | |
| 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("All models successfully ran.") | |
| } | |
| shell: Rscript {0} | |
| - name: Run comparison | |
| run: | | |
| source("test-models-repo/.github/r_scripts/compare.R") | |
| orig_wd <- getwd() | |
| setwd("test-models-repo") | |
| on.exit(orig_wd) | |
| dir.create("run_R") | |
| # get model folder names | |
| mod_fold <- file.path("model_runs") | |
| mod_names <- list.dirs(mod_fold, full.names = FALSE, recursive = FALSE) | |
| message("Will compare ref runs to new results for these models:") | |
| print(mod_names) | |
| message("Notable changes in total likelihood, max gradients, ", | |
| " and number of warnings:") | |
| compare_list <- vector(mode = "list", length = length(mod_names)) | |
| for(i in mod_names) { | |
| pos <- which(mod_names == i) | |
| sum_file <- file.path(mod_fold, i, "ss_summary.sso") | |
| if (i == "Simple") { | |
| file.copy(sum_file, file.path("run_R", paste0(i, "_ss_summary.sso"))) | |
| } | |
| ref_sum_file <- file.path(mod_fold, i, "ss_summary_ref.sso") | |
| par_file <- file.path(mod_fold, i, "ss3.par") | |
| ref_par_file <- file.path(mod_fold, i, "ss3_ref.par") | |
| warn_file <- file.path(mod_fold, i, "warning.sso") | |
| ref_warn_file <- file.path(mod_fold, i, "warning_ref.sso") | |
| fail_file <- file.path("run_R", "test_failed.csv") | |
| compare_list[[pos]] <- compare_ss_runs(mod_name = i, | |
| sum_file = sum_file, ref_sum_file = ref_sum_file, | |
| par_file = par_file, ref_par_file = ref_par_file, | |
| warn_file = warn_file, ref_warn_file = ref_warn_file, | |
| hessian = TRUE, | |
| new_file = NULL, fail_file = fail_file) | |
| } | |
| # write out all model results | |
| compare_df <- do.call("rbind", compare_list) | |
| compare_df_print <- format(compare_df, digits = 6, nsmall = 3, | |
| justify = "left") | |
| message("see saved artifact all_results.csv for all compared values and their differences.") | |
| # write all model comparison results to csv | |
| write.csv(compare_df_print, "run_R/all_results.csv", row.names = FALSE) | |
| # write all | |
| message("see saved artifact all_changes.csv for only changed values (even if the threshold was too low to fail the job)") | |
| filtered_df <- compare_df[compare_df$diff != 0, ] | |
| filtered_df <- format(filtered_df, digits = 6, nsmall = 3, | |
| justify = "left") | |
| write.csv(filtered_df, "run_R/all_changes.csv", row.names = FALSE) | |
| shell: Rscript {0} | |
| - name: Determine results of test | |
| run: cd test-models-repo && Rscript .github/r_scripts/check_failed.R | |
| - name: Archive results | |
| uses: actions/upload-artifact@main | |
| if: always() | |
| with: | |
| name: 'result_textfiles' | |
| path: test-models-repo/run_R/ |