remove linux-related lines #2
Workflow file for this run
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| name: update-ss3-test-models-mac | |
| on: | |
| push: | |
| jobs: | |
| update-ss3-test-models-mac: | |
| runs-on: macos-14 | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: install remotes | |
| run: Rscript -e 'install.packages("remotes")' | |
| - name: install r4ss | |
| run: Rscript -e 'remotes::install_github("r4ss/r4ss")' | |
| - name: install other r packages | |
| run: Rscript -e 'install.packages("purrr","furrr","parallely","future")' | |
| - name: Get the latest SS3 executable | |
| run: | | |
| wget -O ss3 https://github.com/nmfs-ost/ss3-source-code/releases/latest/download/ss3_osx | |
| sudo chmod a+x ss3 | |
| mv ss3 /usr/local/bin/ss3 | |
| export PATH=/usr/local/bin/ss3:$PATH | |
| echo "/usr/local/bin/ss3" >> $GITHUB_PATH | |
| - name: Run models | |
| run: | | |
| mod_names <- list.dirs(file.path("models"), full.names = FALSE, recursive = FALSE) | |
| mod_paths <- list.dirs(file.path("models"), 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} |