update-ss3-test-models #35
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| name: update-ss3-test-models | |
| on: | |
| workflow_dispatch: | |
| jobs: | |
| update-ss3-test-models: | |
| runs-on: ubuntu-latest | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: install libcurl | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| - name: setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: install remotes | |
| run: Rscript -e 'install.packages("remotes")' | |
| - name: install r4ss | |
| run: Rscript -e 'remotes::install_github("r4ss/r4ss")' | |
| - name: install purrr | |
| run: Rscript -e 'install.packages("purrr")' | |
| # - name: Get the latest SS3 executable | |
| # run: | | |
| # wget -O ss3 https://github.com/nmfs-ost/ss3-source-code/releases/latest/download/ss3_linux | |
| # sudo chmod a+x ss3 | |
| # mv ss3 /usr/local/bin/ss3 | |
| # mv models/ss3 | |
| # export PATH=/usr/local/bin/ss3:$PATH | |
| # echo "/usr/local/bin/ss3" >> $GITHUB_PATH | |
| - name: run models | |
| run: | | |
| dirs_test <- list.dirs(recursive = FALSE) | |
| mod_dir_name <- dirs_test[grepl("model", dirs_test)] | |
| mod_dir_name <- gsub(".*\\./", "", mod_dir_name) | |
| update_ref_files <- function(new_mod_path, mod_dir_name) { | |
| ss_examples_folder <- file.path(getwd(), mod_dir_name) | |
| mod_name <- basename(new_mod_path) | |
| git_mod_path <- file.path(ss_examples_folder, mod_name) | |
| # list model files that need to be moved | |
| files_to_move <- c("ss.par", "ss3.par", "ss_summary.sso", "warning.sso") | |
| # copy model files from new_mod_path folder to the git_mod_path folder, | |
| results_of_move <- lapply(files_to_move, | |
| function(x, new_mod_path, git_mod_path) { | |
| # file.remove(file.path(git_mod_path, x)) | |
| file.copy(from = file.path(new_mod_path, x), | |
| to = file.path(git_mod_path, x), | |
| overwrite = TRUE) | |
| #to make sure worked: | |
| worked <- file.exists(file.path(git_mod_path, x)) | |
| }, new_mod_path = new_mod_path, git_mod_path = git_mod_path) | |
| if(all(unlist(results_of_move) == TRUE)) { | |
| files_replaced <- TRUE | |
| } else { | |
| files_replaced <- FALSE | |
| } | |
| files_replaced | |
| } | |
| new_mod_dir_name <- "new_models" | |
| r4ss::populate_multiple_folders(outerdir.old = mod_dir_name, | |
| outerdir.new = new_mod_dir_name, | |
| exe.file = NULL, verbose = FALSE) | |
| run_ssnew <- function(dir) { | |
| wd <- getwd() | |
| print(wd) | |
| on.exit(system(paste0("cd ", wd))) | |
| system(paste0("cd ", dir, " && ../ss3")) | |
| model_ran <- file.exists(file.path(dir, "control.ss_new")) | |
| return(model_ran) | |
| } | |
| r4ss::get_ss3_exe(dir = file.path(getwd(), new_mod_dir_name)) | |
| new_mod_runs_folder <- file.path(new_mod_dir_name) | |
| new_mod_path_list <- list.dirs(new_mod_runs_folder, recursive = FALSE, | |
| full.names = TRUE) | |
| # Run models in parallel using .ss_new files and print out error messages | |
| purrr::map( | |
| .x = new_mod_path_list, | |
| .f = run_ssnew) | |
| # purrr::map( | |
| # .x = file.path(new_mod_dir_name, list.files(new_mod_dir_name)), | |
| # .f = r4ss::run, | |
| # exe = "ss3", | |
| # verbose = TRUE) | |
| run_result <- purrr::map( | |
| .x = new_mod_path_list, | |
| .f = update_ref_files, | |
| mod_dir_name = mod_dir_name) | |
| run_result | |
| r4ss::populate_multiple_folders(outerdir.old = new_mod_dir_name, | |
| outerdir.new = mod_dir_name, | |
| exe.file = NULL, verbose = FALSE, | |
| use_ss_new = TRUE, overwrite = TRUE) | |
| unlink(new_mod_dir_name, recursive = TRUE) | |
| shell: Rscript {0} | |
| - name: Setup git user | |
| uses: fregante/setup-git-user@v1 | |
| - name: Commit | |
| run: | | |
| git add . | |
| git commit -m "update test model files for new ss3 release" | |
| - name: Create Pull Request | |
| uses: peter-evans/create-pull-request@v3 | |
| with: | |
| commit_message: Update model files for new ss3 release | |
| branch: update-test-models | |
| title: 'Update test model files for new ss3 release' |