add offset option for ENV Q #300
Workflow file for this run
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| # Check that SS_output and SS_plots run with changes in ss3. | |
| name: test-r4ss-with-ss3 | |
| on: | |
| workflow_dispatch: | |
| push: | |
| paths: | |
| - '**.tpl' | |
| branches: | |
| - main | |
| pull_request: | |
| types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review'] | |
| paths: | |
| - '**.tpl' | |
| branches: | |
| - main | |
| # run models without estimation, then run r4ss SS_plots and SS_output | |
| jobs: | |
| test-r4ss-with-ss3: | |
| if: github.event.pull_request.draft == false | |
| 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 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: 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 R packages | |
| run: Rscript -e 'install.packages(c("remotes","parallely", "furrr", "future"))' | |
| - name: install r4ss | |
| run: Rscript -e 'remotes::install_github("r4ss/r4ss")' | |
| # - 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 | |
| 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 models without estimation | |
| run: | | |
| cd test-models-repo && Rscript run_from_par.R | |
| - name: run SS3 output and SS3 plots | |
| run: | | |
| ncores <- parallelly::availableCores(omit = 1) | |
| future::plan(future::multisession, workers = ncores) | |
| mod_names <- list.dirs("test-models-repo/model_runs", full.names = FALSE, recursive = FALSE) | |
| print(mod_names) | |
| if(length(mod_names) == 0) { | |
| stop("Did not r4ss on any models; perhaps path to models is not correct?") | |
| } | |
| out <- furrr::future_map(mod_names, function(i) { | |
| tryCatch(r4ss::SS_output(file.path("test-models-repo", "model_runs", i), | |
| verbose = FALSE, hidewarn = TRUE, printstats = FALSE), | |
| error = function(e) { | |
| print(e) | |
| } | |
| ) | |
| }) | |
| plots <- furrr::future_map(out, function(x) { | |
| tryCatch(r4ss::SS_plots(x, verbose = FALSE, openfile = FALSE), | |
| error = function(e) { | |
| print(e) | |
| }) | |
| }) | |
| # determine if job fails or not | |
| out_issues <- mod_names[unlist(lapply(out, function(x) "error" %in% class(x)))] | |
| plotting_issues<- mod_names[unlist(lapply(plots, function(x) "error" %in% class(x)))] | |
| if(length(out_issues) == 0 & length(plotting_issues) == 0) { | |
| message("all r4ss functions completed successfully") | |
| } else { | |
| message("There were some errors. SS_output failed to run for model_runs ", | |
| paste0(out_issues, collapse = ", "), "; SS_plots failed to run for ", | |
| "models ", paste0(plotting_issues, collapse = " ,"), ". More info ", | |
| "below.") | |
| message("Problems with SS_output:") | |
| for(i in out_issues) { | |
| message(i) | |
| tmp_loc <- which(mod_names == i) | |
| print(out[[tmp_loc]]) | |
| } | |
| for(p in plotting_issues) { | |
| message(p) | |
| tmp_loc <- which(mod_names == p) | |
| print(plots[[tmp_loc]]) | |
| } | |
| q(status = 1) | |
| } | |
| shell: Rscript {0} | |
| # could archive files, but the archive will be large, so may not be worth it. |