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run-ss3-no-est.yml
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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/