Merge pull request #45 from nmfs-ost/test-convert-output

Add SS3 integration tests for testing convert_output()

DESCRIPTION

@@ -30,12 +30,17 @@ Imports:
 Suggests: 
     knitr,
     rmarkdown,
+    parallel,
+    snowfall, 
+    r4ss,
     testthat (>= 3.0.0)
 VignetteBuilder: 
     knitr
 Remotes:
-    nmfs-ost/satf
+    nmfs-ost/satf,
+    r4ss/r4ss
 Config/testthat/edition: 3
+Config/testthat/parallel: true
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2

tests/testthat/fixtures/prepare_ss3_output_files.R

@@ -0,0 +1,60 @@
+# Download SS3 models and place them in the specified directory
+ss3_models <- r4ss::download_models(
+  dir = test_path("fixtures", "ss3_models")
+)
+
+# Get the SS3 executable for running the models
+ss3_exe <- r4ss::get_ss3_exe(
+  dir = test_path("fixtures", "ss3_models")
+)
+
+# Function to run a specific SS3 model
+run_ss3_models <- function(model_id, model_dir, exe_dir){
+  # Define the working directory for the model
+  working_dir <- model_dir[model_id]
+
+  # Copy the SS3 executable to the model's working directory
+  file.copy(Sys.which(file.path(exe_dir, "ss3")), working_dir)
+
+  # Run SS3 model
+  r4ss::run(dir = working_dir)
+}
+
+# List all the model directories to be processed
+all_models <- list.dirs(
+  file.path(test_path("fixtures", "ss3_models"), "models"),
+                      full.names = TRUE,
+                      recursive = FALSE
+)
+
+# Detect the number of available CPU cores, leaving one free
+core_num <- parallel::detectCores() - 1
+
+# Initialize snowfall for parallel processing, using the detected core count
+snowfall::sfInit(parallel = TRUE, cpus = core_num)
+
+# Run the SS3 models in parallel using the snowfall library
+snowfall::sfLapply(
+  1:length(all_models),
+  run_ss3_models,
+  all_models,
+  test_path("fixtures", "ss3_models")
+)
+
+# Stop the snowfall parallel session
+snowfall::sfStop()
+
+# Remove the SS3 files except Report.sso from the working directory after the run is complete
+all_files <- list.files(
+  test_path("fixtures", "ss3_models", "models"),
+  full.names = TRUE,
+  recursive = TRUE
+)
+report_files <- file.path(all_models, "Report.sso")
+
+report_id <- match(report_files, all_files)
+files_to_delete <- all_files[-report_id]
+file.remove(files_to_delete)
+
+# Clean up by removing the SS3 executable from the main directory after running all models
+file.remove(Sys.which(test_path("fixtures", "ss3_models", "ss3")))