refactor(tests): update integration test setup

- Create helper functions (`load_*()`) to load or create
  data for a FIMS model run, or run a FIMS model with
  wrappers to save the fit output. These functions
  check if the corresponding `.RDS` file exists; if not,
  they generate the data or run the model and save
  the output to an `.RDS` file. If the file exists,
  they read and return the object from the `.RDS` file.
  This ensures that test data is generated only once
  and is available for subsequent test runs,
  speeding up the process.
- Add error handling (e.g., `tryCatch()`) in data loading
  functions to provide clearer messages when file
  operations fail.
- Update README to document new helper functions
  for loading data and running FIMS with wrappers.
- Rename `test-integration-caa-mle.R` to
  `test-integration-caa-mle-without-wrappers.R` so it
  can be filtered when running tests
  (`devtools::test(filter = "xxx")`), speeding up
  single-test execution.
- Update snapshot tests outputs from `.md` files
  to `.csv` files.
- Replace nan with -999 in JSON files. Thanks to
  @msupernaw for the fix to issue #940.

Author: Bai-Li-NOAA

.devcontainer/devcontainer.json

@@ -18,7 +18,7 @@
 			"updatePackages": true			
 		},
 		 "ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
-			"packages": "covr,dplyr,devtools,ggplot2,jsonlite,methods,Rcpp,RcppEigen,scales,snowfall,TMB,tibble,tidyr,usethis,spelling",
+			"packages": "covr,dplyr,devtools,diffviewer,ggplot2,jsonlite,methods,Rcpp,RcppEigen,scales,snowfall,TMB,tibble,tidyr,usethis,spelling",
 			"installSystemRequirements": true
 		  },
 		 // option to run rstudio. you can type rserver into the command line to

inst/WORDLIST

@@ -277,6 +277,7 @@ DWORD
 dynam
 elif
 ELT
+emph
 emplace
 emptyDoubleLogistic
 emptyLogistic

inst/include/utilities/fims_json.hpp

@@ -49,6 +49,9 @@ enum JsonValueType {
  */
 class JsonValue {
  public:
+  /** Represents the string representation of NaN in JSON. */
+  static std::string NaN_Representation;
+
   /** Default constructor, initializes to Null value. */
   JsonValue() : type(JsonValueType::Null) {}
 
@@ -100,6 +103,9 @@ class JsonValue {
   JsonArray array;    /**< JSON array. */
 };
 
+/**< Default representation for NaN in JSON. */
+std::string JsonValue::NaN_Representation = "999"; 
+
 /**
  * Parses JSON strings and generates JSON values.
  */
@@ -181,8 +187,37 @@ class JsonParser {
           break;
       }
     }
+    // Replace NaN with the specified representation
+    JsonParser::replaceNaN(result);
     return result;
   }
+  
+  /**
+   * @brief Replace occurrences of "NaN" or "nan" in a string with the 
+   * specified representation.
+   * @param s The string to modify.
+   */
+  static void replaceNaN(std::string &s)
+    {
+      std::string target = "NaN";
+      std::string replacement = JsonValue::NaN_Representation;
+      size_t pos = 0;
+
+      while ((pos = s.find(target, pos)) != std::string::npos)
+      {
+        s.replace(pos, target.size(), replacement);
+        pos += replacement.size(); // move past the replacement
+      }
+
+      target = "nan";
+      pos = 0;
+
+      while ((pos = s.find(target, pos)) != std::string::npos)
+      {
+        s.replace(pos, target.size(), replacement);
+        pos += replacement.size(); // move past the replacement
+      }
+    }
 
  private:
   /** Skip whitespace characters in the input string. */

tests/README.md

@@ -17,13 +17,8 @@ Prepare the test data in the new file or in a separate file if you plan on reusi
 - In-line test data: make the data directly in the new test file within the `setup` section.
 - C++ reusable test data: create a fixture file, e.g., `tests/gtest/test_XXX_test_fixture.hpp`, to prepare reusable unit-test data, or create an integration file, e.g., `tests/gtest/integration/XXX.hpp`, to set up integration-test data for C++ tests.
 - If you used a test fixture from GoogleTest to use the same data configuration for multiple tests, `TearDown()` can be used to clean up the test and then the test fixture will be deleted. See [GoogleTest user's guide](https://google.github.io/googletest/primer.html#same-data-multiple-tests) for more details.
-- R reusable test data: add code to the `prepare_test_data()` function in [`tests/testthat/helper-integration-tests-setup-run.R`](https://github.com/NOAA-FIMS/FIMS/blob/main/tests/testthat/helper-integration-tests-setup-run.R), including code to save the new data object, e.g., `base::saveRDS(object, file = testthat::test_path("fixtures", "data_name.RDS"))`, and call `prepare_test_data()` in the `setup` section of the new test file to load the data using
-  ```r
-  if (!file.exists(test_path("fixtures", "data_name.RDS"))) {
-    prepare_test_data()
-  }
-  ```
-- Use pre-existing integration data, e.g., `tests/testthat/fixtures/integration_test_data_components.RData` and `tests/testthat/fixtures/integration_test_data.RData`, by loading them within the `setup` section, e.g., `load(test_path("fixtures", "integration_test_data.RData"))` or within `prepare_test_data()`, where these data objects can be updated by running `R/data1.R`.
+- R reusable test data: add code to the [`tests/testthat/helper-integration-tests-setup-wrappers.R`](https://github.com/NOAA-FIMS/FIMS/blob/main/tests/testthat/helper-integration-tests-setup-wrappers.R) file, including code to save a new data or fit object for tests that use wrapper functions, e.g., `base::saveRDS(object, file = testthat::test_path("fixtures", "data_name.RDS"))` or `base::saveRDS(object, file = testthat::test_path("fixtures", "fit_name.RDS"))`, and call `load_fit_*()` in the `setup` section of the new test file to load the data.
+- Use pre-existing integration data, e.g., `tests/testthat/fixtures/integration_test_data_components.RData` and `tests/testthat/fixtures/integration_test_data.RData`, by loading them within the `setup` section, e.g., `load(test_path("fixtures", "integration_test_data.RData"))`, where these data objects can be updated by running `R/data1.R`.
 
 ### :pencil: Edit the code in the new test file
 
@@ -33,8 +28,8 @@ Follow the structure of the new test file to write appropriate correctness, edge
 
 The following :hammer: helper functions are available to assist with writing integration tests in R.
 
-- `setup_and_run_FIMS_without_wrappers()`: Set up a FIMS model without wrappers (in [`tests/testthat/helper-integration-tests-setup-run.R`](https://github.com/NOAA-FIMS/FIMS/blob/main/tests/testthat/helper-integration-tests-setup-run.R)).
-- `setup_and_run_FIMS_with_wrappers()`: Set up a FIMS model with wrappers (in [`tests/testthat/helper-integration-tests-setup-run.R`](https://github.com/NOAA-FIMS/FIMS/blob/main/tests/testthat/helper-integration-tests-setup-run.R)).
+- `setup_and_run_FIMS_without_wrappers()`: Set up a FIMS model without wrappers (in [`tests/testthat/helper-integration-tests-setup-without-wrappers.R`](https://github.com/NOAA-FIMS/FIMS/blob/main/tests/testthat/helper-integration-tests-setup-without-wrappers.R)).
+- `load_*()`: Load or create data for a FIMS model run, or run a FIMS model with wrappers to save the fit output (in [tests/testthat/helper-integration-tests-setup-wrappers.R](https://github.com/NOAA-FIMS/FIMS/blob/main/tests/testthat/helper-integration-tests-setup-wrappers.R)).
 - `verify_fims_deterministic()`: Compare the model output from a FIMS deterministic run against the expected "truth" from an operating model (in [`tests/testthat/helper-integration-tests-validation.R`](https://github.com/NOAA-FIMS/FIMS/blob/main/tests/testthat/helper-integration-tests-validation.R)).
 - `verify_fims_nll()`: Compare the negative log likelihood (NLL) from a FIMS model against the expected NLL calculated from an operating model (in [`tests/testthat/helper-integration-tests-validation.R`](https://github.com/NOAA-FIMS/FIMS/blob/main/tests/testthat/helper-integration-tests-validation.R)).
 - `validate_fims()`: Compare the output from a FIMS model where parameters are estimated against the expected "truth" from an operating model (in [`tests/testthat/helper-integration-tests-validation.R`](https://github.com/NOAA-FIMS/FIMS/blob/main/tests/testthat/helper-integration-tests-validation.R)).