Merge pull request #2 from KienTTran/main

Update classes and tests

promts/generate_gtest.md

@@ -1,4 +1,97 @@
-```
+```angular2html
+Here is example unit test code
+
+#include <date/date.h>
+#include <gtest/gtest.h>
+
+#include "Configuration/ModelSettings.h"
+
+class ModelSettingsTest : public ::testing::Test {
+        protected:
+                ModelSettings default_settings;
+              
+                void SetUp() override {
+                  // Initialize default ModelSettings object using setters
+                  default_settings.set_days_between_stdout_output(10);
+                  default_settings.set_initial_seed_number(123);
+                  default_settings.set_record_genome_db(true);
+                  default_settings.set_starting_date(
+                      date::year_month_day{date::year{2024}, date::month{10}, date::day{1}});
+default_settings.set_start_of_comparison_period(
+date::year_month_day{date::year{2024}, date::month{10}, date::day{1}});
+default_settings.set_ending_date(
+date::year_month_day{date::year{2024}, date::month{10}, date::day{2}});
+default_settings.set_start_collect_data_day(1);
+}
+        };
+
+// Test encoding functionality
+TEST_F(ModelSettingsTest, EncodeModelSettings) {
+YAML::Node node = YAML::convert<ModelSettings>::encode(default_settings);
+
+EXPECT_EQ(node["days_between_stdout_output"].as<int>(),
+default_settings.get_days_between_stdout_output());
+EXPECT_EQ(node["initial_seed_number"].as<int>(),
+default_settings.get_initial_seed_number());
+EXPECT_EQ(node["record_genome_db"].as<bool>(),
+default_settings.get_record_genome_db());
+EXPECT_EQ(node["starting_date"].as<date::year_month_day>(),
+default_settings.get_starting_date());
+EXPECT_EQ(node["start_of_comparison_period"].as<date::year_month_day>(),
+default_settings.get_start_of_comparison_period());
+EXPECT_EQ(node["ending_date"].as<date::year_month_day>(),
+default_settings.get_ending_date());
+EXPECT_EQ(node["start_collect_data_day"].as<int>(),
+default_settings.get_start_collect_data_day());
+}
+
+// Test decoding functionality
+TEST_F(ModelSettingsTest, DecodeModelSettings) {
+YAML::Node node;
+node["days_between_stdout_output"] = 10;
+node["initial_seed_number"] = 123;
+node["record_genome_db"] = true;
+node["starting_date"] =
+date::year_month_day{date::year{2024}, date::month{10}, date::day{1}};
+node["start_of_comparison_period"] =
+date::year_month_day{date::year{2024}, date::month{10}, date::day{1}};
+node["ending_date"] =
+date::year_month_day{date::year{2024}, date::month{10}, date::day{2}};
+node["start_collect_data_day"] = 1;
+
+ModelSettings decoded_settings;
+EXPECT_NO_THROW(YAML::convert<ModelSettings>::decode(node, decoded_settings));
+
+EXPECT_EQ(decoded_settings.get_days_between_stdout_output(), 10);
+EXPECT_EQ(decoded_settings.get_initial_seed_number(), 123);
+EXPECT_EQ(decoded_settings.get_record_genome_db(), true);
+
+auto expected_starting_date =
+date::year_month_day{date::year{2024}, date::month{10}, date::day{1}};
+EXPECT_EQ(decoded_settings.get_starting_date(), expected_starting_date);
+
+auto expected_start_of_comparison_period =
+date::year_month_day{date::year{2024}, date::month{10}, date::day{1}};
+EXPECT_EQ(decoded_settings.get_start_of_comparison_period(),
+expected_start_of_comparison_period);
+
+auto expected_ending_date =
+date::year_month_day{date::year{2024}, date::month{10}, date::day{2}};
+EXPECT_EQ(decoded_settings.get_ending_date(), expected_ending_date);
+
+EXPECT_EQ(decoded_settings.get_start_collect_data_day(), 1);
+}
+
+// Test missing fields during decoding
+TEST_F(ModelSettingsTest, DecodeModelSettingsMissingField) {
+YAML::Node node;
+node["initial_seed_number"] = 123;  // intentionally omit other fields
+
+ModelSettings decoded_settings;
+EXPECT_THROW(YAML::convert<ModelSettings>::decode(node, decoded_settings),
+std::runtime_error);
+}
+
 As an expert in C++ programming, would you mind help me to write a gtest for the following function.
 Suggest me a test file name and using Test Fixture class.
 

sample_inputs/input.yml

@@ -7,7 +7,7 @@
 # ---------------------------------------------------------------
 # 1. Execution Settings
 # ---------------------------------------------------------------
-execution_settings:
+model_settings:
   # The number of days between each output to the standard output (stdout).
   # This variable defines the frequency at which notifications or logs
   # are sent to stdout, measured in days.
@@ -87,8 +87,8 @@ spatial_settings:
     district_raster: "../input/kag_district.asc"
 
     # Raster files defining treatment probabilities (comment these out for beta calibration)
-    p_treatment_under_5: "../input/kag_treatment.asc"
-    p_treatment_over_5: "../input/kag_treatment.asc"
+    p_treatment_under_5_raster: "../input/kag_treatment.asc"
+    p_treatment_over_5_raster: "../input/kag_treatment.asc"
 
     # Probability that an infected and symptomatic person receives treatment; single value for the entire country
     # If set to '-1', these values are read from 'pr_treatment_under5' and 'pr_treatment_over5' above
@@ -244,7 +244,7 @@ genotype_parameters:
   mutation_mask: "||||111||1111111,0||||||000000000010|1"
 
   # Daily probability that a parasite will mutate at a given locus when drug concentration is not zero
-  mutation_probability_by_locus: 0.001
+  mutation_probability_per_locus: 0.001
 
   pf_genotype_info:
     - chromosome: 5
@@ -826,7 +826,7 @@ epidemiological_parameters:
 
   # Relapse rate used to increase parasite density after treatment failure
   # Multiply by sqrt(20) per day
-  relapseRate: 4.4721
+  relapse_rate: 4.4721
 
   # Minimum update frequency for a host's attributes (especially parasite density)
   # NOTE: consider remove this value as Person will be updated daily