Merge pull request #9 from KienTTran/main

Update core scheduler

sample_inputs/input.yml

@@ -828,6 +828,7 @@ epidemiological_parameters:
 # ---------------------------------------------------------------
 # 15. Mosquito Parameters (default is location based)
 # ---------------------------------------------------------------
+#TODO: Check this implementation in Mosquito class
 mosquito_parameters:
   mosquito_config:
     mode: "location_based" # or "grid_based"

src/CMakeLists.txt

@@ -5,6 +5,7 @@ find_package(sol2 CONFIG REQUIRED)
 find_package(Lua REQUIRED)
 find_package(spdlog REQUIRED)
 find_package(date CONFIG REQUIRED)
+find_package(CLI11 CONFIG REQUIRED)
 
 include_directories(
   ${PROJECT_SOURCE_DIR}/src
@@ -34,6 +35,7 @@ target_link_libraries(MalaSimCore PUBLIC
   sol2
   spdlog::spdlog
   date::date date::date-tz
+  CLI11::CLI11
 )
 
 set_property(TARGET MalaSimCore PROPERTY CXX_STANDARD 20)

src/Configuration/Config.cpp

@@ -13,58 +13,73 @@ int inline get_pipe_count(const std::string &str) {
   return pipe_count;
 }
 
-void Config::load(const std::string &filename) {
+bool Config::load(const std::string &filename) {
   config_file_path_ = filename;
-  YAML::Node config = YAML::LoadFile(filename);
+  try {
+    YAML::Node config = YAML::LoadFile(filename);
 
-  config_data_.model_settings = config["model_settings"].as<ModelSettings>();
-  config_data_.simulation_timeframe  =
-    config["simulation_timeframe"].as<SimulationTimeframe>();
+    std::cout << "Configuration file loaded successfully" << std::endl;
 
-  config_data_.transmission_settings =
-      config["transmission_settings"].as<TransmissionSettings>();
+    config_data_.model_settings = config["model_settings"].as<ModelSettings>();
+    config_data_.simulation_timeframe  =
+      config["simulation_timeframe"].as<SimulationTimeframe>();
 
-  config_data_.population_demographic =
-    config["population_demographic"].as<PopulationDemographic>();
+    config_data_.transmission_settings =
+        config["transmission_settings"].as<TransmissionSettings>();
 
-  config_data_.spatial_settings =
-     config["spatial_settings"].as<SpatialSettings>();
+    config_data_.population_demographic =
+      config["population_demographic"].as<PopulationDemographic>();
 
-  config_data_.seasonality_settings =
-    config["seasonality_settings"].as<SeasonalitySettings>();
+    config_data_.spatial_settings =
+       config["spatial_settings"].as<SpatialSettings>();
 
-  config_data_.movement_settings =
-    config["movement_settings"].as<MovementSettings>();
+    config_data_.seasonality_settings =
+      config["seasonality_settings"].as<SeasonalitySettings>();
 
-  config_data_.parasite_parameters =
-    config["parasite_parameters"].as<ParasiteParameters>();
+    config_data_.movement_settings =
+      config["movement_settings"].as<MovementSettings>();
 
-  config_data_.immune_system_parameters =
-    config["immune_system_parameters"].as<ImmuneSystemParameters>();
+    config_data_.parasite_parameters =
+      config["parasite_parameters"].as<ParasiteParameters>();
 
-  config_data_.genotype_parameters =
-    config["genotype_parameters"].as<GenotypeParameters>();
+    config_data_.immune_system_parameters =
+      config["immune_system_parameters"].as<ImmuneSystemParameters>();
 
-  config_data_.drug_parameters =
-    config["drug_parameters"].as<DrugParameters>();
+    config_data_.genotype_parameters =
+      config["genotype_parameters"].as<GenotypeParameters>();
 
-  config_data_.therapy_parameters =
-    config["therapy_parameters"].as<TherapyParameters>();
+    config_data_.drug_parameters =
+      config["drug_parameters"].as<DrugParameters>();
 
-  config_data_.strategy_parameters =
-    config["strategy_parameters"].as<StrategyParameters>();
+    config_data_.therapy_parameters =
+      config["therapy_parameters"].as<TherapyParameters>();
 
-  config_data_.epidemiological_parameters =
-    config["epidemiological_parameters"].as<EpidemiologicalParameters>();
+    config_data_.strategy_parameters =
+      config["strategy_parameters"].as<StrategyParameters>();
 
-  config_data_.mosquito_parameters =
-    config["mosquito_parameters"].as<MosquitoParameters>();
+    config_data_.epidemiological_parameters =
+      config["epidemiological_parameters"].as<EpidemiologicalParameters>();
 
-  config_data_.population_events =
-    config["population_events"].as<PopulationEvents>();
+    config_data_.mosquito_parameters =
+      config["mosquito_parameters"].as<MosquitoParameters>();
 
-  // Validate all cross field validations
-  validate_all_cross_field_validations();
+    config_data_.population_events =
+      config["population_events"].as<PopulationEvents>();
+
+    std::cout << "Configuration file parsed successfully" << std::endl;
+
+    // Validate all cross field validations
+    validate_all_cross_field_validations();
+
+    std::cout << "Configuration file validated successfully" << std::endl;
+
+    return true;
+  }
+  catch (YAML::BadFile) {
+    std::cerr << "Error: File not found" << std::endl;
+    return false;
+  }
+  return false;
 }
 
 void Config::validate_all_cross_field_validations() {

src/Configuration/Config.h

@@ -19,7 +19,7 @@ class Config {
   Config &operator=(Config &&) = delete;
 
   // Load configuration from a YAML file
-  void load(const std::string &filename);
+  bool load(const std::string &filename);
 
   // Reload configuration (useful for dynamic updates)
   void reload();

src/Configuration/README.md

@@ -1 +1,47 @@
 # Core Config
+
+The Configuration module is responsible for loading, validating, and managing the configuration settings for the simulation. It reads configuration data from a YAML file and provides access to various configuration parameters through getter methods.
+
+## Files
+
+- `Config.h` and `Config.cpp`: Defines the `Config` class, which handles loading and validating the configuration file.
+- `ConfigData.h`: Defines the `ConfigData` struct, which holds all the configuration parameters.
+- `ConfigData.cpp`: Implements the methods for the `ConfigData` struct.
+
+## Classes
+
+### Config
+
+The `Config` class is responsible for:
+
+- Loading configuration data from a YAML file.
+- Validating the configuration data.
+- Providing access to the configuration parameters.
+
+#### Methods
+
+- `bool load(const std::string &filename)`: Loads the configuration from the specified YAML file.
+- `void reload()`: Reloads the configuration file.
+- `void validate_all_cross_field_validations()`: Validates all cross-field validations.
+- Various getter methods to access specific configuration parameters.
+
+### ConfigData
+
+The `ConfigData` struct holds all the configuration parameters. It includes the following fields:
+
+- `ModelSettings model_settings`: Configuration for the model settings.
+- `TransmissionSettings transmission_settings`: Configuration for transmission settings.
+- `PopulationDemographic population_demographic`: Configuration for population demographics.
+- `SimulationTimeframe simulation_timeframe`: Configuration for the simulation timeframe.
+- `SpatialSettings spatial_settings`: Configuration for spatial settings.
+- `SeasonalitySettings seasonality_settings`: Configuration for seasonality settings.
+- `MovementSettings movement_settings`: Configuration for movement settings.
+- `ParasiteParameters parasite_parameters`: Configuration for parasite parameters.
+- `ImmuneSystemParameters immune_system_parameters`: Configuration for immune system parameters.
+- `GenotypeParameters genotype_parameters`: Configuration for genotype parameters.
+- `DrugParameters drug_parameters`: Configuration for drug parameters.
+- `TherapyParameters therapy_parameters`: Configuration for therapy parameters.
+- `StrategyParameters strategy_parameters`: Configuration for strategy parameters.
+- `EpidemiologicalParameters epidemiological_parameters`: Configuration for epidemiological parameters.
+- `MosquitoParameters mosquito_parameters`: Configuration for mosquito parameters.
+- `PopulationEvents population_events`: Configuration for population events.

src/Configuration/SimulationTimeframe.h

@@ -4,6 +4,7 @@
 #include <spdlog/spdlog.h>
 
 #include "Utils/YamlFile.h"
+#include "Utils/Time.h"
 
 // Class to hold the simulation timeframe data
 class SimulationTimeframe {
@@ -53,11 +54,20 @@ class SimulationTimeframe {
     start_collect_data_day_ = value;
   }
 
+  void set_total_time(int total_time) {
+    total_time_ = total_time;
+  }
+
+  [[nodiscard]] int get_total_time() const {
+    return total_time_;
+  }
+
 private:
   date::year_month_day starting_date_;
   date::year_month_day start_of_comparison_period_;
   date::year_month_day ending_date_;
   int start_collect_data_day_;
+  int total_time_;
 };
 
 // Specialization of convert for the SimulationTimeframe class
@@ -93,6 +103,7 @@ struct convert<SimulationTimeframe> {
     rhs.set_ending_date(node["ending_date"].as<date::year_month_day>());
     rhs.set_start_collect_data_day(node["start_collect_data_day"].as<int>());
 
+    rhs.set_total_time(utils::Time::instance().get_day_count(rhs.get_starting_date(), rhs.get_ending_date()));
     return true;
   }
 };

src/Core/Scheduler/README.md

@@ -1 +1,37 @@
 # Core Scheduler
+
+The Scheduler module is responsible for managing the simulation's time progression and scheduling events. It interacts with the `Model` class to execute daily, monthly, and yearly updates.
+
+## Files
+
+- `Scheduler.h` and `Scheduler.cpp`: Defines the `Scheduler` class, which handles the simulation's time management and event scheduling.
+
+## Classes
+
+### Scheduler
+
+The `Scheduler` class is responsible for:
+
+- Managing the simulation's current time and total available time.
+- Interacting with the `Model` class to perform updates.
+- Handling the simulation's calendar date.
+- Providing methods to start, run, and stop the simulation.
+
+#### Methods
+
+- `Scheduler(Model *model = nullptr)`: Constructor that initializes the scheduler with an optional `Model` instance.
+- `~Scheduler()`: Destructor that clears all events.
+- `void extend_total_time(int new_total_time)`: Extends the total available time for the simulation.
+- `void clear_all_events()`: Clears all scheduled events.
+- `void initialize(const date::year_month_day &starting_date, const int &total_time)`: Initializes the scheduler with a starting date and total time.
+- `void run()`: Runs the simulation.
+- `void begin_time_step() const`: Begins a time step in the simulation.
+- `void end_time_step() const`: Ends a time step in the simulation.
+- `bool can_stop() const`: Checks if the simulation can stop.
+- `int current_day_in_year() const`: Returns the current day in the year.
+- `int current_month_in_year() const`: Returns the current month in the year.
+- `bool is_today_last_day_of_month() const`: Checks if today is the last day of the month.
+- `bool is_today_first_day_of_month() const`: Checks if today is the first day of the month.
+- `bool is_today_first_day_of_year() const`: Checks if today is the first day of the year.
+- `bool is_today_last_day_of_year() const`: Checks if today is the last day of the year.
+- `void daily_update() const`: Performs daily updates in the simulation.

src/Core/Scheduler/Scheduler.cpp

@@ -0,0 +1,111 @@
+#include "Scheduler.h"
+
+#include <Configuration/Config.h>
+
+Scheduler::Scheduler(Model* model)
+    : current_time_(-1), total_available_time_(-1), model_(model), is_force_stop_(false) {}
+
+Scheduler::~Scheduler() {
+  clear_all_events();
+}
+
+void Scheduler::extend_total_time(int new_total_time) {
+  if (total_available_time_ < new_total_time) {
+    // for (auto i = total_available_time_; i <= new_total_time; i++) {
+    //   individual_events_list_.push_back(EventPtrVector());
+    //   population_events_list_.push_back(EventPtrVector());
+    // }
+  }
+  total_available_time_ = new_total_time;
+}
+
+void Scheduler::clear_all_events() {
+  // clear_all_events(individual_events_list_);
+  // clear_all_events(population_events_list_);
+}
+
+void Scheduler::initialize(const date::year_month_day& starting_date, const int& total_time) {
+  set_total_available_time(total_time + 720); // Prevent scheduling at the end of simulation
+  set_current_time(0);
+  calendar_date = date::sys_days(starting_date);
+}
+
+// Methods not declared in the header have been removed
+
+void Scheduler::run() {
+  current_time_ = 0;
+  for (current_time_ = 0; !can_stop(); current_time_++) {
+    if (current_time_ % model_->get_config()->get_model_settings().get_days_between_stdout_output() == 0) {
+      spdlog::info("Day: {}", current_time_);
+    }
+    begin_time_step();
+    daily_update();
+    end_time_step();
+    calendar_date += date::days{1};
+  }
+}
+
+void Scheduler::begin_time_step() const {
+  if (model_ != nullptr) {
+    model_->begin_time_step();
+  }
+}
+
+void Scheduler::daily_update() const {
+  if (model_ != nullptr) {
+    model_->daily_update();
+
+    if (is_today_first_day_of_month()) {
+      model_->monthly_update();
+    }
+
+    if (is_today_first_day_of_year()) {
+      model_->yearly_update();
+    }
+
+    // Executing population-related events
+    // execute_events_list(population_events_list_[current_time_]);
+
+    // Executing individual-related events
+    // execute_events_list(individual_events_list_[current_time_]);
+  }
+}
+
+void Scheduler::end_time_step() const {
+  if (model_ != nullptr) {
+    model_->end_time_step();
+  }
+}
+
+bool Scheduler::can_stop() const {
+  return current_time_ > model_->get_config()->get_simulation_timeframe().get_total_time();
+}
+
+int Scheduler::current_day_in_year() const {
+  return utils::Time::instance().day_of_year(calendar_date);
+}
+
+int Scheduler::current_month_in_year() const {
+  return utils::Time::instance().month_of_year(calendar_date);
+}
+
+bool Scheduler::is_today_last_day_of_year() const {
+  date::year_month_day ymd{calendar_date};
+  return ymd.month() == date::month{12} && ymd.day() == date::day{31};
+}
+
+bool Scheduler::is_today_first_day_of_month() const {
+  date::year_month_day ymd{calendar_date};
+  return ymd.day() == date::day{1};
+}
+
+bool Scheduler::is_today_first_day_of_year() const {
+  date::year_month_day ymd{calendar_date};
+  return ymd.month() == date::month{1} && ymd.day() == date::day{1};
+}
+
+bool Scheduler::is_today_last_day_of_month() const {
+  const auto next_date = calendar_date + date::days{1};
+  date::year_month_day ymd{next_date};
+  return ymd.day() == date::day{1};
+}