Release V1.0.0

.clang-format

@@ -1,4 +1,4 @@
-BasedOnStyle: llvm 
+BasedOnStyle: gnu 
 BraceWrapping:
   AfterFunction: true
 AllowShortFunctionsOnASingleLine: None

README.md

@@ -1,7 +1,7 @@
 <div align="left">
 
   [![License: Apache-2.0](https://img.shields.io/badge/License-Apache-blue.svg)](LICENSE)
-  [![Version: 0.9.7](https://img.shields.io/badge/Version-0.9.7-red.svg)](LICENSE)
+  [![Version: 1.0.0](https://img.shields.io/badge/Version-0.9.7-red.svg)](LICENSE)
 </div>
 
 

apps/api/public/api/api.hpp

@@ -22,7 +22,11 @@
  */
 namespace Api
 {
-  std::array<int, 3> get_version();
+  constexpr std::array<int, 3>
+  get_version()
+  {
+    return { _BIOMC_VERSION_MAJOR, _BIOMC_VERSION_MINOR, _BIOMC_VERSION_DEV };
+  }
 
   void finalise();
 
@@ -76,6 +80,8 @@ namespace Api
          char** argv,
          std::optional<std::size_t> run_id = std::nullopt) noexcept;
 
+    static std::vector<std::string> get_model_list() noexcept;
+
     /**
      * @brief Default constructor.
      */
@@ -136,7 +142,7 @@ namespace Api
      * @param recursive Flag indicating if recursive registration is required.
      * @return True if the path was successfully registered; false otherwise.
      */
-    bool register_cma_path(std::string_view path);
+    ApiResult register_cma_path(std::string_view path);
 
     /**
      * @brief Register a serialization/deserialization (serde) path.
@@ -171,6 +177,10 @@ namespace Api
                                                  std::size_t output_position,
                                                  bool gas = false);
 
+    ApiResult set_mtr(Simulation::MassTransfer::Type::MtrTypeVariant&& variant);
+
+    void set_auto_mtr();
+
     // /**
     //  * @brief Configure feed constants for the simulation.
     //  *
@@ -222,13 +232,15 @@ namespace Api
      */
     ApiResult exec() noexcept;
 
-    void set_logger(std::shared_ptr<IO::Logger> _logger)
+    void
+    set_logger(std::shared_ptr<IO::Logger> _logger)
     {
 
       logger = std::move(_logger);
     }
 
-    [[nodiscard]] auto& get_logger() const
+    [[nodiscard]] auto&
+    get_logger() const
     {
       return logger;
     }
@@ -250,17 +262,19 @@ namespace Api
 
     std::shared_ptr<IO::Logger> logger;
 
-    std::optional<Core::ScalarFactory::ScalarVariant>
-        scalar_initializer_variant = std::nullopt;
+    std::optional<Core::ScalarFactory::ScalarVariant> scalar_initializer_variant
+        = std::nullopt;
     Core::CaseData _data;               ///< Case data for the simulation.
     Core::UserControlParameters params; ///< User-defined control parameters.
     bool loaded = false;  ///< Flag indicating if the instance is loaded.
     bool applied = false; ///< Flag indicating if the configuration is applied.
     bool registered = false; ///< Flag indicating if resources are registered.
-    std::optional<Simulation::Feed::SimulationFeed> feed =
-        std::nullopt; ///< Optional feed configuration.
-    std::optional<Simulation::MassTransfer::Type::MtrTypeVariant> mtr_type =
-        std::nullopt;
+    std::optional<Simulation::Feed::SimulationFeed> feed
+        = std::nullopt; ///< Optional feed configuration.
+    std::optional<Simulation::MassTransfer::Type::MtrTypeVariant> mtr_type
+        = std::nullopt;
+
+    bool auto_mtr;
   };
 
 } // namespace Api

apps/api/public/api/api_raw.h

@@ -43,6 +43,9 @@ typedef struct Opaque* Handle; // NOLINT //In C we only need ptr type so Opaque
    */
   void delete_handle(Handle* handle);
 
+  // TODO
+  void get_model_list(char** names, const int* n_model);
+  void free_model_list(char** names, int n_model);
   // void finalize(); //Do not use it
 
   int exec(Handle handle);

apps/api/public/api/results.hpp

@@ -12,7 +12,8 @@ struct ApiResult : Result<Success, std::string>
   }
 
   explicit constexpr ApiResult() noexcept = default;
-  constexpr int to_c_ret_code()
+  constexpr int
+  to_c_ret_code()
   {
     return (valid()) ? 0 : -1;
   }

apps/api/python/__init__.py

@@ -10,6 +10,10 @@
 if hasattr(handle_module, "__all__"):
     __all__ = handle_module.__all__
 
+__all__.extend(
+    ["pyinit_handle", "init_simulation", "set_initial_concentrations", "fast_run"]
+)
+
 
 def pyinit_handle(sim_id: int):
     """
@@ -85,25 +89,30 @@ def fast_run(
     is_serde: bool = False,
     f_init=None,
     serde_path=None,
+    uniform=None,
 ):
     """Run the simulation with optional recursion or serde handling."""
 
     # Prepare parameters
     params = handle_module.make_params(**params)
-    handle = handle_module.init_simulation(
-        outfolder, name, cma_path, params
-    )
+
+    if uniform is not None:
+        params.uniform_particle_init = True
+
+    handle = init_simulation(outfolder, name, cma_path, params)
 
     # Liquid feed configuration
     if liquid_flow_rate != 0:
         handle_module.set_liquid_feed_constant(handle, liquid_flow_rate, s_feed, 0, 0)
 
+    handle_module.register_model_name(
+        handle, model_name
+    )  # Needed to set it even if serde with UDF
     # Model setup
     if not is_serde:
         if f_init is None:
             raise ValueError("f_init must be provided when is_serde is False")
-        handle_module.set_initial_concentrations(handle, *f_init(n_compartment))
-        handle_module.register_model_name(handle, model_name)
+        set_initial_concentrations(handle, *f_init(n_compartment))
     else:
         if not serde_path:
             raise ValueError("serde_path must be provided when is_serde is True")
@@ -116,9 +125,4 @@ def fast_run(
         return -1
 
     handle_module.exec(handle)
-    return 0
-
-
-__all__.extend(
-    ["pyinit_handle", "init_simulation", "set_initial_concentrations", "fast_run"]
-)
+    return handle_module.i_rank(handle)