Reorganize the file for code generation a bit.

src/codegeneration.jl

@@ -1,4 +1,8 @@
-########## Check units ###############
+####################################################################################
+####################################################################################
+########################### CHECK UNITS #################################
+####################################################################################
+####################################################################################
 
 function calculate_units(exp::Expr, units::Dict{Symbol, Dimension}, c::Int64)
  ex = deepcopy(exp)
@@ -44,9 +48,12 @@ The right hand side expression was $(val.Expr)")
  end
 end
 
-########## Generate Jacobian ###############
+####################################################################################
+####################################################################################
+######################## GENERATE JACOBIAN ##############################
+####################################################################################
+####################################################################################
 
-using Calculus
 
 # Calculation Jacobian matrix of the model
 function generate_jacobian_matrix(compressed_model::OdeSorted)
@@ -66,7 +73,11 @@ function generate_jacobian_matrix(compressed_model::OdeSorted)
  return Jacobian
 end
 
-########## Generate Extended System ###############
+####################################################################################
+####################################################################################
+################### GENERATE EXTENDED SYSTEM ############################
+####################################################################################
+####################################################################################
 
 # Calculate array of sensitivities
 function generate_sensitivity_array(compressed_model::OdeSorted)
@@ -89,7 +100,7 @@ end
 
 ####################################################################################
 ####################################################################################
-########################## JULIA CODE GENERATION #################################
+########################## SOURCE CODE GENERATION ################################
 ####################################################################################
 ####################################################################################
 
@@ -177,6 +188,73 @@ function generate_extended_system_julia(compressed_model::OdeSorted, name)
 end
 
 
+####################################################################################
+####################################################################################
+########################### FULL MODEL GENERATION ################################
+####################################################################################
+####################################################################################
+
+"""
+`generate_code_Julia!` will generate a Julia source file containing the code necessary
+to load the model and simulate (using the SimulationModels packge). This function
+will return nothing. As a side effect, it will write a file to the hard-drive.
+
+Arguments
+----------
+
+`source`: Compulsory argument that contains a path to the ode file
+
+`unit_analysis`: Keyword boolean argument to indicate whether we want to perform
+analysis of physical dimensions and unit conversion
+
+`name`: Keyword string argument with the name of the model we want to generate.
+This name will be appended to the default names of the functions being generated
+as well as the factory function from which we can generate new instances of the model.
+
+`file`: Keyword string argument with the path to the file where we want to generate
+the model. It does not have to coincide with the `name` argument given before. Note that
+the extension should not be included.
+
+`jacobian`: Keyword boolean argument to indicate whether the Jacobian of the model should
+be generated or not.
+
+`sensitivities`: Keyword boolean argument to indicate whether the sensitivity functions
+associated to the model should be generated or not.
+"""
+function generate_code_Julia!(source::String; unit_analysis = false, name = "autogenerated_model", file = "autogenerated_model", jacobian = false, sensitivities = false)
+ parsed_model = process_file(source)
+ reaction_model = convert_master_equation(parsed_model)
+ ode_model = convert_reaction_model(reaction_model)
+ generate_code_Julia!(ode_model, unit_analysis = unit_analysis, name = name, file = file, jacobian = jacobian, sensitivities = sensitivities)
+end
+
+"""
+`generate_code_Julia!` will generate a Julia source file containing the code necessary
+to load the model and simulate (using the SimulationModels packge). This function
+will return nothing. As a side effect, it will write a file to the hard-drive.
+
+Arguments
+----------
+
+`source`: Compulsory argument that contains an OdeSource model
+
+`unit_analysis`: Keyword boolean argument to indicate whether we want to perform
+analysis of physical dimensions and unit conversion
+
+`name`: Keyword string argument with the name of the model we want to generate.
+This name will be appended to the default names of the functions being generated
+as well as the factory function from which we can generate new instances of the model.
+
+`file`: Keyword string argument with the path to the file where we want to generate
+the model. It does not have to coincide with the `name` argument given before. Note that
+the extension should not be included.
+
+`jacobian`: Keyword boolean argument to indicate whether the Jacobian of the model should
+be generated or not.
+
+`sensitivities`: Keyword boolean argument to indicate whether the sensitivity functions
+associated to the model should be generated or not.
+"""
 
 function generate_code_Julia!(ode_model::OdeSource; unit_analysis = true, name = "autogenerated_model", file = "autogenerated_model", jacobian = false, sensitivities = false)
 
@@ -244,6 +322,13 @@ function generate_code_Julia!(ode_model::OdeSource; unit_analysis = true, name =
  nothing
 end
 
+
+"""
+`write_model_Julia!` will write the source file required to run the models in julia.
+
+It is generated according to the interface provided by SimulationModels which will take care
+of wrapping the corresponding solvers, converting units, etc.
+"""
 function write_model_Julia!(States::OrderedDict{ASCIIString, Float64},
  Coef_states::OrderedDict{ASCIIString, Float64},
  Parameters::OrderedDict{ASCIIString, Float64},
@@ -302,37 +387,3 @@ function write_model_Julia!(States::OrderedDict{ASCIIString, Float64},
  close(f)
  nothing
 end
-
-"""
-`generate_code_Julia!` will generate a Julia source file containing the code necessary
-to load the model and simulate (using the SimulationModels packge). This function
-will return nothing. As a side effect, it will write a file to the hard-drive.
-
-Arguments
-----------
-
-`source`: Compulsory argument that contains a path to the ode file
-
-`unit_analysis`: Keyword boolean argument to indicate whether we want to perform
-analysis of physical dimensions and unit conversion
-
-`name`: Keyword string argument with the name of the model we want to generate.
-This name will be appended to the default names of the functions being generated
-as well as the factory function from which we can generate new instances of the model.
-
-`file`: Keyword string argument with the path to the file where we want to generate
-the model. It does not have to coincide with the `name` argument given before. Note that
-the extension should not be included.
-
-`jacobian`: Keyword boolean argument to indicate whether the Jacobian of the model should
-be generated or not.
-
-`sensitivities`: Keyword boolean argument to indicate whether the sensitivity functions
-associated to the model should be generated or not.
-"""
-function generate_code_Julia!(source::String; unit_analysis = false, name = "autogenerated_model", file = "autogenerated_model", jacobian = false, sensitivities = false)
- parsed_model = process_file(source)
- reaction_model = convert_master_equation(parsed_model)
- ode_model = convert_reaction_model(reaction_model)
- generate_code_Julia!(ode_model, unit_analysis = unit_analysis, name = name, file = file, jacobian = jacobian, sensitivities = sensitivities)
-end