Merge pull request #580 from StochSS/develop

Release v1.6.3

gillespy2/__version__.py

@@ -24,7 +24,7 @@
 # =============================================================================
 
 
-__version__      = '1.6.2'
+__version__      = '1.6.3'
 
 __title__        = 'GillesPy2'
 __description__  = 'Python interface for Gillespie-style biochemical simulations'

gillespy2/core/functiondefinition.py

@@ -35,30 +35,31 @@ class FunctionDefinition(SortableObject, Jsonify):
     """
 
     def __init__(self, name="", function=None, args=[]):
-
-        import math
-        eval_globals = math.__dict__
+        if function is None:
+            raise TypeError("Function string provided for FunctionDefinition cannot be None")
 
         self.name = name
         self.function_string = function
-
-        self.args = ', '.join(args)
-        self.function = eval('lambda ' + self.args + ': ' + function, eval_globals)
-
-        if self.function is None:
-            raise TypeError
+        self.args = args
 
 
     def __str__(self):
-        return f"self.name: Args: {self.args}, Expression: {self.function_string}"
+        return f"{self.name}: Args: {self.args}, Expression: {self.function_string}"
+
+    def get_arg_string(self) -> str:
+        """
+        Convert function's argument list into a comma-separated formatted string.
 
+        :returns: Argument list as a comma-separated formatted string.
+        """
+        return ','.join(self.args)
 
     def sanitized_function(self, species_mappings, parameter_mappings):
         names = sorted(list(species_mappings.keys()) + list(parameter_mappings.keys()), key=lambda x: len(x),
                        reverse=True)
         replacements = [parameter_mappings[name] if name in parameter_mappings else species_mappings[name]
                         for name in names]
-        sanitized_function = self.function
+        sanitized_function = self.function_string
         for id, name in enumerate(names):
             sanitized_function = sanitized_function.replace(name, "{" + str(id) + "}")
         return sanitized_function.format(*replacements)

gillespy2/sbml/SBMLexport.py

@@ -131,7 +131,7 @@ def __add_function_definitions(function_definition_list, model):
     for name, function_def in function_definition_list.items():
         func_def = model.createFunctionDefinition()
         func_def.setId(name)
-        func_str = f"lambda({func_def.args}, {func_def.function_string})"
+        func_str = f"lambda({function_def.get_arg_string()}, {function_def.function_string})"
         function = __get_math(func_str)
         func_def.setMath(function)
 

gillespy2/solvers/cpp/__init__.py

@@ -21,6 +21,7 @@
 from gillespy2.solvers.cpp.ode_c_solver import ODECSolver
 from gillespy2.solvers.cpp.tau_leaping_c_solver import TauLeapingCSolver
 from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver
+from gillespy2.solvers.cpp.tau_hybrid_c_solver import TauHybridCSolver
 
 # Check to see if we're missing any dependencies.
 from .build.build_engine import BuildEngine
@@ -34,4 +35,4 @@
     )
 
 __all__ = ['SSACSolver', 'VariableSSACSolver']
-__all__ = ['SSACSolver', 'ODECSolver', 'TauLeapingCSolver', 'VariableSSACSolver']
+__all__ = ['SSACSolver', 'ODECSolver', 'TauLeapingCSolver', 'VariableSSACSolver', 'TauHybridCSolver']

gillespy2/solvers/cpp/build/build_engine.py

@@ -29,6 +29,7 @@
 
 class BuildEngine():
     template_definitions_name = "template_definitions.h"
+    template_options_name = "template_opts.h"
 
     def __init__(self, debug: bool = False, output_dir: str = None):
         self.self_dir = Path(__file__).parent
@@ -68,7 +69,7 @@ def get_missing_dependencies(cls) -> "list[str]":
 
         return missing
 
-    def prepare(self, model: Model, variable=False) -> str:
+    def prepare(self, model: Model, variable=False, custom_definitions: "dict[str, str]" = None) -> str:
         """
         Prepare the template directory for compilation.
         The following operations will be performed:
@@ -109,6 +110,10 @@ def prepare(self, model: Model, variable=False) -> str:
         template_file = self.template_dir.joinpath(self.template_definitions_name)
         template_file.unlink()
         template_gen.write_template(str(template_file), model, variable)
+        if custom_definitions is not None:
+            options_file = self.template_dir.joinpath(self.template_options_name)
+            options_file.unlink()
+            template_gen.write_definitions(str(options_file), custom_definitions)
 
         # With all required information gathered, create a Make instance.
         self.make = Make(str(self.makefile), str(self.output_dir), str(self.obj_dir))

gillespy2/solvers/cpp/build/make.py

@@ -57,17 +57,11 @@ def __init__(self, makefile: str, output_dir: str, obj_dir: str = None):
         self.output_file = Path(self.output_dir, self.output_file)
 
     def prebuild(self):
-        self.__execute("prebuild")
+        self.__execute("build")
 
     def build_simulation(self, simulation_name: str, **kwargs):
         self.__execute(simulation_name, **kwargs)
 
-    def clean(self):
-        self.__execute("clean")
-
-    def clean_all(self):
-        self.__execute("clean_all")
-
     def __execute(self, target: str, **kwargs):        
         # Default make arguments.
         args_dict = {