def __init__(self, model: Model = None, output_directory: str = None, delete_directory: bool = True, resume=None, variable: bool = False):
if model is None:
raise gillespyError.SimulationError("A model is required to run the simulation.")
if len(BuildEngine.get_missing_dependencies()) > 0:
raise gillespyError.SimulationError(
"Please install/configure 'g++' and 'make' on your system, to ensure that GillesPy2 C solvers will run properly."
)
if platform.system() == "Windows" and " " in gillespy2.__file__:
raise gillespy2Error.SimulationError("GillesPy2 does not support spaces in its path on Windows systems.")
self.delete_directory = False
self.model = copy.deepcopy(model)
self.resume = resume
self.variable = variable
self.build_engine: BuildEngine = None
# Validate output_directory, ensure that it doesn't already exist
if isinstance(output_directory, str):
output_directory = os.path.abspath(output_directory)
if os.path.exists(output_directory):
raise gillespyError.DirectoryError(
f"Could not write to specified output directory: {output_directory}"
" (already exists)"
)
self.output_directory = output_directory
self.delete_directory = delete_directory
if self.model is not None:
self._set_model()
self.is_instantiated = True
def __init__(self, makefile: str, output_dir: str, obj_dir: str = None):
self.makefile = Path(makefile).resolve()
self.self_dir = Path(__file__).parent
self.cbase_dir = self.self_dir.joinpath("../c_base").resolve()
self.output_dir = Path(output_dir).resolve()
# obj_dir is, presumably, only supplied if caching is enabled.
# If not supplied, it should be assumed ethereal and cleaned up
# with the rest of the tmp directory.
if obj_dir is None:
self.obj_dir = self.output_dir.joinpath("gillespy2_obj").resolve()
else:
self.obj_dir = Path(obj_dir).resolve()
for path in [self.output_dir, self.obj_dir]:
if path.is_file():
raise gillespyError.DirectoryError(
f"Error while attempting to open directory:\n"
f"- {path} is actually a file."
)
if not path.is_dir():
path.mkdir()
self.output_file = "GillesPy2_Simulation.out"
if os.name == "nt":
self.output_file = "GillesPy2_Simulation.exe"
self.output_file = Path(self.output_dir, self.output_file)
def __init__(self,
model=None,
output_directory=None,
delete_directory=True,
resume=None):
super(SSACSolver, self).__init__()
self.__compiled = False
self.delete_directory = False
self.model = model
self.resume = resume
if self.model is not None:
# Create constant, ordered lists for reactions/species/
self.species_mappings = self.model.sanitized_species_names()
self.species = list(self.species_mappings.keys())
self.parameter_mappings = self.model.sanitized_parameter_names()
self.parameters = list(self.parameter_mappings.keys())
self.reactions = list(self.model.listOfReactions.keys())
if isinstance(output_directory, str):
output_directory = os.path.abspath(output_directory)
if isinstance(output_directory, str):
if not os.path.isfile(output_directory):
self.output_directory = output_directory
self.delete_directory = delete_directory
if not os.path.isdir(output_directory):
os.makedirs(self.output_directory)
else:
raise gillespyError.DirectoryError(
"File exists with the same path as directory.")
else:
self.temporary_directory = tempfile.TemporaryDirectory()
self.output_directory = self.temporary_directory.name
if not os.path.isdir(self.output_directory):
raise gillespyError.DirectoryError(
"Errors encountered while setting up directory for Solver C++ files."
)
cutils._copy_files(self.output_directory, GILLESPY_C_DIRECTORY)
self.__write_template()
self.__compile()