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HOTFIX: Export StochSS Live! Models #942

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merged 2 commits into from
Apr 27, 2023
Merged

HOTFIX: Export StochSS Live! Models #942

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c1a047f
Fixed timespan convert when exporting model as stochss models.
BryanRumsey Apr 27, 2023
48998de
Pylint updates.
BryanRumsey Apr 27, 2023
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44 changes: 25 additions & 19 deletions gillespy2/stochss/StochSSexport.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@

# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.

''' Module for exporting GillesPy2 model as StochSS Live! models. '''
import ast
import json

Expand Down Expand Up @@ -55,8 +55,8 @@ def __add_function_definitions(model, function_definitions):
for name, function_definition in function_definitions.items():
variables = function_definition.get_arg_string()
expression = function_definition.function_string
function = "lambda({0}, {1})".format(variables, expression)
signature = "{0}({1})".format(name, variables)
function = f"lambda({variables}, {expression})"
signature = f"{name}({variables})"

s_function_definition = {"compID":model['defaultID'],
"name":name,
Expand All @@ -73,7 +73,7 @@ def __add_parameters(model, parameters):
for name, parameter in parameters.items():
try:
expression = ast.literal_eval(parameter.expression)
except:
except Exception: # pylint: disable=broad-except
expression = parameter.expression
s_parameter = {"compID":model['defaultID'],
"name":name,
Expand Down Expand Up @@ -185,7 +185,7 @@ def __get_species(species, name):


def __write_to_file(model, path):
with open(path, "w") as model_file:
with open(path, "w", encoding="utf-8") as model_file:
json.dump(model, model_file, indent=4, sort_keys=True, cls=ComplexJsonCoder)


Expand All @@ -207,25 +207,31 @@ def export(model, path=None, return_stochss_model=False):

if model.tspan is None:
model_settings = {"endSim": 20, "timeStep": 0.05}
elif type(model.tspan).__name__ == "TimeSpan":
model_settings = {
"endSim": model.tspan.items[-1],
"timeStep": model.tspan.items[1] - model.tspan.items[0]
}
else:
model_settings = {
"endSim": model.tspan[-1],
"timeStep": model.tspan[-1] / len(model.tspan)
"timeStep": model.tspan[1] - model.tspan[0]
}

s_model = {"is_spatial": False,
"defaultID": 1,
"annotation": "",
"volume": model.volume,
"modelSettings": model_settings,
"species": [],
"initialConditions": [],
"parameters": [],
"reactions": [],
"rules": [],
"eventsCollection": [],
"functionDefinitions": []
}
s_model = {
"is_spatial": False,
"defaultID": 1,
"annotation": "",
"volume": model.volume,
"modelSettings": model_settings,
"species": [],
"initialConditions": [],
"parameters": [],
"reactions": [],
"rules": [],
"eventsCollection": [],
"functionDefinitions": []
}

__add_species(model=s_model, species=model.get_all_species())
__add_parameters(model=s_model, parameters=model.get_all_parameters())
Expand Down