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Remove Result dictionary inheritance & add timeout flag #92

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Merged
BryanRumsey merged 2 commits into from
Mar 9, 2021
Merged

Remove Result dictionary inheritance & add timeout flag #92

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091dedd
Removed Result Dict inheritance
makdl Mar 8, 2021
cd9609b
Added Result timeout flag
makdl Mar 8, 2021
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6 changes: 4 additions & 2 deletions spatialpy/Result.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,16 +50,18 @@ def _plotly_iterate(types, size=5, property_name=None, cmin=None, cmax=None, col
trace_list.append(trace)
return trace_list

class Result(dict):
""" Result object for a URDME simulation, extends the dict object. """
class Result():
""" Result object for a URDME simulation. """

def __init__(self, model=None, result_dir=None, loaddata=False):
self.model = model
self.U = None
self.tspan = None
self.data_is_loaded = False
self.success = False
self.stdout = None
self.stderr = None
self.timeout = False
self.result_dir = result_dir


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3 changes: 2 additions & 1 deletion spatialpy/Solver.py
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Expand Up @@ -195,6 +195,7 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None, number_of_threa
if stderr is not None:
print(stderr.decode('utf-8'))
except subprocess.TimeoutExpired:
result.timeout = True
# send signal to the process group
os.killpg(process.pid, signal.SIGINT)
stdout, stderr = process.communicate()
Expand All @@ -220,7 +221,7 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None, number_of_threa
raise SimulationError(
"Solver execution failed, return code = {0}".format(return_code))

result["Status"] = "Success"
result.success = True
if profile:
self.read_profile_info(result)
if stdout is not None:
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