Python bindings to a C++ implementation of the source code accompanying: Jagiella, Rickert, Theis, Hasenauer "Parallelization and high-performance computing enables automated statistical inference of multiscale models" (2017)
License: BSD 3-Clause "New" or "Revised" License
Is there a reason for the lines https://github.com/ICB-DCM/tumor2d/blob/master/tumor2d/simulate.py#L63 generating a subprocess for the call to tumor2d_simulate? The package still seems to work directly calling res = tumor2d_simulate(**kwargs), and removes a "daemons may not create subprocesses" error in pyABC.
@neuralyzer @drickert @ any developer? Thanks!
trying the test invocation fails:
$ python
Python 3.8.5 (default, Jul 21 2020, 10:48:26)
[Clang 11.0.3 (clang-1103.0.32.62)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import tumor2d
>>> simulate()
>>> tumor2d.simulate()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/System/Volumes/Data/rikData/virtualenv/pyABC/tumor2d-master/tumor2d/simulate.py", line 70, in simulate
proc.start()
File "/usr/local/Cellar/[email protected]/3.8.5/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/usr/local/Cellar/[email protected]/3.8.5/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/usr/local/Cellar/[email protected]/3.8.5/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/context.py", line 284, in _Popen
return Popen(process_obj)
File "/usr/local/Cellar/[email protected]/3.8.5/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/usr/local/Cellar/[email protected]/3.8.5/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/usr/local/Cellar/[email protected]/3.8.5/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 47, in _launch
reduction.dump(process_obj, fp)
File "/usr/local/Cellar/[email protected]/3.8.5/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/reduction.py", line 60, in dump
ForkingPickler(file, protocol).dump(obj)
AttributeError: Can't pickle local object 'simulate.<locals>.pipe_call'
All I'm trying to do is use this to demo pyABC, and so i've just commented out the offending line#5:
tumor2d/tumor2d/src/Mathematix.cpp
Line 5 in bb68a58
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