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I'm sorry, this is just a duplicate of my previous report: viewtopic.php?f=2&t=3221

Greetings, I have a problem where point processes are not being removed from NEURON (7.3) even though all python references are apparently lost. Here is my simple point process: NEURON { POINT_PROCESS TestPointProc RANGE rangeval } ASSIGNED { rangeval (1) } ..and a script that demonstrates the probl...

This is an issue I ran into while debugging unit tests in pynrn: from neuron import h s = h.Section() c = h.IClamp(0.5, s) g = c.get_segment() del s del c del g print "Sections:", len(list(h.allsec())) print "IClamps: ", len(list(h.List('IClamp'))) The output looks like: Sections...

I am trying to understand how to use MechanismStandard, but it is returning inconsistent results in some situations. For example: from neuron import h #s = h.Section() #s.insert('hh') ms = h.MechanismStandard('k_ion', 1) print ms.count() As written, the output is 3. If I uncomment the line that crea...

The behavior you describe is a property of Python not of NEURON. That's exactly my point. You and I are aware of sys.last_traceback, but the vast majority of NEURON users are not (and even I would have to do a lot of digging to fix this issue). As I have said, there are many different ways referenc...

Thanks again, Michael! I'd like to return to this issue of object deletion, because there seems to be some doubt about my concern that reference management in python is hard. Let's take the following example: from neuron import h sections = {} def make_sec(name): sec = h.Section(name=name) if name i...

Thanks Michael, I want to clarify that I am working on a wraper around the existing NEURON+Python; my suggestion to use ctypes is a separate issue. The focus of this is to see whether I can build an API that is a bit more natural to use in python. I only intend to have partial backward compatibility...

. . . have everything else work with a weakref proxy object. Unfortunately, weakrefs are not allowed to most (all?) neuron objects. I'd think you'd be reset if you reset globals, removed all sections (check h.allsec), all point processes (get a list of possible types with h.MechanismType and of ins...

Is the issue that you have no control over the code that is being run? We are writing a general-purpose model that we hope will be useful to a larger community. So in that sense we have complete control over the code within the model, but we do no control the ways it will be used (except by writing...

This is a big deal when using NEURON from Python? It has been a big deal for me, but perhaps I have some basic misunderstanding of how the API works. The problem is that there is no way to explicitly remove objects from the NEURON kernel; instead this is done indirectly when Python collects the obj...

I am looking for a comprehensive set of guidelines on how to correctly run two different simulations (serially) within the same process (or alternatively, whether this is even supported behavior in the first place). Ideally, the results of the second simulation should be in no way affected by any de...

I have been working with Python + NEURON lately and found myself frustrated with the API on several occasions. Some of the problems are related to the original translation from HOC to Python, some are historical API issues inherited from early versions of the Python interface, and some appear to be ...

Thanks, Michael!

Take the following session example: >>> s = h.Section() >>> s.nseg 1 >>> s.allseg() <nrn.Section object at 0x7f50c483fd50> >>> list(s) [<nrn.Segment object at 0x7f50bc8ab058>, <nrn.Segment object at 0x7f50bc8ab8c8>, <nrn.Segment object at 0x7f50bc8ab7d8>] >>> list(s.allseg()) [<nrn.Segment object at...

Example:
It appears the first statement generated a python error, but the exception was not raised until the error check in the following statement.