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NeuralEnsemble / PyNN

A Python package for simulator-independent specification of neuronal network models.

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TypeError following the "Initialising the simulator" step in the documentation

rberg2 opened this issue · comments

commented

Hello,
I am attempting to validate my installation of PyNN and Nest-simulator in a rather large miniconda environment. While running the example code I run into the following error. Do you have any idea whats going wrong?

Python 3.8.10 (default, Jun  4 2021, 15:09:15)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pyNN.nest import *

Apr 13 18:05:23 CopyFile [Error]:
    Could not open source file.
Error in nest resource file: /BadIO in CopyFile_

              -- N E S T --
  Copyright (C) 2004 The NEST Initiative

 Version: 3.3
 Built: Apr 13 2022 17:17:35

 This program is provided AS IS and comes with
 NO WARRANTY. See the file LICENSE for details.

 Problems or suggestions?
   Visit https://www.nest-simulator.org

 Type 'nest.help()' to find out more about NEST.

>>> setup()
0
>>> setup(timestep=0.1, min_delay=0.1, max_delay=10.0)
0
>>> from pyNN.utility import init_logging
>>> init_logging("logfile", debug=True)
<Logger PyNN (DEBUG)>
>>> p1 = Population(100, IF_curr_alpha, structure=space.Grid2D())
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/apps/conda/lib/python3.8/site-packages/pyNN/nest/populations.py", line 141, in __init__
    super(Population, self).__init__(size, cellclass,
  File "/apps/conda/lib/python3.8/site-packages/pyNN/common/populations.py", line 672, in __init__
    self.celltype = cellclass(**cellparams)
TypeError: type object argument after ** must be a mapping, not NoneType

Thanks in advance!

commented

Hi @rberg2,

There's just a small bug in your code, it should be

p1 = Population(100, IF_curr_alpha(), structure=space.Grid2D())

not

p1 = Population(100, IF_curr_alpha, structure=space.Grid2D())

[By the way, I note you're using NEST 3.3, which is not fully compatible with the current release of PyNN (0.10.0) - NEST 3.1 is preferred. PyNN 0.10.1 will be released very soon (this week or next), and will include support for NEST 3.3, so please update your PyNN installation once the new version comes out].

commented

Thanks for the correction! It looks like I was following the instructions for PyNN 0.7.