Added IPython notebook example using pyNeuroML

[rgerkin]

No description provided.

[rgerkin]

9bb51c0 is a bug fix.

[sanjayankur31]

Looking into this. Unfortunately, I can't get sciunit to install on my Fedora 33 system with pip here. The AllenSDK seems to have quite a few deps that do not include wheels from the looks of it, and pip fails when it tries to compile them from source for various reasons.

Example errors with PyTables:

  tables/hdf5extension.c: In function ‘__Pyx_modinit_type_init_code’:
  tables/hdf5extension.c:32959:42: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’
  32959 |   __pyx_type_6tables_13hdf5extension_Node.tp_print = 0;
        |                                          ^
  tables/hdf5extension.c:32971:42: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’
  32971 |   __pyx_type_6tables_13hdf5extension_Leaf.tp_print = 0;
        |                                          ^

Similarly with statsmodels:

  statsmodels/tsa/kalmanf/kalman_loglike.c:24553:25: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’
  24553 |   __pyx_type___pyx_array.tp_print = 0;
        |                         ^
  statsmodels/tsa/kalmanf/kalman_loglike.c:24558:31: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’
  24558 |   __pyx_type___pyx_MemviewEnum.tp_print = 0;
        |                               ^
  statsmodels/tsa/kalmanf/kalman_loglike.c:24573:30: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’
  24573 |   __pyx_type___pyx_memoryview.tp_print = 0;
        |                              ^
  statsmodels/tsa/kalmanf/kalman_loglike.c:24586:35: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’
  24586 |   __pyx_type___pyx_memoryviewslice.tp_print = 0;
        |                                   ^

Could be python3.9 related. It'll require some digging in and bug-reports with all these projects. On my TODO list now.

[sanjayankur31]

https://docs.python.org/release/3.9.0/whatsnew/3.9.html#id3 says:

• The tp_print slot of PyTypeObject has been removed. It was used for printing objects to files in Python 2.7 and before. Since Python 3.0, it has been ignored and unused. (Contributed by Jeroen Demeyer in bpo-36974.)

So, that's probably it. Will file issues upstream and see what can be done here.

[rgerkin]

SciUnit should install fine (it doesn't have AllenSDK or any of that other stuff as dependencies). It is probably NeuronUnit you are having trouble with. Pip is probably hopeless for AllenSDK on many architectures/environments, and a conda environment or something like that will probably work better for now. On my to-do list is to refactor NeuronUnit to move dependencies like AllenSDK, which are only required for a subset of behaviors (and not relevant to this particular example) to become optional dependencies. You could even just comment that dependency out for the purposes of this example.

[sanjayankur31]

Hi @rgerkin .

Thanks, that sounds good. I'll comment out the AllenSDK dependency in NeuronUnit for the time being and see how far I get.

Cheers,
Ankur

[rgerkin]

@sanjayankur31 You may have to comment out some import AllenSDK type lines as well. I don't recall how carefully I tried to isolate them in the past.

[sanjayankur31]

Sure, I'll have a look and see how far I get :)