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OpenSourceBrain / AllenInstituteNeuroML

Example files to test interaction between models developed at the Allen Brain Institute and NeuroML
http://www.opensourcebrain.org/projects/alleninstituteneuroml
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All-active celltype #19

Closed anujanegi closed 2 years ago

anujanegi commented 2 years ago

@pgleeson can you review? Also, I'm unsure how to fix the fail in the checks(hard to recreate as I don't get them locally).

anujanegi commented 2 years ago

Also, I would love to get tips on how do I go about verifying the generated LEMS/NML models? @sanjayankur31 @pgleeson

pgleeson commented 2 years ago

@anujanegi Just to check, the ParseAll.py is failing when I run it locally, as well as on these tests. Is it running for you? What version of the allen sdk do you have?

Also re running the tests locally, are you managing to run the LEMS files (i.e. using https://docs.neuroml.org/Userdocs/Software/Tools/NEURON.html#simulating-neuroml-models-in-neuron). Have you installed omv (https://github.com/OpenSourceBrain/osb-model-validation) to test the models automatically?

One of the issues with the test failing is due to the new cell file not being valid nml. This is easier to check using pynml -validate xx.cell.nml

anujanegi commented 2 years ago

My allensdk version is 2.13.4 My tests also don't pass locally, but they don't pass on the current master branch as well (although gh-actions pass there).

Something to do with versions? This is my omv list -V:

[omv] The following engines are currently supported by OMV (v0.1.14):
[omv] 
[omv]   Arbor                         (installed: False)
[omv]   Brian2                        (installed: False)
[omv]   EDEN                          (installed: False)
[omv]   Moose                         (installed: False)
[omv]   NEST                          (installed: False)
[omv]   NEURON                        (installed: v8.1.0)
[omv]   NetPyNE                       (installed: vWarning: could not import interactive plotting functions; make sure the "bokeh" package is installed.
1.0.2.1)
[omv]   NetPyNE_NP2                   (installed: vWarning: could not import interactive plotting functions; make sure the "bokeh" package is installed.
1.0.2.1)
[omv]   NetPyNE_NP4                   (installed: vWarning: could not import interactive plotting functions; make sure the "bokeh" package is installed.
1.0.2.1)
[omv]   Octave                        (installed: v5.2.0)
[omv]   PyLEMS                        (installed: v0.5.9)
[omv]   PyLEMS_NeuroML2               (installed: False)
[omv]   PyNEST                        (installed: False)
[omv]   PyNEURON                      (installed: v8.1.0)
[omv]   PyNN                          (installed: False)
[omv]   PyNN_NEURON                   (installed: False)
[omv]   PyNN_Nest                     (installed: False)
[omv]   PyNN_NeuroML                  (installed: False)
[omv]   Py_neuroConstruct             (installed: False)
[omv]   genesis                       (installed: False)
[omv]   jLEMS                         (installed: False)
[omv]   jNeuroML                      (installed: v0.11.1)
[omv]   jNeuroML_Brian2               (installed: False)
[omv]   jNeuroML_EDEN                 (installed: False)
[omv]   jNeuroML_Moose                (installed: False)
[omv]   jNeuroML_NEURON               (installed: v8.1.0)
[omv]   jNeuroML_NetPyNE              (installed: vWarning: could not import interactive plotting functions; make sure the "bokeh" package is installed.
1.0.2.1)
[omv]   jNeuroML_NetPyNE_NP2          (installed: vWarning: could not import interactive plotting functions; make sure the "bokeh" package is installed.
1.0.2.1)
[omv]   jNeuroML_NetPyNE_NP4          (installed: vWarning: could not import interactive plotting functions; make sure the "bokeh" package is installed.
1.0.2.1)
[omv]   jNeuroML_PyNN_NEURON          (installed: False)
[omv]   jNeuroML_validate             (installed: v0.11.1)
[omv]   jNeuroML_validatev1           (installed: v0.11.1)
[omv]   pyNeuroML                     (installed: v0.5.20)
[omv] 
[omv] Additional Python (v3.7.13) packages:
[omv] 
[omv]   matplotlib                    (installed: v3.4.2)
[omv]   numpy                         (installed: v1.21.6)
[omv]   pandas                        (installed: v1.3.5)
[omv]   scipy                         (installed: v1.7.3)
[omv]   sympy                         (installed: False)
[omv]   tables                        (installed: v3.6.1)
[omv]   h5py                          (installed: v3.7.0)
[omv]   neo                           (installed: False)
[omv]   lazyarray                     (installed: False)
[omv]   pyelectro                     (installed: v0.2.4)
[omv]   neurotune                     (installed: v0.2.5)
[omv]   lems                          (installed: v0.5.9)
[omv]   pyneuroml                     (installed: v0.5.20)
[omv]   neuroml                       (installed: v0.3.1)
[omv]   neuromllite                   (installed: v0.5.1)
[omv]