simplify process for initializing cell-to-cell connections

[rythorpe]

Currently, various functions and wrappers are involved in allowing a NeuronNetwork instance to establish cell-to-cell (i.e., local network and feed) connections:

1. NeuronNetwork()._build() calls _parnet_connect()

2. NeuronNetwork()._parnet_connect() then calls parconnect(), parreceive(), and parconnect_ext() within one of the child cell classes (e.g., Pyramidal).

3. Pyramidal().parconnect() then calls Pyramidal._connect() and Pyramidal().parreceive() and Pyramidal().parconnect_ext() calls Pyramidal()._parconnect_from_src() (all of which are inherited from the parent _Cell class). (Same for the basket cell class.)

4. Finally, _PC.gid_connect() is called from the Pyramidal()._parconnect_from_src() which is the lowest common python element in establishing a cell-to-cell connection.

It would be nice to rearrange and simply this process so that it is more transparent to Network how and when network connections are made. Ideally, there would be a single function, a method in _Cell, that Network could call in order to create a given cell-to-cell connection.

[jasmainak]

I would love to discuss this. +100, I literally had the same issue the other day wrapping my head around these methods

[blakecaldwell]

Agreed! The reason that it was moved out of Network was because it used _PC. However, moving to _Cell with a from .neuron import _PC inside the function sounds great.

[rythorpe]

Agreed! The reason that it was moved out of Network was because it used _PC. However, moving to _Cell with a from .neuron import _PC inside the function sounds great.

I think it's a great policy to keep all hoc references out of Network - good call @blakecaldwell. We should definitely try to maintain this moving forward. Should we anticipate encountering any pickling or parallelization errors by moving this _PC reference to _Cell?

[blakecaldwell]

Should we anticipate encountering any pickling or parallelization errors by moving this _PC reference to _Cell?

We should be fine. _PC is already imported in cell.py and existing functions heavily rely on h. objects.

[jasmainak]

is there still stuff to do here after #164 ?

[rythorpe]

is there still stuff to do here after #164 ?

Nope, I think you covered it! Thanks @jasmainak!