openbraininstitute / neurodamus / 13305127832

90%

Build Type

push

github

Committed by web-flow

Commit Message

Add a SONATA circuit for the ringtest (#49)

## Context
As per discussion in
https://github.com/openbraininstitute/neurodamus/issues/11, this PR adds
the ringtest circuit which creates 2 rings of simple `BallStick` cells.
```
Nodes:
- RingA: 3 cells, 2 sections/cell, 2 segments/section
- RingB: 2 cells, 2 sections/cell, 2 segments/section
Edges:
- RingA: 0 -> 1 -> 2 ->0
- RingB: 0 -> 1 -> 0
- RingA: 0 -> RingB: 0
```
## Scope

1. In the test folder: adds a SONATA version of the ring test circuit
including 2 nodes files + 3 edges files, the relevant SONATA config
files, reference cell dump output json files.
2. In neurodamus/utils, a new function `dump_cellstate` to dump
cell/section/segments/netcons/synapse attributes from the NEURON context

## Testing
1. `test/integration/test_ringcells.py` can be run with `tox -e
integration`
     `test_dump_RingB_2cells`: dump 1 population with 2 cells
     `test_dump_RingA_RingB`: dump 2 populations 

## Review
* [x] PR description is complete
* [x] Coding style (imports, function length, New functions, classes or
files) are good
* [x] Unit/Scientific test added
* [ ] Updated Readme, in-code, developer documentation

Run Details

70 of 71 new or added lines in 1 file covered. (98.59%)

1 existing line in 1 file now uncovered.

5043 of 9080 relevant lines covered (55.54%)

1.06 hits per line