openbraininstitute / neurodamus / 14749248271

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Build Type

push

github

Committed by web-flow

Commit Message

Replace base_circuit and extra_circuits with sonata_circuits (#205)

## Context
In Neurodamus code base, for the legacy BlueConfig config file,
`base_circuit` was used for the circuit defined in the `Run` section and
`extra_circuits` was used for the extra `Circuit` section if existing.
After migrating to the SONATA config file, only `extra_circuits` was
used for SONATA circuits to be distinguished from the legacy BlueConfig.
Now that we only support SONATA config files, there is no need to have
such separation. This PR merges them to a single object
`sonata_circuits`.

## Scope

- In configuration.py, `SimConfig` class: replace `base_circuit` and
`extra_circuits` with `sonata_circuits`.
- In Node.py, `Node` class: replace `_base_circuit` and
`_extra_circuits` with ` _sonata_circuits`
- In Node.py: remove the creation of `base_cell_manager` based on the
empty `base_circuit` by default, i.e. node_pop=None. The
`base_cell_manager` is needed to hold fake cells in Coreneuron run when
we have empty ranks. So only create such dummy cell_manager when the
fake cells are needed.
- Remove `CircuitPath` in the `CircuitConfig` class.
- Load circuit edges for loadbalance computation

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

---------

Co-authored-by: Alessandro Cattabiani <cattabiani@users.noreply.github.com>

Run Details

7 of 56 new or added lines in 5 files covered. (12.5%)

6 existing lines in 2 files now uncovered.

7003 of 8903 relevant lines covered (78.66%)

1.03 hits per line