Allow API configuration to preserve the axons during setup #155
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I wrote here my findings: https://bbpteam.epfl.ch/project/issues/browse/BBPBGLIB-984. Let me know if you prefer the reports directly here instead |
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WeinaJi
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not from me |
jorblancoa
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WeinaJi
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Logfiles from GitLab pipeline #223382 (:white_check_mark:) have been uploaded here! Status and direct links: |
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## Context
With BlueConfig one could ask a circuit to preserve the axons in full
detail via a config entry `DetailedAxons`.
However, that options was never made globally available via a flag,
which enables it also for Sonata simulations.
This PR covers that.
## Scope
- Introduce the new Neurodamus top-level option `keep_axon`
- Propagate to all Detailed neuron circuits which don't set the option
explicitly.
## Testing
in the testing environment under `test/ngv_wip` with the patched
`emodels_atp_1p4` one must see
**Script:**
```python
nd = neurodamus.Neurodamus(
"simulation_config.json",
keep_axon=True,
auto_init=False,
cleanup_atexit=False,
logging_level=2,
)
nd.init()
nd.run()
```
**Output:**
```
[VERB] -> Keeping axons ENABLED
...
[INFO] Executing actions after stdinit...
[INFO] Now deleting the axon!
REPLACING AXON!
[INFO] Now deleting the axon!
REPLACING AXON!
```
## Review
* [x] PR description is complete
* [x] Coding style (imports, function length, New functions, classes or
files) are good
* [ ] Unit/Scientific test added
* [ ] Updated Readme, in-code, developer documentation
Co-authored-by: Weina Ji <[email protected]>
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Context
With BlueConfig one could ask a circuit to preserve the axons in full detail via a config entry
DetailedAxons.However, that options was never made globally available via a flag, which enables it also for Sonata simulations.
This PR covers that.
Scope
keep_axonTesting
in the testing environment under
test/ngv_wipwith the patchedemodels_atp_1p4one must seeScript:
Output:
Review