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Allow API configuration to preserve the axons during setup #155

Merged
merged 6 commits into from
Jul 24, 2024
Merged

Allow API configuration to preserve the axons during setup #155

merged 6 commits into from
Jul 24, 2024

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ferdonline
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@ferdonline ferdonline commented Apr 18, 2024 •
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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:

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

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

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@cattabiani
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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

@WeinaJi WeinaJi marked this pull request as ready for review May 13, 2024 11:32
@WeinaJi WeinaJi force-pushed the leite/propagate_cli_keep_axon_to_circuits branch from d8bbb28 to ed80d0b Compare May 13, 2024 11:32
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WeinaJi
WeinaJi previously approved these changes Jun 12, 2024
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LGTM!
Just one question: is there any need to add a CLI option for this parameter?

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not from me

jorblancoa
jorblancoa previously approved these changes Jun 12, 2024
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@WeinaJi WeinaJi dismissed stale reviews from jorblancoa and themself via 4ead169 July 24, 2024 10:20
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Logfiles from GitLab pipeline #223382 (:white_check_mark:) have been uploaded here!

Status and direct links:

@WeinaJi WeinaJi merged commit 75fa632 into main Jul 24, 2024
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@WeinaJi WeinaJi deleted the leite/propagate_cli_keep_axon_to_circuits branch July 24, 2024 11:04
WeinaJi added a commit that referenced this pull request Oct 14, 2024
@ferdonline @WeinaJi
Allow API configuration to preserve the axons during setup (#155)
773915f 
## 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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@WeinaJi WeinaJi WeinaJi approved these changes

@jorblancoa jorblancoa jorblancoa left review comments

@cattabiani cattabiani Awaiting requested review from cattabiani

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5 participants
@ferdonline @bbpbuildbot @cattabiani @WeinaJi @jorblancoa