Allow API configuration to preserve the axons during setup

[ferdonline]

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

[cattabiani]

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]

LGTM!
Just one question: is there any need to add a CLI option for this parameter?

[cattabiani]

not from me

[bbpbuildbot]

Logfiles from GitLab pipeline #219662 (:white_check_mark:) have been uploaded here!

Status and direct links:

• ✅ docs
• ✅ test-unit
• ✅ test-integration
• ✅ test-integration-e2e
• ✅ test-scientific
• ✅ test-scientific-ngv
• ✅ set_alt_branches
• ✅ build-package
• ⚙️ publish-package
• ⚙️ publish-docs