Add Nexus integration #major

[ilkilic]

The Nexus integration enables users to store and manage e-models on Nexus. This extension offers a dedicated access point, NexusAccessPoint, and a set of functions designed to create e-model-related resources. These resources are automatically linked to existing electrophysiological data, mechanisms, and morphology registered on Nexus. Additionally, this PR includes an export script that facilitates the exporting of local e-models to Nexus, as well as an example demonstrating how to run a simulation of an e-model stored on Nexus using BlueCellulab.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 32.66069% with 901 lines in your changes missing coverage. Please review.

Project coverage is 53.45%. Comparing base (8d5b0ab) to head (341b3bf).
Report is 22 commits behind head on main.

Files	Patch %	Lines
bluepyemodel/access_point/nexus.py	19.44%	468 Missing ⚠️
bluepyemodel/access_point/forge_access_point.py	28.70%	380 Missing ⚠️
bluepyemodel/export_emodel/export_emodel.py	4.16%	46 Missing ⚠️
bluepyemodel/emodel_pipeline/emodel_pipeline.py	60.00%	4 Missing ⚠️
tests/unit_tests/test_nexus_access_point.py	97.70%	2 Missing ⚠️
bluepyemodel/tasks/emodel_creation/optimisation.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #137      +/-   ##
==========================================
- Coverage   60.07%   53.45%   -6.63%     
==========================================
  Files         109      122      +13     
  Lines        7838     9666    +1828     
==========================================
+ Hits         4709     5167     +458     
- Misses       3129     4499    +1370     

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[AurelienJaquier]

I could not comment directly on file examples/run_emodel/run_emodel.ipynb so I do it here:
"Below is a list of Nexus ID of some of the detailed canonical emodel" -> I don't see any though?

[ilkilic]

I could not comment directly on file examples/run_emodel/run_emodel.ipynb so I do it here: "Below is a list of Nexus ID of some of the detailed canonical emodel" -> I don't see any though?

good catch. I will remove that sentence or do you want to list some Nexus IDs?

[AurelienJaquier]

I could not comment directly on file examples/run_emodel/run_emodel.ipynb so I do it here: "Below is a list of Nexus ID of some of the detailed canonical emodel" -> I don't see any though?

good catch. I will remove that sentence or do you want to list some Nexus IDs?

It is ok for me to just remove the sentence

[ilkilic]

I haven't read everything yet. I think we could keep the EModel_pipeline_nexus, and just use it make it a child of EModel_pipeline with data_access_point="nexus". That way people that were using it just have to change the import, and don't have to re-write their pipeline call.

Good idea, I have reintroduced it and placed it in emodel_pipeline.py

[ilkilic]

@darshanmandge thanks for the suggestions. Perhaps these could be addressed in a separate PR since we want to merge this as soon as possible

[darshanmandge]

Ok, Sure. Thanks. You can address the suggestions in a separate PR

[AurelienJaquier]

@ilkilic before merging could you make sure that this has all the latest commits from bluepyemodelnexus? I see that e.g. examples/memodel/memodel.py is missing

[ilkilic]

yes, all the latest commits should be there, I was planning to add the examples at a later point since some are still not ready to be open-sourced, but I guess I can already add the memodel example in this PR, let me add it

[ilkilic]

Tested and I confirm that everything works. This is ready to merge...

[AurelienJaquier]

Last small changes required before merging ;)

[AurelienJaquier]

Looks great, thanks a lot!