Seclamp stimulus

[AurelienJaquier]

New seclamp stimulus following latest SONATA standards.

[codecov]

Codecov Report

❌ Patch coverage is 90.19608% with 5 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
bluecellulab/cell/injector.py	85.71%	2 Missing ⚠️
...ecellulab/stimulus/circuit_stimulus_definitions.py	84.61%	2 Missing ⚠️
bluecellulab/circuit_simulation.py	85.71%	1 Missing ⚠️

Files with missing lines	Coverage Δ
tests/test_cell/test_injector.py	98.72% <100.00%> (+0.06%)	⬆️
...test_stimulus/test_circuit_stimulus_definitions.py	100.00% <ø> (ø)
bluecellulab/circuit_simulation.py	85.38% <85.71%> (-1.13%)	⬇️
bluecellulab/cell/injector.py	94.21% <85.71%> (-1.40%)	⬇️
...ecellulab/stimulus/circuit_stimulus_definitions.py	78.00% <84.61%> (+1.14%)	⬆️

... and 17 files with indirect coverage changes

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[AurelienJaquier]

for reference:
sonata latest standards: openbraininstitute/sonata-extension#20
neurodamus impementation: openbraininstitute/neurodamus#481

[AurelienJaquier]

@ilkilic please do not forget to review when you have some time ;)

[darshanmandge]

Where is stimulus.duration coming from if the user does not use SONATA simulation config for injection?

[darshanmandge]

The argument names are very similar, stimulus.duration and stimulus.durations. Below, you use delay=stimulus_entry["delay"],. Could the first be renamed to stimulus.delay?

[darshanmandge]

Is the initial delay fixed across all the steps?

[AurelienJaquier]

• SEClamp expects duration. User has to give it, SONATA or otherwise.
• duration and delay are two different things. duration is the total duration of the stimulus, i.e. the time during which the clamp is active. delay is actually not used but is needed, as stated in SONATA, mainly for backwards compatibility and consistency across stimuli.
• there is no initial delay, the clamp is always active at t=0

[darshanmandge]

Ok. Thanks.