Add noise stimuli in StimulusFactory

[ilkilic]

• adds StepNoise, ShotNoise, and OrnsteinUhlenbeck in StimulusFactory with support for both amplitude-based and threshold-based calculation
• adds threshold-based support for Ramp
• updates the example notebook 5-stimuli to showcase all stimuli
• refactores factory.py
• adds unit-tests

[codecov]

Codecov Report

Attention: Patch coverage is 98.09524% with 8 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
bluecellulab/stimulus/factory.py	88.88%	5 Missing ⚠️
bluecellulab/stimulus/stimulus.py	98.81%	3 Missing ⚠️

Files with missing lines	Coverage Δ
bluecellulab/analysis/inject_sequence.py	97.61% <100.00%> (ø)
bluecellulab/cell/injector.py	95.30% <100.00%> (ø)
tests/test_stimulus/test_factory.py	100.00% <100.00%> (ø)
tests/test_stimulus/test_stimulus.py	100.00% <100.00%> (ø)
bluecellulab/stimulus/stimulus.py	98.81% <98.81%> (ø)
bluecellulab/stimulus/factory.py	91.11% <88.88%> (ø)

[darshanmandge]

There are some lines in stimulus/factory.py for which codecov complains are not covered tests. Add only if necessary.:).

[ilkilic]

@AurelienJaquier Thanks! I have standardised parameter names across all protocols to consistently use standard deviation (sigma) instead of variance:

• amp_mean → mean
• amp_var → sigma
• variance → sigma
• sd_percent → sigma_percent

And I have added pre_delay and post_delay to replace the hardcoded zero delays

[darshanmandge]

Regarding argument names: I hope you have used the names to same as in neurodamus and sonata-extension.

For this comment, I see these type warnings when I "Load diff" for stimulus.py and factory.py:

[AurelienJaquier]

looks good to me!

[ilkilic]

@darshanmandge

Regarding argument names: I hope you have used the names to same as in neurodamus and sonata-extension.

We decided to unify them in the factory but the the circuit stimulus class uses the same argument names as in Neurodamus

And for the Codecov comment, I tried to increase the test coverage as much as possible

[darshanmandge]

Thanks @ilkilic ! 🎉 Let's other remaining stimuli from neurodamus in new PRs.