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Add Linear stimulus support and update RelativeLinear to enable ramping #10

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Merged
merged 11 commits into from
Mar 10, 2025

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ilkilic
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@ilkilic ilkilic commented Mar 6, 2025

  • Add Linear stimulus support in circuit simulation
  • Update RelativeLinear to support ramping behavior. BlueCelluLab's RelativeLinear previously lacked amp_end, making it function as a step instead of a ramp. This update aligns it with Neurodamus by adding support for ramping

@ilkilic ilkilic self-assigned this Mar 6, 2025
@ilkilic ilkilic requested a review from AurelienJaquier March 6, 2025 15:36
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codecov bot commented Mar 6, 2025

Codecov Report

Attention: Patch coverage is 97.01493% with 2 lines in your changes missing coverage. Please review.

Files with missing lines Patch % Lines
bluecellulab/circuit_simulation.py 50.00% 2 Missing ⚠️
Files with missing lines Coverage Δ
bluecellulab/cell/injector.py 95.37% <100.00%> (+0.06%) ⬆️
...ab/circuit/circuit_access/sonata_circuit_access.py 97.85% <100.00%> (+0.01%) ⬆️
...ecellulab/stimulus/circuit_stimulus_definitions.py 77.31% <100.00%> (+6.44%) ⬆️
tests/test_cell/test_injector.py 98.92% <100.00%> (+0.06%) ⬆️
tests/test_circuit/test_simulation_config.py 100.00% <100.00%> (ø)
...test_stimulus/test_circuit_stimulus_definitions.py 100.00% <100.00%> (ø)
bluecellulab/circuit_simulation.py 86.01% <50.00%> (-0.52%) ⬇️
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@@ -259,12 +261,39 @@ def add_replay_hypamp(self, stimulus: Hyperpolarizing):
self.persistent.append(tstim) # type: ignore
return tstim

def add_replay_relativelinear(self, stimulus):
def add_replay_linear(self, stimulus: Linear):
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You could call self.add_ramp() here for less duplication

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Thanks! done in the last commit

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@AurelienJaquier AurelienJaquier left a comment

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looks nice!

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@darshanmandge darshanmandge left a comment

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Thanks @ilkilic.

Later, we should verify if all the stimuli that we code in bluecellulab reproduce the neurodamus stimuli as the implementations look slightly different in neurodamus stimulus_manager.py and stimuli.py. This will be essential for reproducibility of neurodamus network simulation results at the single-cell level using bluecellulab.

@ilkilic ilkilic merged commit 855ed13 into main Mar 10, 2025
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@ilkilic ilkilic deleted the linear-stimulus branch March 10, 2025 11:02
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3 participants