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Refine SONATA output handling #22

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Merged
merged 6 commits into from
Jun 18, 2025
Merged

Refine SONATA output handling #22

merged 6 commits into from
Jun 18, 2025

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ilkilic
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@ilkilic ilkilic commented Jun 18, 2025

This PR improves SONATA output handling by:

  • Fixing the default spikes_file name (to out.h5) if not specified
  • Using spike_location from config when recording spikes
  • Correcting dt logic in report writing:
    • Downsampling now applies if report_dt > sim_dt
    • If report_dt < sim_dt, it’s clamped to sim_dt with a warning

@ilkilic ilkilic requested a review from darshanmandge June 18, 2025 13:34
@ilkilic ilkilic self-assigned this Jun 18, 2025
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codecov bot commented Jun 18, 2025

Codecov Report

Attention: Patch coverage is 84.21053% with 3 lines in your changes missing coverage. Please review.

Files with missing lines Patch % Lines
bluecellulab/simulation/report.py 78.57% 3 Missing ⚠️
Files with missing lines Coverage Δ
...ellulab/circuit/config/sonata_simulation_config.py 96.87% <100.00%> (ø)
bluecellulab/circuit_simulation.py 85.83% <100.00%> (-0.05%) ⬇️
tests/test_circuit/test_iotools.py 90.90% <100.00%> (ø)
bluecellulab/simulation/report.py 82.97% <78.57%> (-0.75%) ⬇️
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@darshanmandge
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darshanmandge commented Jun 18, 2025

I tested the code to generate reports for a small microcircuit and results also work with bluepysnap. Thanks @ilkilic!
Just mentioning here that the report.py code will be refactored later to have a similar structure as Report class of neurodamus. More tests will be added later to increase the coverage, too :)

@ilkilic ilkilic merged commit 24e4900 into main Jun 18, 2025
7 of 8 checks passed
@ilkilic ilkilic deleted the report2 branch June 18, 2025 14:51
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2 participants