feat: compute and plot normalised g-V curve with Boltzmann fit (#177)#207
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Adds GVPoint, BoltzmannFit, GVAnalysisResult dataclasses and compute_gv() / boltzmann() functions to patch_sim.analysis. Exports them from both the analysis subpackage and top-level patch_sim namespace.
16 tests covering boltzmann(), compute_gv() unit behaviour (chord conductance, normalisation, driving-force filtering, Boltzmann fit recovery), edge cases (empty input, <2 valid points), and an integration test against a real HH multi-sweep simulation.
Refactors _compute_iv_data() to return the raw IVAnalysisResult alongside the serialised dict. Adds _compute_gv_data() which calls compute_gv() and pre-computes the Boltzmann fit curve. The neuron's Na+ reversal potential (core_channels[0]) is used as E_rev. gv_data is stored in AnalysisState and cleared in all non-voltage-clamp paths.
- AnalysisState gets gv_data, has_gv_data, and gv_figure - build_gv_figure() renders G/Gmax scatter + Boltzmann fit curve with V_half and k annotation - _iv_curve_tab() embeds the g-V plot below the I-V plot in a scroll_area when g-V data is available
- Replace Union[float, np.ndarray] with float | np.ndarray in boltzmann() - Fix __all__ ordering in analysis/__init__.py (boltzmann/compute_gv now sorted alphabetically among function names) - Add explanatory comment on _null_fit sentinel in compute_gv() - Replace hardcoded core_channels[0] with an explicit Na+ channel lookup via NernstSpec/IonSpecies.SODIUM in simulation.py and integration test
JCorson
commented
Apr 13, 2026
Instead of silently falling back to core_channels[0] (which could be
any channel), set gv_data to {} so the plot stays empty rather than
showing a g-V curve computed against an arbitrary reversal potential.
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Summary
patch_sim/analysis/gv_curve.pywithcompute_gv()andboltzmann()— computes chord conductance G = I / (V − E_rev), normalises to G/Gmax, and fits a two-parameter Boltzmann sigmoid viascipy.optimize.curve_fitcore_channels[0].reversal_potential(neuron)) intorun_simulation()so g-V is computed automatically after every voltage-clamp multi-sweep runbuild_gv_figure()(green scatter + dashed Boltzmann fit curve + V½/k annotation) and embeds it below the existing I-V plot in a scrollable container in the I-V Curve analysis tabboltzmann()properties,compute_gv()unit behaviour (chord conductance, normalisation, driving-force filtering, Boltzmann parameter recovery, edge cases), and an HH integration testTest plan
uv run --frozen --group ui -m pytest)ruff check .andruff format --check .passty checkpassesCloses #177