Fix: VCML writer dropped species velocity components equal to "0.0"#54
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The writer skipped any species advection-velocity component whose string was exactly "0.0", emitting e.g. <Velocity X="0.5"/> for an axis-aligned advection v = (0.5, 0). The FV reader defaults a missing component to 0, so the data-layer round trip survived — but the Moving Boundary solver reads the VCML directly and requires each needed component, failing at runtime with "Expression for VelocityY is null". Emit every component that is set, including "0.0"; the round trip is unchanged. Regression test added (verified end-to-end against pyvcell-mbsolver: velocity_y="0.0" now solves). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The quality job failed because float(reloaded_sm.velocity_x/_y) tripped mypy (velocity components are typed float | str | None). Narrow out None before float() so the assertions type-check; behavior unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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The bug
vcml_writer.pyskipped any species advection-velocity component whose string was exactly"0.0":So an axis-aligned advection
v = (0.5, 0)emitted<Velocity X="0.5"/>with noY. The FV reader defaults a missing component to 0, so the data-layer round trip survived and the bug was invisible there — but the Moving Boundary solver reads the VCML directly and requires each needed component, failing at runtime with:This surfaced while setting a species advection velocity (
v = v_b) for a moving-boundary cross-validation: any 2D velocity with a zero component was unusable.The fix
Emit every component that is set, including
"0.0". The round trip is unchanged (the reader already defaults missing → 0, so emitting"0.0"is equivalent). Regression test added (test_species_advection_velocity_emits_zero_components), and verified end-to-end againstpyvcell-mbsolver:velocity_y="0.0"now solves (previously crashed).mypy clean; the moving-boundary + velocity tests (incl. the gated end-to-end solve) pass.
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