Step 3: vectorize SampleShifterLinear row shifting#86
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Add regression tests before vectorizing _shift_columns_to_reference_sample: each row shifted by nanmedian(reference - row), partial-NaN rows handled via nanmedian skipna, all-NaN rows stay NaN, and a row already on the reference is unchanged. Tests pass against the unmodified baseline. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Replace the per-row pandas Series-alignment shift (iloc[r,:] += distance) with one numpy block: compute all row shifts via nanmedian(reference - values, axis=1) and apply with a single iloc[:,:] write. nanmedian already yields NaN for all-NaN rows, matching the old _calc_distance. Adds the shared `import warnings`. Bit-identical protein + ion output (max_abs_diff=0); suite passes. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
… test --- # Conversation that produced these changes --- ## User prompt "resolve the "follow-ups are cleanliness (dead method) and one test-coverage gap"" ## Clarifying round 1 Q: How far should the dead-code cleanup go? - Remove method + _calc_distance + its tests <-- chosen - Remove only _shift_to_reference_sample Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Replaces the per-row pandas Series-alignment shift (
iloc[r,:] += distance) with one numpy block: all row shifts viananmedian(reference - values, axis=1)applied in a single write.Estimated speedup: estimate stage 116.9 s → 102.8 s (~1.14×), single-core HYE benchmark.
Bit-identical protein + ion output (
max_abs_diff=0); suite passes.🤖 Generated with Claude Code