[3/5] Refactor: extract the charged fragment type annotation and the pointer reannotation - #436
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…tion Move two concerns out of the body of `flatten_fragments`: the per-column annotation of the charged fragment types, and the reannotation of the precursor pointers. The function now reads as its steps, and the memory refactoring that follows changes a named helper instead of a long function body. `_annotate_charged_frag_types` returns typed arrays rather than four parallel lists of Python ints. Tiling a typed array keeps its dtype, so the dense type/loss_type/charge/direction arrays no longer pass through an int64 intermediate of 8 bytes per dense slot. No functional change. Output stays bit-identical to main across 5400 generated configurations of library shape, padding, top-k, intensity threshold and custom_columns. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
GeorgWa
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mschwoer
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Aug 31, 2026
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| # tiling the typed arrays keeps their dtype. A tiled list of Python ints gave |
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"tiling the typed arrays keeps their dtype" -> I feel this is redundant? like "a = 1+1 # this will stay an int" ? also, second part of comment references previous implementation.
(I am not saying the information is not valuable, it's just that code is not the right place for it .. this would be a good example of the PR author commenting his own code to guide the review)
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Pure refactor. No functional change, output bit-identical to main.
Move two concerns out of the body of
flatten_fragments, so the memory changes that follow are diffs in named helpers instead of a long function body.int64intermediate of 8 bytes per dense slot.Stacked on #435. Splitting #429.
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