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[3/5] Refactor: extract the charged fragment type annotation and the pointer reannotation - #436
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flatten_fragments had no unit test. Add black-box tests that pin its contract, so the refactoring that follows can be checked step by step. `_dense_library` builds dense frames with mz == 0 padding from both sources that produce it: unmodified precursors carry no modloss fragments, and some fragments fall outside the mz range. Intensities are distinct, so the top-k selection is unambiguous. `_expected_keep_mask` derives the expected mask per precursor, without flatten_fragments. The tests cover the kept fragments over five combinations of `keep_top_k_fragments` and `min_fragment_intensity`, every annotation column, the reannotated precursor pointers, `custom_df` and `custom_columns`, the path without intensities, an empty library, and a precursor long enough to need more than a uint8 fragment number. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
`parse_fragment`, `fill_in_indices` and `calculate_fragment_numbers` only serve `flatten_fragments`, and nothing in alphabase, alphadia or peptdeep calls them. A leading underscore states that, and frees their signatures for the refactoring that follows. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
…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)
_expected_keep_mask reimplemented the filtering logic, so it could agree with a broken flatten_fragments. Add a minimal_library fixture of two precursors over a forward and a reverse fragment type, with the kept slots written out per filter setting, and assert both the helper and flatten_fragments against it. Derive the long precursor row count from the uint8 boundary it tests instead of picking a number near the fill_in_indices limit, and guard the limit explicitly so exceeding it fails on an assertion rather than on a broadcast error inside numba. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
"fragment number" read as ambiguous between a count and an enumeration. Spell out that it is the MS series numbering, and contrast it with the fragment position that all series share. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
The library was generated from a seeded rng and the expectations came from _expected_keep_mask, which reimplemented the filtering logic and so could agree with a broken flatten_fragments. Replace both with one library fixture over hand-written mz and intensity grids, and hand-written keep masks per filter setting. Two fragment types carry the whole annotation surface: y_z1 is reverse without loss and b_modloss_z1 is forward with loss, so direction, series and loss all vary over two columns. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Comparing column by column left the column set, the column order and the dtypes unchecked. Assert the whole annotated frame against an expected frame instead, and fold the row count of the filter cases into a frame comparison of mz and intensity. type and charge come out as int8, so the expected frame spells that out. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
The three tile calls differed only in column name and source array, and the comment above them explained the dtype of the previous implementation rather than the code it sat on. Loop over the columns instead; the dtypes stay visible where they are set, in _annotate_charged_frag_types. Trim the two comments carried into the extracted helpers. The direction comment claimed a third value of 0 that DIRECTION_MAPPING never produces. Column order of the flat fragment dataframe is unchanged. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
…ragment-parsing-helpers
The merged tests named fill_in_indices, which this branch renamed. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
…e-charged-frag-types
Replace the remaining column comparisons. Each one now also pins the column set, the column order and the dtypes: - without_intensity subsumes its separate missing-column assertion - selects_custom_columns checked only the column names - filters_custom_df_columns now pins where cardinality lands - reannotates_precursor_pointers compares hardcoded flat pointers instead of reslicing mz per precursor, which was the last place the tests recomputed an expectation - empty_precursor_df compares both frames instead of their lengths Five tests assert against the same unfiltered library, so it moves into a flat_unfiltered fixture. test_flatten_fragments_long_precursor keeps its property assertions. It builds 257 rows to push fragment numbers past 255, so a frame of 1542 generated values would bury what it tests. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
…ragment-parsing-helpers
…e-charged-frag-types
The four scalar assertions become two equality comparisons. The dtypes need their own comparison, because .max() over columns of different dtypes upcasts to a common one and would hide a narrowed column. Also drop the tuple rebuild in the parse test, expected is already the tuple being compared. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
…ragment-parsing-helpers
…e-charged-frag-types
Main carries PR #434, the characterization tests of this stack, so the test file arrives identical apart from the helper names this branch makes private. Kept the private names in both conflicts. Main also dropped Python 3.8 and rewrote the typing generics of the whole file. The annotations of the extracted helpers came from main unchanged, so nothing here still references the removed typing imports. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
…e-charged-frag-types
…e-charged-frag-types Brings main in behind it. The merge was textually clean but left the module unimportable: _annotate_charged_frag_types is annotated -> Tuple[...], and main dropped Python 3.8 and with it the typing import. Changed to the builtin tuple, matching the rest of the file. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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September 15, 2026 11:44
Main carries PR #435, so the helper renames of this stack arrive from main and the test file now matches it exactly. One conflict in flatten_fragments. Main still builds frag_directions inline and passes it to _parse_fragment, while this branch takes the directions from _annotate_charged_frag_types. Kept this branch's call, since the variable main passes no longer exists here. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Main carries PRs #434 to #436, so the three branches below this one arrive from main and only fragment.py still differs. Six conflicts, all where this branch had rewritten what main still has: the dense annotation tiling, the cumsum in _reannotate_precursor_pointers that searchsorted replaces, and the helper signatures around them. Kept this branch's version of each, and main's tuple annotation, since main dropped Python 3.8 and the typing imports with it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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…gment-positions Brings main and PRs #434 to #436 in behind it. Two conflicts, both where the annotation of a function this branch reworked met main's builtin generics. Kept this branch's signature and docstring with the builtin tuple, since main dropped Python 3.8 and the typing imports with it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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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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