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[2/5] Refactor: make the fragment parsing helpers private - #435
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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>
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Sep 1, 2026
| number_of_fragment_types: int, | ||
| ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]: | ||
| """ | ||
| Parse fragments to get fragment numbers, fragment positions and not top k excluded indices in one hit |
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"fragment numbers" is kinda ambigous.. is this counts? or enumeration? not sure if it should be renamed now (depends on the radius of this change), but at last a comment would help :-)
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I agree, it's the MS convention fragment numbering. I will add a comment :D
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PS: I'll be creating a PR soon to optimize the translation modules ( I think it will be better to reuse the much more optimized helpers here instead. |
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very nice! |
_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>
…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>
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
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
Base automatically changed from
test/flatten-fragments-characterization
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September 15, 2026 09:52
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>
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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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Pure refactor. Rename only, no functional change.
parse_fragment,fill_in_indicesandcalculate_fragment_numbersonly serveflatten_fragments, and nothing in alphabase, alphadia or peptdeep calls them. A leading underscore states that, and frees their signatures for the refactoring that follows.Stacked on #434. Splitting #429.
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