[1/5] Tests: characterize flatten_fragments before the memory refactor - #434
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[1/5] Tests: characterize flatten_fragments before the memory refactor#434GeorgWa wants to merge 1 commit into
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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>
GeorgWa
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mschwoer
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Aug 31, 2026
| @pytest.mark.requires_numba | ||
| def test_flatten_fragments_long_precursor(): | ||
| """A long precursor keeps fragment numbers above 255, and the columns stay uint32.""" | ||
| n_rows = 260 # close to the max_frag_per_peptide limit of _fill_in_indices |
| def _expected_keep_mask( | ||
| precursor_df, mz_df, intensity_df, keep_top_k_fragments, min_fragment_intensity | ||
| ): | ||
| """Give the keep mask over all dense slots. This does not use flatten_fragments.""" |
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could we add a test for this?
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seriously, could we not work with statically define input data (and data to assert against)?
such minimal data models would also help understand/debug the code better one day
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@mschwoer do you mean we SHOULD work with static examples or we should keep this logic?
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we should "strongly consider"™️ it :-D
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Tests only. No production change.
flatten_fragmentshad no unit test. Add black-box tests that pin its contract, so the refactoring that follows can be checked step by step.All tests pass unchanged on
main.First of 5 stacked PRs splitting #429.
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