[antonsoo]

from pyteomics import parser

print(parser.xcleave('PEPTIDEK', 'trypsin', semi=True,
                    min_length=3, max_length=5))

This returns [] before the change. The expected result is [(0, 'PEP'), (0, 'PEPT'), (0, 'PEPTI'), (3, 'TIDEK'), (4, 'IDEK'), (5, 'DEK')].

Generate semi-specific prefixes and suffixes independently of whether the full cleavage product satisfies the length limit. Include prefixes whose length equals max_length. Two regression tests cover exact bounds and preserve the order and duplicates of the equivalent unbounded result followed by a length filter, including missed cleavages.

An independent enumeration on four UniProt albumin/hemoglobin sequences agrees with all 80 digestion and precursor-planning configurations after the change; 42 configurations previously omitted candidates. All 38 previously correct records remain identical. Another 2,880 constructed short-sequence cases agree with exhaustive interval enumeration.

Validation uses Python 3.10/NumPy 1.26 and Python 3.12/NumPy 2.5, the project's per-file test commands, and an isolated wheel replay. The separate isoelectric-point correction also composes cleanly and preserves these results.

All 27 project CI test files succeed on each dependency profile (491 tests, including one live-PostgreSQL service skip).

[levitsky]

Thank you for the contribution!