Phase 1: audit and regression-backed correctness fixes - #233
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Alexander-Mitrofanov wants to merge 27 commits into
Open
Phase 1: audit and regression-backed correctness fixes#233Alexander-Mitrofanov wants to merge 27 commits into
Alexander-Mitrofanov wants to merge 27 commits into
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Record the 3.4.1 architecture, numeric contracts, bottlenecks, test gaps, and independently reproduced correctness findings for discussion #232. Add focused regressions before fixes: Interaction self-assignment and null-seed equality, zero-capacity result storage, invalid Nussinov paired intervals, base-pair ES semantics, noLP/terminal-GU partition counting, and target/query accessibility option isolation. These regressions intentionally fail on the audited baseline so each correction can follow independently.
Return before clearing owned pairing and seed state when the source and destination are the same Interaction. This makes the assignment contract safe without changing normal copy behavior.
Treat identical seed pointers as equal and compare seed sets only when both interactions own one. Seeded and unseeded interactions now compare unequal instead of dereferencing null.
Continue counting reported candidates when maxToStore is zero, but skip list comparison and insertion. This avoids dereferencing an empty reverse iterator for --outNumber=0 style consumers.
An out-of-range paired state is impossible and must contribute the additive zero of the partition semiring. Returning one incorrectly admitted an invalid pair as a multiplicative identity.
getES1/getES2 promise the ensemble of intramolecular structures containing at least one pair. Subtract the unit-weight empty structure before converting Q to energy, while leaving getEall1/getEall2 based on the complete monomer partition.
The direct continuation after the mandatory left stack already covers the adjacent (1,1) extension. Skip that one loop transition so the heuristic remains a subset of the exact interaction ensemble instead of assigning duplicate weight.
Reject terminal-GU and excessive-ED sites in updateZ before they alter Zall or the boundary partition. Reported candidates and their requested interaction ensemble now use the same scientific domain.
Construct target AccessibilityBasePair with tIntLenMax and tAccW. Query settings must not truncate the target ED matrix; asymmetric target/query CLI options now retain their independent biological domains.
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Hi Alex, For merging, could you please trigger to update the Given that, I will do some local checks and merge it to master! 👍👍 |
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PS. I already reviewed all code base changes and had a close read of the refactoring plan. |
martin-raden
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Aug 16, 2026
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I have checked and approved all changes.
- TODO: update "Changelog" file accordingly
and this will be ready to merge
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Implements phase 1 of discussion #232.
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