Mathews 2004 parameter set (corrected) + paramset plumbing + dangles=2 exterior stacks - #13

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KowalskiBio wants to merge 9 commits into

EmilioVenegas:mainfrom

KowalskiBio:mathews2004-dangles

Commits on Aug 16, 2026

feat(dimer): native Rust port of the dimer MFE candidate DP
KowalskiBio
committed
7ef9cf0
fix(native-dp): alphabet divergence guard, codegen staleness test, param-override guard test
KowalskiBio
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2b81703
ci(native): run both parity suites in the extension CI job
KowalskiBio
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736419d
fix(params): correct Mathews 2004 stack/bulge/interior key conventions + dH interior tables
KowalskiBio
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38f2036
feat(thermo,structure): paramset threading, name resolution, dangles=2 exterior stacks
KowalskiBio
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04314e4
docs(notices): record dna_mathews2004.par provenance for the Mathews 2004 paramset
KowalskiBio
committed
c23cb1b
fix(paramset,dangles): review round for #13 - scope, dimer flag, tests, notices
KowalskiBio
committed
0b0145a
fix(params): resolve DEF hairpin mismatch entries to match ViennaRNA
KowalskiBio
committed
d5e8096

Commits on Aug 17, 2026

perf(ensemble): add pair_probs flag to skip outside recurrence
KowalskiBio
committed
cea7364