Issues

• Optional DFA-based exact sampler for DomainPool

  Feature

  UC-Davis-molecular-computing/nuad#283 · Filter by author dave-doty opened on Aug 7, 2026

• Optional Infrared-based exact sampler for DomainPool

  Feature

  UC-Davis-molecular-computing/nuad#282 · Filter by author dave-doty opened on Aug 6, 2026

• fix potential bug in _independent_domains_in_part

  Bug

  UC-Davis-molecular-computing/nuad#281 · Filter by author dave-doty opened on Jun 25, 2026

• optimize EvaluationSet.update_domain_keyed_dicts

  Feature

  UC-Davis-molecular-computing/nuad#277 · Filter by author dave-doty opened on Mar 25, 2026

• design DNA strand displacement rate constants

  UC-Davis-molecular-computing/nuad#273 · Filter by author dave-doty opened on Aug 29, 2025
  1

• restart should require output directory to be specified explicitly

  invalid
  UC-Davis-molecular-computing/nuad#272 · Filter by author dave-doty opened on Jul 22, 2025

• storable constraints

  UC-Davis-molecular-computing/nuad#271 · Filter by author dave-doty opened on May 23, 2025

• rna_duplex_multiple being called with wrong signature

  UC-Davis-molecular-computing/nuad#269 · Filter by author JoshPetrack opened on Jan 31, 2025

• fix failing unit tests due to ViennaRNA installation failing on CI server

  invalid
  UC-Davis-molecular-computing/nuad#266 · Filter by author dave-doty opened on Jan 6, 2025
  

• use ruff CI

  UC-Davis-molecular-computing/nuad#261 · Filter by author dave-doty opened on Dec 27, 2024
  

• remove strand groups

  invalid
  UC-Davis-molecular-computing/nuad#258 · Filter by author dave-doty opened on Apr 17, 2024
  

• merge Result and Evaluation

  UC-Davis-molecular-computing/nuad#254 · Filter by author dave-doty opened on Mar 26, 2024
  

• allow subdomains to have multiple parents

  enhancement
  UC-Davis-molecular-computing/nuad#252 · Filter by author dave-doty opened on Dec 15, 2023
  1

  

• generalized dependent domains

  enhancement
  UC-Davis-molecular-computing/nuad#251 · Filter by author dave-doty opened on Dec 15, 2023
  

• mismatches

  enhancement
  UC-Davis-molecular-computing/nuad#250 · Filter by author dave-doty opened on Dec 15, 2023
  2

  

• do not require length parameter to Domain constructor when Domain.dependent is True and subdomains are independent

  invalid
  UC-Davis-molecular-computing/nuad#249 · Filter by author dave-doty opened on Dec 13, 2023

• find/use/compare black box stochastic local search optimization software

  UC-Davis-molecular-computing/nuad#247 · Filter by author dave-doty opened on Nov 6, 2023

• RNAplex output missing lines with sufficiently long input

  bug
  UC-Davis-molecular-computing/nuad#244 · Filter by author dave-doty opened on Oct 8, 2023

• use _normalize_domains_pairs_disjoint_parameters and _normalize_strands_pairs_disjoint_parameters

  enhancement
  UC-Davis-molecular-computing/nuad#241 · Filter by author dave-doty opened on Sep 19, 2023

• prevent two strands with the same name

  bug
  UC-Davis-molecular-computing/nuad#228 · Filter by author dave-doty opened on Sep 30, 2022
  

• remove declaration of private properties in classes

  invalid
  UC-Davis-molecular-computing/nuad#210 · Filter by author dave-doty opened on Jul 21, 2022
  

• store StrandPair instead of Tuple[Strand, Strand] in ConstraintWithStrandPairs and make _determine_strand_pairs_to_check more efficient

  enhancement
  UC-Davis-molecular-computing/nuad#209 · Filter by author dave-doty opened on Jul 21, 2022
  

• dependent domains whose independent source is fixed should be fixed

  high priorityinvalid
  UC-Davis-molecular-computing/nuad#208 · Filter by author dave-doty opened on Jul 20, 2022
  

• Allow inclusion of other arguments in description for constraints.

  enhancement
  UC-Davis-molecular-computing/nuad#195 · Filter by author cgevans opened on Jul 4, 2022
  3

• simplify API of evaluate function in constraint

  high priorityinvalid
  UC-Davis-molecular-computing/nuad#148 · Filter by author dave-doty opened on Dec 1, 2021