UC-Davis-molecular-computing/nuad issues and pull requests

#260 - Simd sw constraint

Pull Request - State: closed - Opened by Raj-Bapat 4 months ago

#259 - 258 remove strand groups

Pull Request - State: open - Opened by lia-n2 5 months ago

#258 - remove strand groups

Issue - State: open - Opened by dave-doty 6 months ago
Labels: invalid

#257 - 228 prevent two strands with the same name

Pull Request - State: open - Opened by lia-n2 6 months ago

#256 - closes #255 matplotlib histogram of nearest neighbor energies

Pull Request - State: closed - Opened by dave-doty 6 months ago

#255 - matplotlib histogram of nearest neighbor energies

Issue - State: open - Opened by dave-doty 6 months ago
Labels: enhancement, closed in dev

#254 - merge `Result` and `Evaluation`

Issue - State: open - Opened by dave-doty 6 months ago

#253 - Dev

Pull Request - State: closed - Opened by dave-doty 8 months ago

#252 - allow subdomains to have multiple parents

Issue - State: open - Opened by dave-doty 10 months ago - 1 comment
Labels: enhancement

#251 - generalized dependent domains

Issue - State: open - Opened by dave-doty 10 months ago
Labels: enhancement

#250 - mismatches

Issue - State: open - Opened by dave-doty 10 months ago - 2 comments
Labels: enhancement

#249 - do not require `length` parameter to `Domain` constructor when `Domain.dependent` is True and subdomains are independent

Issue - State: open - Opened by dave-doty 10 months ago
Labels: invalid

#248 - fix Domain.name docstring

Pull Request - State: closed - Opened by cgevans 10 months ago

#247 - find/use/compare black box stochastic local search optimization software

Issue - State: open - Opened by dave-doty 11 months ago

#246 - Dev

Pull Request - State: closed - Opened by dave-doty 12 months ago

#245 - 233 for speed minimize time spent creating `pint.Quantity` objects

Pull Request - State: closed - Opened by dave-doty 12 months ago

#244 - RNAplex output missing lines with sufficiently long input

Issue - State: open - Opened by dave-doty 12 months ago
Labels: bug

#243 - Dev

Pull Request - State: closed - Opened by dave-doty about 1 year ago

#242 - 240 constraint to specify NUPACK/ViennaRNA non complementary domain binding affinities

Pull Request - State: closed - Opened by dave-doty about 1 year ago

#241 - use `_normalize_domains_pairs_disjoint_parameters` and `_normalize_strands_pairs_disjoint_parameters`

Issue - State: open - Opened by dave-doty about 1 year ago
Labels: enhancement

#240 - constraint to specify NUPACK/ViennaRNA non-complementary domain binding affinities

Issue - State: closed - Opened by dave-doty about 1 year ago
Labels: enhancement

#234 - Dev

Pull Request - State: closed - Opened by dave-doty over 1 year ago

#233 - minimize time spent creating `pint.Quantity` objects

Issue - State: closed - Opened by dave-doty over 1 year ago - 2 comments
Labels: enhancement, closed in dev

#232 - Dev

Pull Request - State: closed - Opened by dave-doty over 1 year ago

#231 - How to have DomainPools reuse existing strands when possible and generate new ones if not.

Issue - State: closed - Opened by DurhamSmith over 1 year ago - 2 comments

#230 - Dev

Pull Request - State: closed - Opened by dave-doty almost 2 years ago

#229 - closes #227: rename "hard" constraints `NumpyConstraint` and `SequenceConstraint` to `NumpyFilter` and `SequenceFilter`

Pull Request - State: closed - Opened by dave-doty almost 2 years ago

#228 - prevent two strands with the same name

Issue - State: open - Opened by dave-doty about 2 years ago
Labels: bug

#227 - rename "hard" constraints `NumpyConstraint` and `SequenceConstraint` to `NumpyFilter` and `SequenceFilter`

Issue - State: closed - Opened by dave-doty about 2 years ago
Labels: invalid

#226 - attempt to fix broken setup.py

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#225 - Dev

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#224 - removed niupack from docs/requirements.txt and bumped version

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#223 - bumped version and re-added doc/requirements.txt

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#222 - bumped version again and removed doc/requirements to point at root requirements.txt instead

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#221 - Dev

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#220 - Dev

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#219 - fix readthedocs

Issue - State: closed - Opened by dave-doty about 2 years ago - 1 comment
Labels: bug

#218 - 216 use pipe instead of union for union type annotations

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#217 - Dev

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#216 - use `|` instead of `Union` for union type annotations

Issue - State: closed - Opened by dave-doty about 2 years ago
Labels: enhancement

#215 - 133 implement parallelism for `SingularConstraint`'s

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#214 - closes #213: display constraints report graphically in jupyter notebook

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#213 - display constraints report graphically in jupyter notebook

Issue - State: closed - Opened by dave-doty about 2 years ago
Labels: enhancement, closed in dev

#212 - Dev

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#211 - 209 store strandpair instead of tuplestrand strand in constraintwithstrandpairs and make determine strand pairs to check more efficient

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#210 - remove declaration of private properties in classes

Issue - State: open - Opened by dave-doty about 2 years ago
Labels: invalid

#209 - store `StrandPair` instead of `Tuple[Strand, Strand]` in `ConstraintWithStrandPairs` and make `_determine_strand_pairs_to_check` more efficient

Issue - State: open - Opened by dave-doty about 2 years ago
Labels: enhancement

#208 - dependent domains whose independent source is fixed should be fixed

Issue - State: open - Opened by dave-doty about 2 years ago
Labels: invalid, high priority

#207 - Dev

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#206 - 175 Domains and pools should be stored per-design

Pull Request - State: closed - Opened by dave-doty about 2 years ago - 1 comment

#205 - 134 implement `SearchParameters.report_only_violations`

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#204 - fixes #190: `DomainPool`'s should have distinct names

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#203 - Dev

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#202 - closes #201: fix protocol for choosing dependent domains to change, and independent domains to be weighted to affect change probability

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#201 - fix protocol for choosing dependent domains to change, and independent domains to be weighted to affect change probability

Issue - State: closed - Opened by dave-doty about 2 years ago
Labels: invalid

#200 - Dev

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#199 - 197 introduce SubstringSampler class to store domainpool.possible sequences as a single longer sequence and substring length

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#198 - 191 pre packaged strand pair constraints should allow threshold to depend on number of complementary domains

Pull Request - State: closed - Opened by dave-doty about 2 years ago

#197 - store `DomainPool.possible_sequences` as a single longer sequence and substring length

Issue - State: closed - Opened by dave-doty about 2 years ago
Labels: enhancement, closed in dev

#196 - Description formatting for pre-packaged constraints (example for #195)

Pull Request - State: open - Opened by cgevans about 2 years ago - 5 comments

#195 - Allow inclusion of other arguments in `description` for constraints.

Issue - State: open - Opened by cgevans over 2 years ago - 3 comments
Labels: enhancement

#194 - Dev

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#193 - 192 parallel constraints will fail on single cpu systems

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#192 - Parallel constraints will fail on single-cpu systems

Issue - State: closed - Opened by cgevans over 2 years ago
Labels: bug

#191 - pre-packaged strand pair constraints should allow threshold to depend on number of complementary domains

Issue - State: closed - Opened by dave-doty over 2 years ago - 1 comment
Labels: enhancement, closed in dev

#190 - `DomainPool`'s should have distinct names

Issue - State: closed - Opened by cgevans over 2 years ago
Labels: bug, closed in dev

#189 - Dev

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#188 - Create directory before opening logs (fixes #182)

Pull Request - State: closed - Opened by cgevans over 2 years ago - 1 comment

#187 - fixes #182: `info_log_file=True` should create output directory before opening log file

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#186 - Dev

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#185 - fixes #183: restart runs with different random seeds

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#184 - 181 rna duplex multiple causes keyerror with parallel=true

Pull Request - State: closed - Opened by dave-doty over 2 years ago - 1 comment

#183 - restart runs with different random seeds

Issue - State: closed - Opened by cgevans over 2 years ago - 1 comment
Labels: enhancement, closed in dev

#182 - `info_log_file=True` should create output directory before opening log file

Issue - State: closed - Opened by cgevans over 2 years ago - 4 comments
Labels: bug

#181 - rna_duplex_multiple causes occasional KeyError with parallel=True

Issue - State: closed - Opened by cgevans over 2 years ago - 2 comments
Labels: bug, closed in dev

#180 - Dev

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#179 - Dev

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#178 - Dev

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#177 - Dev

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#176 - Install .par files when installing via pip.

Pull Request - State: closed - Opened by cgevans over 2 years ago

#175 - Domains and pools should be stored per-design

Issue - State: closed - Opened by cgevans over 2 years ago - 1 comment
Labels: invalid, closed in dev

#174 - Change sc_domain.dna_sequence() -> sc_domain.dna_sequence

Pull Request - State: closed - Opened by cgevans over 2 years ago - 2 comments

#173 - Dev

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#172 - Fix readthedocs build error with mock import

Pull Request - State: closed - Opened by UnHumbleBen over 2 years ago - 1 comment

#171 - Update README.md

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#170 - Dev

Pull Request - State: closed - Opened by UnHumbleBen over 2 years ago

#169 - Dev

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#168 - Add nupack docker instructions

Pull Request - State: closed - Opened by UnHumbleBen over 2 years ago

#167 - Add NUPACK copyright notice

Pull Request - State: closed - Opened by UnHumbleBen over 2 years ago - 2 comments

#166 - Closes #138; Automated Release Notes

Pull Request - State: closed - Opened by UnHumbleBen over 2 years ago - 2 comments

#165 - Merging main to dev because #163 was accidentally merged to main instead of dev

Pull Request - State: closed - Opened by UnHumbleBen over 2 years ago

#164 - Get CI working by using nupack docker container

Pull Request - State: closed - Opened by UnHumbleBen over 2 years ago

#163 - Fixes #139; make PyPI package that does not include NUPACK or ViennaRNA

Pull Request - State: closed - Opened by UnHumbleBen over 2 years ago - 10 comments

#162 - added more doc details about subdomain and dependent fields

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#161 - Update README.md

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#160 - closes #159: correct installation instructions for OSX

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#159 - Correct installation instructions for OSX

Issue - State: closed - Opened by JoshPetrack over 2 years ago

#158 - added assign_idt_fields_to_scadnano_design and assign_modifications_to_scadnano_design

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#157 - Dev

Pull Request - State: closed - Opened by dave-doty over 2 years ago

#156 - clarified how to set subdomains in order when dealing with starred domains

Pull Request - State: closed - Opened by dave-doty over 2 years ago

GitHub / UC-Davis-molecular-computing/nuad issues and pull requests