Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / UC-Davis-molecular-computing/scadnano-python-package issues and pull requests

#312 - Close Issue #309: account for helix group rotation properly

Pull Request - State: closed - Opened by DanielHader 4 months ago

#311 - Debugging cadnanov2 export of paranemic crossovers when both segments…

Pull Request - State: open - Opened by tcosmo 4 months ago - 2 comments

#308 - import (previously exported) cadnano design with paranemic crossover

Issue - State: open - Opened by dave-doty 4 months ago - 6 comments
Labels: bug

#307 - 306 allow per helix group geometry

Pull Request - State: closed - Opened by dave-doty 5 months ago

#306 - allow per-helix-group geometry

Issue - State: open - Opened by dave-doty 5 months ago - 1 comment
Labels: enhancement, closed in dev

#305 - update packaging action

Issue - State: open - Opened by dave-doty 7 months ago
Labels: invalid

#304 - Typo in 'set_dna_sequence' comment

Issue - State: open - Opened by Phillip-Drake 8 months ago
Labels: documentation, closed in dev

#303 - implement thermodynamic analysis of stability of origami

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

#302 - separate Github actions for release notes and PyPi publishing

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

#301 - fix PyPi publishing

Issue - State: open - Opened by dave-doty 11 months ago - 1 comment
Labels: bug, high priority

#300 - Dev

Pull Request - State: closed - Opened by dave-doty 11 months ago - 1 comment

#299 - Dev

Pull Request - State: closed - Opened by dave-doty 11 months ago - 1 comment

#298 - fixes #297: fix oxView export exception on Loopouts

Pull Request - State: closed - Opened by dave-doty 11 months ago - 1 comment

#297 - fix oxView export exception with Loopouts

Issue - State: closed - Opened by dave-doty 11 months ago
Labels: bug, closed in dev

#296 - Added pip packages to enviornment.yml

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

#295 - Changed to use mamba

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

#294 - Removed python.version and added back tools.python

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

#293 - 290 fix readthedocs updating

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

#292 - 290 fix readthedocs updating

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

#291 - enable 2FA for PyPI publishing action

Issue - State: closed - Opened by dave-doty about 1 year ago - 3 comments
Labels: invalid, high priority

#290 - fix readthedocs updating

Issue - State: open - Opened by dave-doty about 1 year ago - 4 comments
Labels: bug, high priority, closed in dev

#289 - bumped version

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

#288 - 287 export dna sequences from extensions and loopouts

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

#287 - export DNA sequences from extensions and loopouts

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

#286 - option to display some domains with dashed or squiggly lines

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

#286 - option to display some domains with dashed or squiggly lines

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

#285 - Dev

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

#284 - fixes #283: deal with non-unique Modification vendor codes

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

#284 - fixes #283: deal with non-unique Modification vendor codes

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

#283 - deal with non-unique Modification vendor codes

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

#283 - deal with non-unique Modification vendor codes

Issue - State: open - Opened by dave-doty over 1 year ago
Labels: invalid, closed in dev

#282 - closes #281: remove field `Modification.id`

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

#281 - remove field `Modification.id`

Issue - State: open - Opened by dave-doty over 1 year ago - 1 comment
Labels: invalid

#281 - remove field `Modification.id`

Issue - State: closed - Opened by dave-doty over 1 year ago - 1 comment
Labels: invalid, closed in dev

#280 - closes #279: rename IDTFields to VendorFields

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

#280 - closes #279: rename IDTFields to VendorFields

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

#279 - rename `IDTFields` to `VendorFields`

Issue - State: closed - Opened by dave-doty over 1 year ago - 1 comment
Labels: invalid, closed in dev

#278 - Dev

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

#277 - 276 customize delimiter between domains in exported dna sequences

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

#276 - customize delimiter between domains in exported DNA sequences

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

#275 - Dev

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

#273 - deal with inter-helix-group crossovers when relaxing helix rolls

Issue - State: open - Opened by dave-doty over 1 year ago
Labels: invalid, high priority

#273 - deal with inter-helix-group crossovers when relaxing helix rolls

Issue - State: closed - Opened by dave-doty over 1 year ago - 1 comment
Labels: invalid, high priority, closed in dev

#272 - 270 ignore same helix crossovers when calculating helix rolls

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

#271 - option to make end offsets inclusive

Issue - State: open - Opened by dave-doty over 1 year ago
Labels: invalid, high priority, challenging

#270 - ignore "same helix" crossovers when calculating Helix rolls

Issue - State: open - Opened by dave-doty over 1 year ago
Labels: bug, high priority, closed in dev

#270 - ignore "same helix" crossovers when calculating Helix rolls

Issue - State: closed - Opened by dave-doty over 1 year ago
Labels: bug, high priority, closed in dev

#269 - fixes #268: ignore loopouts when relaxing Helix rolls

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

#269 - fixes #268: ignore loopouts when relaxing Helix rolls

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

#268 - ignore loopouts when relaxing helix rolls

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

#268 - ignore loopouts when relaxing helix rolls

Issue - State: open - Opened by dave-doty over 1 year ago
Labels: bug

#267 - Dev

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

#266 - export newer Excel file format

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

#265 - 234 export newer excel file format

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

#263 - fix unit test installation error

Issue - State: open - Opened by dave-doty over 1 year ago
Labels: bug

#262 - closes #261: change `label` type to `str`

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

#261 - change label type to string

Issue - State: closed - Opened by dave-doty over 1 year ago - 1 comment
Labels: invalid, closed in dev

#260 - Importing deletions on 5'/3' staple end from Cadnano

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

#259 - unit tests failing due to version incompatibility

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

#258 - Dev

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

#257 - automatically set Helix rolls based on crossover locations ("relax" the rolls)

Issue - State: closed - Opened by dave-doty almost 2 years ago - 4 comments
Labels: enhancement, closed in dev

#256 - Dev

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

#255 - closes #238: Domain colors

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

#254 - closes #252: add method `Design.base_pairs()`

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

#254 - closes #252: add method `Design.base_pairs()`

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

#253 - space out nucleotides in oxDNA export of loopouts

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

#253 - space out nucleotides in oxDNA export of loopouts

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

#252 - add method `Design.base_pairs`

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

#251 - drop support for Python 3.6

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

#251 - drop support for Python 3.6

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

#250 - Dev

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

#249 - oxDNA Export with Helix Group Pitch / Yaw Bug

Issue - State: open - Opened by ajvetturini about 2 years ago - 3 comments
Labels: bug, high priority

#248 - shared binding domains

Issue - State: open - Opened by dave-doty over 2 years ago
Labels: enhancement, challenging

#247 - Add filename extensions to oxDNA exports with filename_no_extension set.

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

#247 - Add filename extensions to oxDNA exports with filename_no_extension set.

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

#246 - Oxview export

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

#245 - oxDNA file export with filename does not set extension

Issue - State: open - Opened by cgevans over 2 years ago

#244 - Add warn_duplicate_strand_names argument to from_scadnano_file

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

#241 - 240 support extensions in oxdna export

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

#241 - 240 support extensions in oxdna export

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

#240 - support Extensions in oxDNA export

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

#239 - export Bioneer files

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

#239 - export Bioneer files

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

#238 - Domain colors

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

#237 - Dev

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

#237 - Dev

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

#235 - fix bug in oxDNA export giving zero normal vector on loopouts

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

#235 - fix bug in oxDNA export giving zero normal vector on loopouts

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

#234 - export newer Excel file format

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

#234 - export newer Excel file format

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

#233 - Set Position3D as frozen

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