Scadnano

One new feature: ability to click-drag ends of extensions to change the displayed length and angle of the extension.

Commits
- ace3a4e: closes 791: add guide on installing older webdev (Edwin Chang) [809](https://github.com/UC-Davis-molecular-computing/scadnano/pull/809)
- a5ded50: Add store for potential extensions (Edwin Chang) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- bbe8b29: Add actions and serializers (Edwin Chang) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 06c1f5a: continued implementation of extensions move actions (Ho-Chih) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- c5a0a61: rename potential extension to dnaextensionmove (sarahayu) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 2d10289: fix compile error (sarahayu) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 7426fbc: Update naming, call move start action (Edwin Chang) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 51a28ef: Show extension moving (Edwin Chang) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- ffc39cf: extension end is now pink! (sarahayu) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 74d4e7c: implemented extension move commit! (Ho-Chih) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- f59049e: Extension commit view works (Ho-Chih) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 327f515: bumped version (David Doty) [844](https://github.com/UC-Davis-molecular-computing/scadnano/pull/844)
- 152d707: Add potential extensions and moving multiple extensions (Edwin Chang) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 3c7764f: fix selection box for extension end (sarahayu) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 5008b72: Fix end rotation on extension move (Edwin Chang) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 944beec: closes 799: adjust Extension display length and angle by click-dragging free end (Edwin Chang) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 80e3d15: Merge branch 'dev' into 799-adjust-extension-display-length-and-angle-by-click-dragging-free-end (Edwin Chang) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 3ffbece: Fix compilation error with strand_color (Edwin Chang) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 6706c58: rename stuff (sarahayu) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)
- 9427933: fix wrong extension offsets on helix move (sarahayu) [840](https://github.com/UC-Davis-molecular-computing/scadnano/pull/840)

Commits
- 4243eca: bumped version (David Doty) [839](https://github.com/UC-Davis-molecular-computing/scadnano/pull/839)
- db0b713: switched github deploy action to use Ubuntu 20.04 instead of 18.04 (David Doty) [839](https://github.com/UC-Davis-molecular-computing/scadnano/pull/839)
- 57f5d01: closes 835: option to remove domain/extension/loopout color (David Doty) [837](https://github.com/UC-Davis-molecular-computing/scadnano/pull/837)
- d591730: closes 834: helix backbone arrows should be color of Domain if defined (David Doty) [838](https://github.com/UC-Davis-molecular-computing/scadnano/pull/838)

Release notes

Base pair lines
It is common in DNA nanotech figures to draw lines orthogonal to the DNA strand lines representing base pairs. Although this would not help when designing a scadnano design, it would help when making figures. By enabling View --> Base pairs --> Base pair lines:


Lines between base pairs are drawn. In combination with turning off the view of helices (View --> Helices --> Show main view helices), this makes it easy to make "figure quality" diagrams in scadnano:



Domain/Extension/Loopout colors
This is another feature useful for making paper-figure-quality diagrams with scadnano.

Individual `Domain`'s, `Extension`'s, and `Loopout`'s now have a `color` field. If specified, then this overrides the field `Strand.color` in the display. In the following image, the strand's color is blue, which is the color of the bottommost domain (which has no color specified) and is also the color of all the crossovers. Every other domain/extension/loopout has its own custom color specified:


They can be specified in the Python package, and manually by right-clicking:




Note that although domain/extension/loopout color is optional, strand color is required.


Select all in helix group
Strands from different helix groups cannot be copied or moved. To make it easier to select all strands in a single group (rather than all strands in the whole design), there is now command "Edit --> Select All in Helix Group" (keyboard Ctrl+Shift+A) that selects all strands in the current helix group.



Commits
- 220d670: bumped version (David Doty) [833](https://github.com/UC-Davis-molecular-computing/scadnano/pull/833)
- 07f1cc8: closes 827: add "select all in current helix group" (Edwin Chang) [828](https://github.com/UC-Davis-molecular-computing/scadnano/pull/828)
- 0c5b9b6: Remove extra action and add keyboard shortcut (Edwin Chang) [828](https://github.com/UC-Davis-molecular-computing/scadnano/pull/828)
- e7b0e8b: Add tests for select all strands in helix group (Edwin Chang) [828](https://github.com/UC-Davis-molecular-computing/scadnano/pull/828)
- 3d9c697: Fixed selection issues for strands in multiple groups (Ho-Chih) [828](https://github.com/UC-Davis-molecular-computing/scadnano/pull/828)
- 6c41702: closes 829: Optional base pair lines (David Doty) [831](https://github.com/UC-Davis-molecular-computing/scadnano/pull/831)
- ffcb86e: added support for displaying domains/loopouts/extensions with optional color field; still need to support setting colors in the web interface (David Doty) [832](https://github.com/UC-Davis-molecular-computing/scadnano/pull/832)
- 4d1dde0: closes 796: Domain colors (David Doty) [832](https://github.com/UC-Davis-molecular-computing/scadnano/pull/832)

Bug fixes.

Commits
- 0470c1e: Fixed Copy and Pasting on same tab, pasting on others not working (Cesar Alonso Guzman Avina) [820](https://github.com/UC-Davis-molecular-computing/scadnano/pull/820)
- 82ef8a4: fix int mods not copying (sarahayu) [820](https://github.com/UC-Davis-molecular-computing/scadnano/pull/820)
- 5596aec: undo tuple to list change (sarahayu) [820](https://github.com/UC-Davis-molecular-computing/scadnano/pull/820)
- 7ad0d1d: updating system clipboard null check (rishabhmudradi) [820](https://github.com/UC-Davis-molecular-computing/scadnano/pull/820)
- c1e2445: bumped version (David Doty) [823](https://github.com/UC-Davis-molecular-computing/scadnano/pull/823)
- fb341cb: Merge branch 'dev' into 745-modifications-should-be-copied-with-strand (sarahayu) [820](https://github.com/UC-Davis-molecular-computing/scadnano/pull/820)
- dfa7430: fixes 819 change color of warning star for domain name mismatch (Ho-Chih) [821](https://github.com/UC-Davis-molecular-computing/scadnano/pull/821)
- 52ae6f6: fixes 817 many editable values in Dialog forms should be existing value of strand/domain/etc., not value entered last time dialog was open (Ho-Chih) [822](https://github.com/UC-Davis-molecular-computing/scadnano/pull/822)
- b9f5d8d: fixes 819 change color of warning star for domain name mismatch (Ho-Chih) [821](https://github.com/UC-Davis-molecular-computing/scadnano/pull/821)
- d94cec4: added tooltips explaining copy/paste/autopaste (David Doty) [823](https://github.com/UC-Davis-molecular-computing/scadnano/pull/823)
- 53ac49a: change type to iterable and add comment (sarahayu) [820](https://github.com/UC-Davis-molecular-computing/scadnano/pull/820)
- a0009fb: Update menu.dart (David Doty) [823](https://github.com/UC-Davis-molecular-computing/scadnano/pull/823)

Release notes

new method [`Design.base_pairs()`](https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Design.base_pairs)
This method returns a dict mapping helix idx's where base pairs exist to a list of offsets where those base pairs are.

Domain/Extension/Loopout colors
Individual `Domain`'s, `Extension`'s, and `Loopout`'s now have a `color` field. If specified, then this overrides the field `Strand.color` when displayed in the web interface. There is also a new method `StrandBuilder.with_domain_color()`:

python
helices = [sc.Helix(max_offset=100) for _ in range(4)]
design = sc.Design(helices=helices, grid=sc.square)

red = sc.Color(255, 0, 0)
dark_red = sc.Color(150, 0, 0)
green = sc.Color(0, 255, 0)
dark_green = sc.Color(0, 150, 0)
blue = sc.Color(0, 0, 255)
dark_blue = sc.Color(0, 0, 150)
black = sc.Color(0, 0, 0)

design.draw_strand(0, 0) \
.extension_5p(num_bases=5).with_domain_color(red) \
.move(8).with_domain_color(green) \
.loopout(1, 5).with_domain_color(dark_blue) \
.move(-8).with_domain_color(dark_red) \
.cross(2) \
.move(8).with_domain_color(dark_green) \
.cross(3) \
.move(-8) \
.extension_3p(num_bases=5).with_domain_color(black) \
.with_color(blue)



Commits
- 5586c9f: bumped version (David Doty) [256](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/256)
- 6463865: closes 252: add method `Design.base_pairs()` (David Doty) [254](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/254)
- fec6f43: changed return type of `Design.base_pairs()` to dict and added `allow_mismatches` parameter (David Doty) [254](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/254)
- e795627: fixed unit tests after updating `with_sequence` and `with_domain_sequence` to default to not assigning complement (David Doty) [254](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/254)
- 6b6001a: removed unused _popleft() function (David Doty) [254](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/254)
- e55609d: Update scadnano.py (David Doty) [256](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/256)
- afc44b8: don't put Helix idx in base_pairs dict if Helix has no base pairs (David Doty) [256](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/256)
- 1049cdc: fixed base pair calculation to allow for deletions/insertions/wildcards/None if DNA sequence is not assigned (David Doty) [256](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/256)
- e6c0737: added unit test for no base pairs (David Doty) [256](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/256)
- f81b8ff: Update scadnano_tests.py (David Doty) [256](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/256)
- 7b83a43: fixed bug in `Design.base_pairs()` when no reverse domains on helix (David Doty) [256](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/256)
- 5312a59: Update scadnano_tests.py (David Doty) [256](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/256)
- 1b7e605: closes 238: Domain colors (David Doty) [255](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/255)
- fea3b32: added example with domain colors (David Doty) [256](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/256)

Release notes

Two big updates:

1. support Extensions in oxDNA export (240); note it can have problems with large extensions between two close domains, see 253
2. preliminary oxView export (173)

Commits
- 5cfa122: fixed docstrings for `Extension` (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- 9b0d3e3: Update scadnano.py (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- f84594e: Update scadnano.py (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- 04a4e9d: Update scadnano.py (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- 4ae1d93: formatting (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- 357a59a: updated extensions example (David Doty) [241](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/241)
- b477328: closes 240: support Extensions in oxDNA export (David Doty) [241](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/241)
- 895469e: fix bug in assigning DNA sequence to strand bound to another strand with an extension (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- 897f66d: fixed bug in oxDNA export when extension has no DNA sequence (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- d1c38b9: Add add_extension to file creation (Constantine Evans) [247](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/247)
- 1400ade: add test (Constantine Evans) [247](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/247)
- d9160d6: Initial oxview export implementation (Constantine Evans) [246](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/246)
- 176811f: Add documentation. (Constantine Evans) [246](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/246)
- a823fee: Add tests. (Constantine Evans) [246](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/246)
- 7086a55: probably-working, probably-bad bp implementation (Constantine Evans) [246](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/246)
- 39b29c0: Tests for bp (Constantine Evans) [246](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/246)
- 6f95338: add mismatch exclusion (Constantine Evans) [246](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/246)
- ed71923: added method `Design.add_helix` (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- d32537b: swapped order of `directory` and `filename` in `Design.write_scadnano_file` (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- b0fee20: changed default display angle to 35 to match Web interface default (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- 400cc3e: bumped version (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- b9912ee: drop Python 3.6 on unit tests, add 3.10 and 3.11 (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- 2c3b85f: adding quotes to python versions to try to fix pip install error on github actions (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- e133772: fixed unit test to ensure helix max offset is sufficiently large (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- 03d54ae: fixed unit test to ensure helix max offset is sufficiently large (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- 931f22d: delete temp file manually in unit test for oxDNA export to avoid error where it cannot be read while open for writing (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)
- 8e78237: added example of oxDNA export of extension and loopouts (David Doty) [250](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/250)