Scadnano

Mostly documentation was updated.

Commits
- [[018fdf8](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/018fdf8a4e641171abe668a0e77dd78420a07ddc)]: added CONTRIBUTING doc (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[ac3de4e](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/ac3de4ef8241847bf8682ecdef04d2464a7aa26e)]: removed bad link to images of checks pending/passing (from web repo) (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[3871de6](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/3871de61fb18b5255def4cf790c6bc76cb813672)]: made contributing a subheader (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[b908561](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/b9085618e39b048d5ce85dee62394c871bf3e295)]: Update CONTRIBUTING.md (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[a601ea5](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/a601ea5a03fd6383375788dd3bc1b3eba1076e05)]: added screenshot showing how to download raw Python file from GitHub (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[b5849b9](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/b5849b95c73b439509cfc28e1e15b5da3188645e)]: changed .dna extension to .sc in README and tutorial (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[fbe4c20](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/fbe4c20facd4c29d244bc28e15772350b38f280d)]: lined up tutorial example source code (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[56a5564](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/56a556445ee3ac6ae025ea71634906cb5478d05c)]: replaced --> with → in tutorial (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[66db277](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/66db2774a82eeaadd618d8675c701d2089333f49)]: in tutorial, changed mistaken references from .py files to .sc files (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[e287a88](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/e287a887adb1a096d56a45ab247e6d29ff443b23)]: added link to API in tutorial (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[edadadc](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/edadadc6b235c3bde79bd97a50920a6b2c1ba7e4)]: in tutorial explained why we use add_strand, and changed default rotation for assigning M13 to 5587 from 5588 (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[8c9daf6](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/8c9daf677a75aaac3191c4dc186e3faec33db4bf)]: updated relative links in README and tutorial (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[4b27c51](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/4b27c510263e615962dd300a395b0e8f3436d4e8)]: added explanation in tutorial for why you need to manually reload .sc file after making changes with scripting library locally (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[6b78b81](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/6b78b816b442aadd7249572036c6b2c10f44f3d5)]: removed local variable scaffold in tutorial code (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[dfe38fa](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/dfe38fac9a429ce05e2bebcaacbe493f38efd079)]: added detail to tutorial about automatically adding nicks when calling add_full_crossover (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[068162a](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/068162ad1be49add7eea11b15100f20b257f878c)]: changed title in README (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[ae2c223](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/ae2c223c29c7401c4a3a00719da17b72e11b0c0c)]: Update README.md (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[96fadf9](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/96fadf994c714bf29052a524fd47326cb98dcc19)]: removed incorrect word "literal" from docstrings (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[7266c62](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/7266c62808f9c4c4700d51bf38cd4090c36827cc)]: corrected reference to StrandBuilder methods in docstrings (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[97e133c](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/97e133cdb24c493b1146ed7fd4a296ff61a9ed36)]: updated README to be explicit about what steps are needed for pip install and what is troubleshooting (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[cab05a4](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/cab05a483685642392099e6a4d918d2a77d8c6d2)]: added link to PYTHONPATH documentation in README (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[3e17fb0](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/3e17fb041100d94b914597f7ead9433bd0ea446e)]: separated out installation instructions for Python from pip in README (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[b15a33d](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/b15a33def5271e9dc204fadabb6dbdb613e9978c)]: Update README.md (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)
- [[256bcb0](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/256bcb092fd0e2678329307cc391cdc3268efd02)]: bumped version (David Doty) [#119](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/119)

Calling this release 0.10.1a, but really it's just to correct for the fact that I messed up the version number 0.10.1 in the source code on the last PR.

Commits
- [[4d82e70](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/4d82e702d815f9522d6fc6fddcb27f7d977a5a11)]: incorrectly bumped version last time; bumping it in _version.py now (David Doty) [#120](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/120)

**BREAKING CHANGE**: The name of the class `DNADesign` has been changed to `Design`. You will have to update scripts to reflect this new name. From now on, it would be good practice to name local variables `design` instead of `dna_design`, for instance. I found it was common for novices to abbreviate these as only `dna`, which is confusing since that could be DNA sequence, for example.

Also, the default file extension has been changed from `.dna` to `.sc`. Most short file extensions are taken, but in this case, the most popular for `.dna` is [SnapGene](https://www.snapgene.com/), which is software for biological DNA, and for `.sc`, it's [SuperCollider](https://supercollider.github.io/), a music synthesis tool. There's much less chance that we'll be confused with SuperCollider than SnapGene. However, the web interface still recognizes `.sc`, `.dna`, and `.json` as file extensions for scadnano files that can be opened using the Menu->Load option, or dragged from a file browser onto the web browser with scadnano open.

Commits
- [[bb8d62d](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/bb8d62de30c7730868db4be253f8ae3311638cc1)]: updated name of function from main() to create_design() in example script in README (David Doty) [#118](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/118)
- [[6db03e8](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/6db03e85314df3e549d345dd5589fb3fd75b9e40)]: changed name of function main() to create_design() in tutorial (David Doty) [#118](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/118)
- [[b4548da](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/b4548daa8d3fefa28ccc9d952751c719e46ca413)]: modified intro to README (David Doty) [#118](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/118)
- [[d0b58d2](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/d0b58d28f06b64be6c28a5e0fc77e7bf8526333e)]: updated tutorial to link directly to raw design file (David Doty) [#118](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/118)
- [[f87b219](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/f87b219bc3e8a93c9560c0092d36e46cdb5c1729)]: fixes #110; updated default file extension from .dna to .sc (David Doty) [118](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/118)
- [[5f9bf45](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/5f9bf4512470652ee4cfc9556a943ee289f279d4)]: closes #91; BREAKING CHANGE: change DNADesign class name to Design (David Doty) [118](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/118)

I messed up this merging this release by committing directly to master and then reverting it. So the release notes are not automatically generated now.

Briefly, this release handles this issue: 370, which involved moving a state information about the current edit and select modes out of the view components, so that they do not need to be re-rendered when those modes change.

It involved significantly re-working the React/Redux action pipeline, because the view components now don't have enough state information to dispatch the proper actions, or know when they should be dispatched. Much of this is now handled in `mode_sensitive_actions_filter_middleware`.

It also required dynamically changing the CSS style rules (for highlighting selectable items) without re-rendering the view components to mark them as selectable.

I also forgot to bump the version number, so this version is 0.9.7-2.

To see all the commits that fixed it, see this PR: 377

Commits
- [[9b1f2e6](https://github.com/UC-Davis-molecular-computing/scadnano/commit/9b1f2e6a53987f3d8ccae8a31495be0a63049da3)]: Update README.md (David Doty) [#333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)
- [[6017c5e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6017c5e95402eb849585bb887d947b77700823b6)]: Now using _initializeBuilder to set default values of AppUIStateStorable. (David Doty) [#333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)
- [[ac77e4b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ac77e4b307a3822ac15847a06a77b6a9e8817f8e)]: removed word "opinionated" from README (David Doty) [#333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)
- [[5b2068c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/5b2068c53094609849afef1f85c5d6c4cdf10366)]: bumped OverReact minimum to 3.6.0, added _initializeBuilder to classes that have a default instance defined as canonical way to set default values for fields (David Doty) [#333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)
- [[240b7db](https://github.com/UC-Davis-molecular-computing/scadnano/commit/240b7db0451d8cedee865b410a7d2a694224e200)]: fixed bug with incorrect x position in setting gridless 3D position of parallel helices from crossovers between pairs of helices (fixes #331) (David Doty) [333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)
- [[4b5d02c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4b5d02c9a03cf56356bc8773d0845c9e54608206)]: refactored MenuNumber into its own React component and refactored modification font size to be one (David Doty) [#333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)
- [[9f9c880](https://github.com/UC-Davis-molecular-computing/scadnano/commit/9f9c880f8300d11a68dc10fd7177e417619f095a)]: refactored view menu into sub-menus in between dividers (David Doty) [#333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)
- [[441e1ef](https://github.com/UC-Davis-molecular-computing/scadnano/commit/441e1efd22e0c47c582ac0115bf6c2b295635a42)]: minor cleanup of menu callbacks (David Doty) [#333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)
- [[f9e7df1](https://github.com/UC-Davis-molecular-computing/scadnano/commit/f9e7df16132805bd546bb808114a0a317f34283c)]: add option in View menu to change font size of major tick offset and major tick widths (closes #309) (David Doty) [333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)
- [[d560fcb](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d560fcbc693b697aab24ad912093d6881ed5d57b)]: fixed bug where changing grid does not redraw main view helices (fixes #246) (David Doty) [333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)
- [[0eb8000](https://github.com/UC-Davis-molecular-computing/scadnano/commit/0eb800084cb880b6b84ca1799f6d4ae12ff0380e)]: fixed bug in GridChange_none_to_square that had incorrect expected svg_position (David Doty) [#333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)
- [[aac3eda](https://github.com/UC-Davis-molecular-computing/scadnano/commit/aac3edae0fb31c72a32757e47ecbc1b39d3ccc23)]: issue alert when attempting to convert from gridless design to grid where two helices will map to the same grid position (fixes #332) (David Doty) [333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)
- [[85e333a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/85e333a94dc0fad588c899ef4f709a3e279a0d18)]: bumped version (David Doty) [#333](https://github.com/UC-Davis-molecular-computing/scadnano/pull/333)

So that we don't have to bump the version on the Python repo every time we put out a new version on the Dart repo, and vice versa, I'm going to try this convention: `MAJOR.MINOR.PATCH-REALLYMINOR`, where we don't bother keeping the REALLYMINOR versions in sync. bumping anything else means that both repos should put out a new version, for example for the web interface to display something that was just implemented in the Python package.

Commits
- [[672a0cc](https://github.com/UC-Davis-molecular-computing/scadnano/commit/672a0ccec50b95c185e7288843950b14ea8368f4)]: added instructions to CONTRIBUTING.md for automatic versioning (David Doty) [#330](https://github.com/UC-Davis-molecular-computing/scadnano/pull/330)
- [[44e0895](https://github.com/UC-Davis-molecular-computing/scadnano/commit/44e0895546cec1399bfc0e3cdaea094f2aff6e46)]: added note to CONTRIBUTING.md about PyPI .tar.gz files being ignored by git (David Doty) [#330](https://github.com/UC-Davis-molecular-computing/scadnano/pull/330)
- [[1f87255](https://github.com/UC-Davis-molecular-computing/scadnano/commit/1f872552de2c0b1080f7d94131f35b4f2f81a348)]: cleaned up some code and tooltip hover text for menu items (David Doty) [#330](https://github.com/UC-Davis-molecular-computing/scadnano/pull/330)
- [[ae43ba3](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ae43ba3e7f42c94aa35d6c6071bbe278da7ffd12)]: closes #327 (invert side view y-axis when "Invert y axis" option is selected) (David Doty) [330](https://github.com/UC-Davis-molecular-computing/scadnano/pull/330)
- [[6f4673a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6f4673a35c5c87bb5fac9e6bdaaba254078ef6b9)]: closes #328 (display major tick offsets directly above base to the right of the tick); closes 329 (display major tick widths below helix) (David Doty) [330](https://github.com/UC-Davis-molecular-computing/scadnano/pull/330)
- [[550c170](https://github.com/UC-Davis-molecular-computing/scadnano/commit/550c170642334c799106af07b6f6296590f70e49)]: fixed bug when major_tick_distance is not specified in JSON for either the design or for individual helices and grid is none; now defaults to showing no major ticks in this case (David Doty) [#330](https://github.com/UC-Davis-molecular-computing/scadnano/pull/330)
- [[d65f545](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d65f545a29dc354d4da96b3b8a0b1d5e36a8cc5a)]: fixed bug with default DNADesign not having major_tick_distance specified (David Doty) [#330](https://github.com/UC-Davis-molecular-computing/scadnano/pull/330)
- [[7a66d11](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7a66d111313f784732b39f82dced8c948d0e29c1)]: bumped version (David Doty) [#330](https://github.com/UC-Davis-molecular-computing/scadnano/pull/330)