Scadnano

Added loopout labels. Now you can do this:

python
(design.strand(0, 0).to(8)
.loopout(1, 4).with_domain_label('loopout label')
.to(0))




Commits
- [[ed0ea3b](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/ed0ea3bebf7ea1ae3d6af62e0872977c69c0fc5d)]: removed example; made StrandBuilder._strand private and added getter that raiases exception if Strand has not been created yet (David Doty) [#130](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/130)
- [[23d5a1c](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/23d5a1c3e302f2e81e62461b3e3493d3a8e72585)]: fixed unit test after changing indenting JSON behavior if Helix.position is specified (David Doty) [#130](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/130)
- [[9a969ce](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/9a969ce3a538f342339d824d5198c5c0ddd06a58)]: added loopout labels; bumped version (David Doty) [#130](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/130)

The main new feature is a method `StrandBuilder.move` and parameter `move` in the existing methods `StrandBuilder.cross` and `StrandBuilder.loopout`. `move` is like `to`, but is a relative offset rather than an absolute offset.

For example, to make a strand that, starting at helix 0, offset 123, goes 8 bases forward, then crosses over to the same offset on helix 1 and goes 16 bases in reverse, then crosses over to helix 2 (but the crossover jumps 2 offsets back), then goes 10 bases forward:

python
(design.strand(0, 123)
.move(8)
.cross(1)
.move(-16)
.cross(2, move=-2)
.move(10))



where the parameter to the method `move`, as well as the parameter named `move`, are relative to the current offset. This is equivalent to the more cumbersome absolute offsets with `to`:

python
(design.strand(0, 123)
.to(131)
.cross(1)
.to(115)
.cross(2, offset=113)
.to(123))


Commits
- [[37db033](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/37db033c9827c1ea9390210c8bc26ec4dc0976cd)]: updated tutorial with correct parameter names for Crossover constructor (David Doty) [#129](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/129)
- [[0808d88](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/0808d88b6b298286224cd2b63350cb4479cfb436)]: fixed code display in docstrings (David Doty) [#129](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/129)
- [[2499733](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/2499733a64fe328befe948e1fd3577ff2f2b9851)]: added move method to StrandBuilder and move parameter to StrandBuilder.cross and StrandBuilder.loopout to enable relative (instead of absolute) specification of offsets when creating Domains through chained methodso (David Doty) [#129](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/129)
- [[0b43e14](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/0b43e14f36464d5672857f5ace455d9886ffa7ac)]: added examples; bumped version (David Doty) [#129](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/129)
- [[4760354](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/4760354cb189915fd379f33bcf5fd2e0d15d8b3f)]: fixed unit test now that positions are automatically created in Helix when grid is None (David Doty) [#129](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/129)

Note there are two breaking changes:

- removed helix_template and num_helices from Design constructor. This feature wasn't carrying its weight, given the complexity it introduced to parse optional parameters in the `Design` constructor. It's simple enough to simply type something like
python
helices=[Helix(idx=idx, <other properties you want>) for idx in range(num_helices)]


- removed `major_tick_distance` from `Design`. Similarly, this feature wasn't carrying its weight and REALLY complicated parsing optional parameters. To assign the same `major_tick_distance` to every `Helix`, simply give the same value in every `Helix` constructor, e.g.,
python
helices=[Helix(idx=idx, major_tick_distance=10) for idx in range(num_helices)]


Commits
- [[b9e7eb6](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/b9e7eb6f9ea9386cba65001b7b56b68c6afab9c3)]: ensures default helices view order is assigned properly in each helix group (David Doty) [#128](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/128)
- [[6874906](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/6874906a7f2fa0bb1714b66f929a86a7831ff919)]: BREAKING CHANGE: removed helix_template and num_helices from Design constructor (David Doty) [#128](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/128)
- [[419caeb](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/419caeb637de5587157915b2af73576b20ae504d)]: bumped version for breaking change (removed helix_template and num_helices from Design constructor parameters) (David Doty) [#128](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/128)
- [[e7e223f](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/e7e223fc408052557119be6d3371ad7377541ba3)]: ignoring .sc files in tests_inputs/cadnano_v2_export directory (David Doty) [#128](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/128)
- [[fb78aa1](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/fb78aa16a1e476bf9a026fa6d2348bd76b4122ad)]: BREAKING CHANGE: removed major_tick_distance from Design (David Doty) [#128](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/128)
- [[d36d457](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/d36d457d53b00c0278e97e1be14209a1ac53742f)]: added example with helix groups (David Doty) [#128](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/128)
- [[507c601](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/507c60166fb254696229b23acf403e631bccd7a2)]: closes #104; add support for Helix.major_tick_start and Helix.major_tick_periodic_distances (David Doty) [128](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/128)
- [[3f59e6d](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/3f59e6dc25e4fecbc71a9910d12d4fef9b816aa5)]: re-ran examples to produce latest version (David Doty) [#128](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/128)
- [[107b677](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/107b677381e0e98c60c275e92bb1af154f8d934a)]: removed DomainLabel and StrandLabel as types in typing hints (David Doty) [#128](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/128)
- [[dceefc1](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/dceefc169b6c25d5788162342d00899795ff24b1)]: fixes #126; fix bug where strands are not always assigned a color (David Doty) [128](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/128)

This was mainly to test some functionality with auto-generating docs and PyPI releases.

Commits
- [[42e6fbd](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/42e6fbdfe5e7cffbcdcbab6a60d3bad125638801)]: fixed version-finding function in setup.py (David Doty) [#124](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/124)
- [[2e81a57](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/2e81a57cc78c3929d631608139ced75055a0e478)]: moved __version__ up closer to top of scadnano.py (David Doty) [#124](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/124)
- [[ab79777](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/ab7977746a34e8c83ae360bc333da585a37c6190)]: removed print statement from setup.py (David Doty) [#124](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/124)
- [[a2c4763](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/a2c476383e7ba403e00c37cc962c436bee26d220)]: Update conf.py (David Doty) [#124](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/124)

Introduces Helix groups in preparation for implementing them in the web interface: https://github.com/UC-Davis-molecular-computing/scadnano/issues/249

Helix groups allow groups of helices to be grouped and given their own position, orientation, and grid, to help with designs where not all helices are parallel.

Commits
- [[acd4e81](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/acd4e819712e43a9909e03fe63ba7b214c340f1f)]: Update README.md (David Doty) [#123](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/123)
- [[f5bbd38](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/f5bbd38c5baa6a3dc474b292655e5eea0997ba56)]: updated version in test files (David Doty) [#123](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/123)
- [[05db22d](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/05db22d3a7fc782b98b5db54777f110ffc509c40)]: removed in_browser test from examples and re-ran with new version (David Doty) [#122](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/122)
- [[24bd68e](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/24bd68e89a0ef068bfc30fdea78f77a9ada08f23)]: closes #121; introduces Helix groups to allow groups of helices to be grouped and given their own position, orientation, and grid, to help with designs where not all helices are parallel (David Doty) [122](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/122)
- [[299e9ea](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/299e9eababcf91f7e3ae4c0ec04f995e40828362)]: removed _version.py so it only needs to be specified in scadnano.py (David Doty) [#123](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/123)
- [[631c1f3](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/631c1f3a8bf3f73907fa65f99ef2f8c7a3ca0464)]: minor docstring changes (David Doty) [#123](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/123)

This version is mostly here to get some fixes in the tutorial, although there's a few app updates as well. Since I forgot to change the version number in the library (which outputs the version in the .sc file), I kept this at 0.10.0 for now.)

Commits
- [[eb15816](https://github.com/UC-Davis-molecular-computing/scadnano/commit/eb158168d8b9a0c4db08446957f12fe3044d6839)]: closes #396; add option to save design to localStorage periodically, and option to save design to localStorage unconditionally on exit (David Doty) [398](https://github.com/UC-Davis-molecular-computing/scadnano/pull/398)
- [[9239659](https://github.com/UC-Davis-molecular-computing/scadnano/commit/92396593484731023306b725d41c8bc3cb64ec7f)]: bumped version (David Doty) [#398](https://github.com/UC-Davis-molecular-computing/scadnano/pull/398)
- [[e23710c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e23710cc3c954b814c1f7d9f7ac5f0bc4d09450c)]: turned off React DevTools (David Doty) [#398](https://github.com/UC-Davis-molecular-computing/scadnano/pull/398)
- [[6e62469](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6e62469f48c733c71f34a51f6f3359c418d3d503)]: updated tutorial with instructions for how to unselect items and what Shift and Ctrl mean (David Doty) [#401](https://github.com/UC-Davis-molecular-computing/scadnano/pull/401)
- [[5d5f717](https://github.com/UC-Davis-molecular-computing/scadnano/commit/5d5f717005dca5d002c68be7c0e0d281561ae6ed)]: Update CONTRIBUTING.md (David Doty) [#401](https://github.com/UC-Davis-molecular-computing/scadnano/pull/401)
- [[4a2eea3](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4a2eea379caf2139f1bf179d50ecf958ae9df818)]: added some details to CONTRIBUTING (David Doty) [#401](https://github.com/UC-Davis-molecular-computing/scadnano/pull/401)
- [[e301f65](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e301f65149cca4a968641890fbc4501e4ca762b7)]: updated CONTRIBUTING (David Doty) [#401](https://github.com/UC-Davis-molecular-computing/scadnano/pull/401)
- [[f6f02a2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/f6f02a27500a20dcb9801c764efbda0b6a3c9b0e)]: updated CONTRIBUTING with more accurate instructions above getting PRs approved (David Doty) [#401](https://github.com/UC-Davis-molecular-computing/scadnano/pull/401)
- [[dfc5c97](https://github.com/UC-Davis-molecular-computing/scadnano/commit/dfc5c972f8296a0180a37cc6480a7a70a4371c99)]: added link to CONTRIBUTING in README (David Doty) [#401](https://github.com/UC-Davis-molecular-computing/scadnano/pull/401)
- [[b7bc444](https://github.com/UC-Davis-molecular-computing/scadnano/commit/b7bc4443d33643e92e6ef1ab3703e37cfd000f32)]: Update fix-index.sh (David Doty) [#401](https://github.com/UC-Davis-molecular-computing/scadnano/pull/401)
- [[811489e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/811489e3b656d7be72f5c48535ce3dd4093becdb)]: fixed link to sc file in tutorial (David Doty) [#401](https://github.com/UC-Davis-molecular-computing/scadnano/pull/401)
- [[4667e0f](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4667e0fa0202e4d096ca15e8dcc73dad2f46f538)]: fixed link to completed design in tutorial (David Doty) [#401](https://github.com/UC-Davis-molecular-computing/scadnano/pull/401)