Scadnano

No changes to software itself so web application is identical to [v0.13.0](https://github.com/UC-Davis-molecular-computing/scadnano/releases/tag/v0.13.0).

Fixes Github Action for deploying website.

Commits
- [[5d9a910](https://github.com/UC-Davis-molecular-computing/scadnano/commit/5d9a91048f54f441c612cf0840d667da3f6bfa36)]: Fixes #522; Fix build error in gh-pages action (Benjamin Lee) [526](https://github.com/UC-Davis-molecular-computing/scadnano/pull/526)
- [[630ec30](https://github.com/UC-Davis-molecular-computing/scadnano/commit/630ec301ea34642a8ff445913f3c8ea30f4f4790)]: Update version to v0.13.1 (Benjamin Lee) [#526](https://github.com/UC-Davis-molecular-computing/scadnano/pull/526)

Breaking Change: Swap x and z coordinates

Python scripts using the "none" grid and specifying 3D coordinates will need to be rewritten so that x and z coordinates are swapped.

Previously, positive x moved right in the main view and into the screen in the side view, and positive z moved right in the side view and out of the screen in the main view. Now these are swapped.

If you are only using the web interface, you shouldn't see any change. But Python scripts that specify (*x*,*y*,*z*) coordinates will need to be updated to swap the roles of *x* and *z*.

If you are curious why this was done, read here: https://github.com/UC-Davis-molecular-computing/scadnano/issues/488

Commits
- [[c6385f0](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/c6385f0b49d982a3edf321d6c627e170beac0b2e)]: Fixes #138; add Python 3.6 CI tests (Benjamin Lee) [140](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/140)
- [[0546749](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/0546749c85001edc77ed26f22a69851a1af0ff3c)]: Fixes #125; CI checks for docs and PyPI packaging (Benjamin Lee) [141](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/141)
- [[76a85be](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/76a85be1c4922099a12a1f9fcfd0c3d80b0c92d2)]: Remove misplaced name field (Benjamin Lee) [#141](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/141)
- [[8699cb7](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/8699cb7d9350b5f87e308058d45820c6305b6898)]: Remove publish from task name for clarity (Benjamin Lee) [#141](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/141)
- [[b137c80](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/b137c8080cc663ff82406fe792998383a869500e)]: added FAM, ROX, and Fluorescein modifications; added code to automatically population field Modification.id with Modification.idt_text if latter is specified and former is not (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[7486223](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/74862239bbf6fce21e5935b6c2722eb6fe47da3c)]: fixed error in setting Modification.id from Modification.idt_text (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[b6f75d4](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/b6f75d488d93d94abb14ecadb61510d735ab34a1)]: included everything in modifications and origami_rectangle when importing scadnano (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[61ba537](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/61ba5377bb9bed178431553a776749e5469e56cb)]: updated defaults for Design.set_default_idt (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[11d6606](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/11d6606b9131a2de46273373dc945f361539887b)]: fixed some mypy errors, and added unique_names argument to set_default_idt to break with cadnano's naming convention and ensure strand names are unique (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[11d9d67](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/11d9d675028d82c2dd8e0c7be88c909653547be6)]: changed default IDT purification with modifications from PAGE to HPLC (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[c24784f](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/c24784f79ac53fab16344ba24521d13325bc24c5)]: added code to import IDT fields from JSON, along with unit tests (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[ecf5ced](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/ecf5ced2ebd2d194f07630d6145c4583c5148596)]: Adds PR to CI workflow (Benjamin Lee) [#143](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/143)
- [[0bd0082](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/0bd0082f824c7088f5b69a81a48b5482ec594d35)]: Remove push events from CI workflow (Benjamin Lee) [#143](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/143)
- [[8787c6d](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/8787c6da83a01aed7897b7abbb18a26bbfadc0d2)]: Update README.md (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[0e5b323](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/0e5b323c3788a981961b63e68ce3ca45dbdbbca7)]: corrected relative link to .sc file in tutorial (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[2ad4868](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/2ad4868e3f26ed3c8cf0967fb50cac6d6703186a)]: Fixes #144; swap position x z coordinate interpretation (Benjamin Lee) [145](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/145)
- [[34d24fe](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/34d24fe4116fd1dcda04e610c89b7738e0b825b5)]: Rewrite none-grid example scripts for #144 (Benjamin Lee) [145](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/145)
- [[a2a31f6](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/a2a31f60baf5001936cd8f613cb6a7bfe2350fa9)]: Update proposal example for #144 (Benjamin Lee) [145](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/145)
- [[3382247](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/33822476167006e60bcc896abf328a60e68b017c)]: updated docstrings for Position3D (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[10eca78](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/10eca786ccfc87611230b047c97f0af0ab571a0a)]: updated StrandBuilder docstrings (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[1c36eeb](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/1c36eeb3595e74bf982a57fd07b1c41511336985)]: Update scadnano.py (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[b91ef99](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/b91ef990e6296f9b439a954423f316317b54a8b7)]: reverted previous edit of docstrings (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)
- [[a94102c](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/a94102cf0d72548f3d09163b606d451d82f596ff)]: fixed erroneous reference to method to() to be move() (David Doty) [#146](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/146)

For Python 3.6, dataclasses backport library is now automatically installed when installing via pip.

The README still contains instructions for installing it manually, in case a user wants to simply download the scadnano.py file to use with Python 3.6. But they should be updated to emphasize that it is unnecessary to install it manually when installing scadnano via pip.

Commits
- [[1102804](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/11028041680e1f8e5595fed67df9f8ba31e95d9e)]: Adding installation instruction for python dataclasses for Python 3.6 (Cosmo) [#135](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/135)
- [[1999445](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/1999445cc1e09db2e15fb43a3b7763ef242109db)]: Require python 3.6 min (Cosmo) [#135](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/135)
- [[2061a9f](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/2061a9fb7e67e99e8c98f5e601a65d4744111375)]: added instructions about commit messages to CONTRIBUTING; bumped version (David Doty) [#137](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/137)

cadnano export upgraded
Can now export to cadnano from design that uses multiple helix groups.

rotate domains
Added method `Strand.rotate_domains` allowing domains to be "rotated" on a strand. Think of it like adding a crossover between the 5' and 3' ends, and removing another crossover.

type hints
Beefed up type hints, in particular making type variables `StrandLabel` and `DomainLabel` for the types of strand labels and domain labels, allowing `Design`, `Strand`, and `Domain` to be parameterized by them, so that a static type checker such as [mypy](http://mypy-lang.org/) will catch errors such as

python
domain: Domain[str] = Domain(label=123) error
domain2: Domain[str] = Domain(label='123') fine
domain2.label = 123 error


NOTE: this particular type hint no longer makes sense since labels are now assumed to be strings: https://github.com/UC-Davis-molecular-computing/scadnano-python-package/releases/tag/v0.18.0

Also got rid of all previous [mypy](http://mypy-lang.org/) type errors.

Commits
- [[41a7f70](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/41a7f701aabf56fba4e48dc04c2859b3e9cf470d)]: updated paper URL now that DNA 2020 paper is published (David Doty) [#136](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/136)
- [[304e120](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/304e120c1a0de989ce375cacbe3ab83c3c918cd5)]: added rotate_domains method to Strand to "rotate" domains of strand (i.e., like adding a crossover between the 5' and 3' ends, and removing another crossover) (David Doty) [#136](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/136)
- [[b7e41d0](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/b7e41d0de73d5b94cbf398f8e2ec0a9d6efcef89)]: Design.write_scadnano_file now warns if a Loopout is the first or last substrand on a Strand (still allowed in intermediate designs) (David Doty) [#136](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/136)
- [[903510d](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/903510d7f27b19b6275ef6c1d9475cc7e72b9ba7)]: fixed all mypy warnings; closes #109 (David Doty) [136](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/136)
- [[b2012e9](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/b2012e9964437532cc5ee81bd9e0707961f3c50f)]: fixed mypy warnings in origami_rectangle (David Doty) [#136](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/136)
- [[a3248bc](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/a3248bca145ddde9725cc0a16b191ed692248c4a)]: made Design, Strand and Domain generic parameterized by StrandLabel and DomainLabel. Made strand label not indented in serialized JSON (David Doty) [#136](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/136)
- [[080bf6d](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/080bf6de7f005cbdde6b6613953a536f03b9e5a4)]: added example with domains names (some mismatching) (David Doty) [#136](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/136)
- [[a2a6b07](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/a2a6b072a21f83578c9aea5802eb25cc7e5eb829)]: updated names example to have more kinds of mismatches (David Doty) [#136](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/136)
- [[27baee2](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/27baee2d4e27ee7d8d5995418105acb6b7610ea9)]: annotated variable to quiet mypy (David Doty) [#136](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/136)
- [[c5bdb1c](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/c5bdb1c39744612df82f16d8a5cd3b32509a605b)]: Update names_domains_strands.py (David Doty) [#136](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/136)
- [[9b54b1e](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/9b54b1e5fc8d18960aef068fae487862a5d8eac9)]: Export code supports helix groups and associated unittest. test_6_helix_bundle_honeycomb restored. (Cosmo) [#133](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/133)
- [[4d62212](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/4d622123c3bbc11bbb99c2c826a9d3504fd9ac49)]: Export code supports helix groups and associated unittest. test_6_helix_bundle_honeycomb restored. (Cosmo) [#133](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/133)
- [[399f905](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/399f9055f16a80e01f22bcdd1fb767c07711ff73)]: Export code supports helix groups and associated unittest. test_6_helix_bundle_honeycomb restored. (Cosmo) [#133](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/133)
- [[6233075](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/62330752fbe511c95c6a1d1e8688f03467c99639)]: Export code supports helix groups and associated unittest. test_6_helix_bundle_honeycomb restored. (Cosmo) [#133](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/133)
- [[a274a98](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/a274a98999c94f7c5bf11b9c64a1b4af1ef50b0c)]: Forcing the add of test_6_helix_bundle_honeycomb.sc which was ignored (Cosmo) [#133](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/133)
- [[3753e36](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/3753e36022364d91fc9f4d6b55e739ee00f4234c)]: Correct type annotation (Cosmo) [#133](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/133)
- [[627d45b](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/627d45b993c9ebbbecd9aeaa493dafbadf2102ca)]: Correcting syntax error (Cosmo) [#133](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/133)
- [[db82d47](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/db82d47fd3fdb7f208afe78d978a30a11217a083)]: bumped version (David Doty) [#136](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/136)

Optional field `name` now supported in Strand, Domain, and Loopout.

The domain/loopout name is displayed (optionally) in the scadnano web interface main view. The strand name is displayed on mouseover, in the tooltip that pops up, and if "backbone mode" is selected, in the footer at the bottom of the page.

All three are also used with the dsd DNA sequence designer (not public yet).

Commits
- [[3ebcb86](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/3ebcb86aaabaa970ee8610ad86b79619cd340f20)]: added move (relative offset) chained method to README (David Doty) [#131](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/131)
- [[eb7563f](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/eb7563f549e4cadc4db58a4a2cea8884a55f89e7)]: added link to json.dumps documentation in docstrings for Loopout.label and Domain.label (David Doty) [#131](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/131)
- [[ca482ba](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/ca482ba8708cb8a775dd2ac5bb9058a906cd0daa)]: added parameter `check_length` to Design.assign_dna that enforces the sequence is exactly the length of the Strand/Domain being assigned (David Doty) [#131](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/131)
- [[2afc921](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/2afc921db30bdedac712d1b4932c78dab420b3a4)]: added optional name fields to Strand, Domain, and Loopout; these are used now instead of label to assign names to Strands, Domains, and Loopouts in the dsd DNA strand designer (though Strand labels are still used to assign Strand groups in the dsd sequence designer) (David Doty) [#131](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/131)
- [[db5d31f](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/db5d31ff46824607c95667390a2b85a45ce53a43)]: bumped version to 0.12.0 (David Doty) [#131](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/131)
- [[5bec304](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/commit/5bec30477e0a5b42e452294eb8d87df459b68acd)]: removed _version.py file (David Doty) [#131](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/pull/131)

Minor feature enhancements.

Commits
- [[31f49eb](https://github.com/UC-Davis-molecular-computing/scadnano/commit/31f49eb7864f92d5c372ebebdefceba2003732d3)]: closes #442; add option to right-click on helix away from circle in main view (e.g., on gray lines, or the white space in between them) to bring up the context menu; WARNING: currently only works when not in backbone mode (David Doty) [452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[a52093a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/a52093ab66eef5225ff3adb0beedee34708106d0)]: updated README to point at simpler URL in Python library README (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[821ccff](https://github.com/UC-Davis-molecular-computing/scadnano/commit/821ccfffe3a750322d2983cef10b76b00ade618c)]: fixed context menu for right-clicking on helix lines/white offset squares, even when in backbone mode (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[8fe1506](https://github.com/UC-Davis-molecular-computing/scadnano/commit/8fe15060f4d5c719bc6bcb73964f8be2e5c422a6)]: Create 2_helix_origami.sc (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[30f4f38](https://github.com/UC-Davis-molecular-computing/scadnano/commit/30f4f38c8d30b1d69d5c00a20e64da4541b6f37b)]: add view option to show length of loopout next to loopout; closes #426 (rishabhmudradi) [443](https://github.com/UC-Davis-molecular-computing/scadnano/pull/443)
- [[6e50857](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6e50857f9416a7bbf5ebe60843467f923c33cf22)]: updated examples (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[3f9e221](https://github.com/UC-Davis-molecular-computing/scadnano/commit/3f9e2213417beca04686afcd2da20e0eb24a628a)]: fixes #414; make copy/paste "anchor" be top left even when y-axis is inverted (David Doty) [452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[4d2142b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4d2142b5c8a3c9312b6f1d67c973c5b6534613fe)]: changed footer display from "substrand length" to "domain length" (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[96698c0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/96698c06aa2d237af9539b0656bd7bbfc6666792)]: Update 2_helix_origami.sc (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[e403526](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e40352607900614ca4c2e0ca9375561abc26a2ef)]: Disable redux dev tools for release (Benjamin Lee) [#444](https://github.com/UC-Davis-molecular-computing/scadnano/pull/444)
- [[6092209](https://github.com/UC-Davis-molecular-computing/scadnano/commit/60922095e01d0527adc87ee2518d4ca9571338ca)]: Updating required issues (rishabhmudradi) [#443](https://github.com/UC-Davis-molecular-computing/scadnano/pull/443)
- [[31777c1](https://github.com/UC-Davis-molecular-computing/scadnano/commit/31777c14490656bcacc2853cee6f782cf32d3688)]: Adding new design_main_loopout_length class (rishabhmudradi) [#443](https://github.com/UC-Davis-molecular-computing/scadnano/pull/443)
- [[ddbdab1](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ddbdab1b8356bd9179d209169233d1c7332b44f8)]: Adding css_selector called loopout_length (rishabhmudradi) [#443](https://github.com/UC-Davis-molecular-computing/scadnano/pull/443)
- [[1bef1e2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/1bef1e2e3b9192fafd7b81f26854a77ebc4ea770)]: Merge branch 'dev' into add-view-option-to-show-length-of-loopout-next-to-loopout (David Doty) [#443](https://github.com/UC-Davis-molecular-computing/scadnano/pull/443)
- [[f0ae4bc](https://github.com/UC-Davis-molecular-computing/scadnano/commit/f0ae4bcdb57082c43299ce9d1665d35b37e3fae1)]: Merge branch 'dev' into add-view-option-to-show-length-of-loopout-next-to-loopout (rishabhmudradi) [#443](https://github.com/UC-Davis-molecular-computing/scadnano/pull/443)
- [[e77e54d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e77e54d820f5b24e12df65c21e95ce0d724eb0e9)]: Removing loopout parameter (rishabhmudradi) [#443](https://github.com/UC-Davis-molecular-computing/scadnano/pull/443)
- [[e29933a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e29933a2e61d0f14726dda08f6bf62f39ff439c1)]: Update README.md (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[d8d004c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d8d004c76151c1a895dd2f2d2f7f14bd1afc621f)]: removed redundant imports (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[a4146b7](https://github.com/UC-Davis-molecular-computing/scadnano/commit/a4146b73ce03d7902efe658a62113d161474f0ce)]: Fixes #436; properly display cached PNG of DNA sequences, when some helix group is translated to negative y position; Fixes 438; exported SVG main set bounding box just large enough to contain elements (Benjamin Lee) [448](https://github.com/UC-Davis-molecular-computing/scadnano/pull/448)
- [[79c2d35](https://github.com/UC-Davis-molecular-computing/scadnano/commit/79c2d35d09043f2c33d26484a71e78079d4939e2)]: Update CONTRIBUTING.md (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[78eaff8](https://github.com/UC-Davis-molecular-computing/scadnano/commit/78eaff85a81335ed742407900aab74458d5f69ff)]: added two examples (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[466202a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/466202aa2b17cd2a4611daca1e52e5d11b0cc8fd)]: changed default inter-helix gap to be 1 nm (previously was 0.5 nm) (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[83f35f9](https://github.com/UC-Davis-molecular-computing/scadnano/commit/83f35f9df53e466941975a5093a8c0b765f720ac)]: updated Design constructor to allow geometry to be specified; fixed unit tests to be less brittle about geometry parameters (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[16e3d60](https://github.com/UC-Davis-molecular-computing/scadnano/commit/16e3d60bb28781685ac2204b345e3a148ca84623)]: disabled Google analytics on localhost (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)
- [[e4b4db4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e4b4db42024fc5d232421a683d3872153e00b4e5)]: bumped version (David Doty) [#452](https://github.com/UC-Davis-molecular-computing/scadnano/pull/452)