v0.10.1

Mostly documentation was updated.

Commits

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

v0.10.0

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, which is software for biological DNA, and for .sc, it's SuperCollider, 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]: updated name of function from main() to create_design() in example script in README (David Doty) #118
• [6db03e8]: changed name of function main() to create_design() in tutorial (David Doty) #118
• [b4548da]: modified intro to README (David Doty) #118
• [d0b58d2]: updated tutorial to link directly to raw design file (David Doty) #118
• [f87b219]: fixes #110; updated default file extension from .dna to .sc (David Doty) #118
• [5f9bf45]: closes #91; BREAKING CHANGE: change DNADesign class name to Design (David Doty) #118

v0.9.10

Not much changed; this release was to test the automated publishing of the package to PyPI through a new GitHub Action.

Commits

• [a0e9f7f]: updated installation instructions with detailed pip cases (David Doty) #115
• [358e389]: corrected grammar in README (David Doty) #115
• [d8249ae]: updated README instructions on using Python 3.6 (David Doty) #115
• [4992423]: Setup workflow to publish to PyPI (Benjamin Lee) #114
• [a3e6b1c]: bumped version to test automated package updating on PyPI (David Doty) #115
• [b3a880e]: Append python publish to release workflow (Benjamin Lee) #116

v0.9.9

This release supports Python version 3.6, if the dataclasses backport package is also installed. See the installation instructions for details.

Commits

• [c2b3b1d]: removed <ins> tag from README (for underlining name of paper) since PyPI doesn't recognize it (David Doty) #112
• [54f0e12]: added note to README that relative links do not work when viewing on PyPI (David Doty) #112
• [385fb29]: added mypy directory to .gitignore, added squarenut design to examples, updated README on using Python 3.6, and fixed a few mypy warnings in scadnano.py (David Doty) #112
• [8be2817]: to support Python 3.6, replaced forward annotations with pre-3.7 string-based hack; bumped version (David Doty) #112
• [054a8bf]: updated examples to v0.9.9 (David Doty) #112

v0.9.8

Forgot to bump version number in source code in last release, so doing it now.

Commits

• [4a3abae]: bumped version (David Doty) #106

v0.9.7

Just trying to test out some new repo settings. Note the version number is not updated in the source code because I forgot. The next version will fix that.

Commits

• [57a1eae]: changed comment on rise_per_base_pair (David Doty) #105
• [a081e59]: fixed newline in README (David Doty) #105
• [12ff50d]: removed requirements.txt (David Doty) #105
• [a4d2bcd]: added CODEOWNERS for protected branches PR review requests (David Doty) #105
• [dff2ec8]: added very large origami example (David Doty) #105
• [58bb6bc]: fixed example code in README to reference design.scaffold (David Doty) #105
• [85d0f9d]: changed to relative links to Python files in installation by download method in README, so viewing the README in another branch will link to the version in that branch (David Doty) #105

v0.9.6

Commits

• [24ff64f]: bumped version and updated doc/requirements.txt in response to dependabot alerts (David Doty) #103

v0.9.5

Based on this: readthedocs/readthedocs.org#4868, seems like "latest" tag is confusing readthedocs. This release fixes that.

v0.9.4

Commits

• [128baa0]: ignoring dist/ directory from now on (where PyPI .tar.gz files are created) (David Doty) #98
• [0b830a2]: removed dist/ directory from tracking (David Doty) #98
• [c3e2c12]: add with_domain_label for method chaining; closes #93 (David Doty) #98
• [18ba037]: corrected README link to write_idt_plate_excel_file (David Doty) #98
• [8d86dff]: updated citation for paper from arXiv to DNA 26 (David Doty) #98
• [fed5149]: bumped version (David Doty) #98

v0.9.3

Commits

• [c4db84a]: bumped version from 0.9.2 to 0.9.3 (David Doty) #97