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Koeng101 committed Dec 7, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- `fastq` now handles optionals correctly [(#323)](https://github.com/TimothyStiles/poly/issues/323)
- Adds functional test and fix for [(#313)](https://github.com/TimothyStiles/poly/issues/313).
- In addition to expanding the set of genbank files which can be validly parsed, the parser is more vocal when it encounters unusual syntax in the "feature" section. This "fail fast" approach is better as there were cases where inputs triggered a codepath which would neither return a valid Genbank object nor an error, and should help with debugging.
- Fixed bug that produced wrong overhang in linear, non-directional, single cut reactions. #408

## [0.26.0] - 2023-07-22
Oops, we weren't keeping a changelog before this tag!
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2 changes: 1 addition & 1 deletion CODE_OF_CONDUCT.md
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Expand Up @@ -61,7 +61,7 @@ representative at an online or offline event.

Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the community leaders responsible for enforcement at
[INSERT CONTACT METHOD].
[email protected]
All complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the
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6 changes: 2 additions & 4 deletions CONTRIBUTING.md
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Expand Up @@ -60,8 +60,6 @@ As one final guideline please be welcoming to newcomers and encourage new contri

Unsure where to begin contributing to Poly? You can start by looking through these beginner and help-wanted issues:

[Beginner issues](https://github.com/TimothyStiles/poly/issues?q=is%3Aissue+is%3Aopen+label%3A%22beginner%22+) - issues which should only require a few lines of code, and a test or two.

[Good first issues](https://github.com/TimothyStiles/poly/contribute) - issues which are good for first time contributors.

[Help wanted issues](https://github.com/TimothyStiles/poly/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22+) - issues which should be a bit more involved than beginner issues.
Expand Down Expand Up @@ -109,14 +107,14 @@ Additionally, you may want to [install](https://golangci-lint.run/usage/install/

### Security disclosures

If you find a security vulnerability, do NOT open an issue. I've yet to set up a security email for this so please in the interim DM me on twitter for my email [@timothystiles](https://twitter.com/TimothyStiles).
If you find a security vulnerability, do NOT open an issue. Instead, email [email protected] with a description of the vulnerability and we will get in contact with you ASAP.

In order to determine whether you are dealing with a security issue, ask yourself these two questions:

* Can I access something that's not mine, or something I shouldn't have access to?
* Can I disable something for other people?

If the answer to either of those two questions are "yes", then you're probably dealing with a security issue. Note that even if you answer "no" to both questions, you may still be dealing with a security issue, so if you're unsure, just DM me [@timothystiles](https://twitter.com/TimothyStiles) for my personal email until I can set up a security related email.
If the answer to either of those two questions are "yes", then you're probably dealing with a security issue. Note that even if you answer "no" to both questions, you may still be dealing with a security issue, so if you're unsure, shoot an email to [email protected].

### Non-security related bugs

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29 changes: 9 additions & 20 deletions README.md
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# (Poly)merase <img align="right" src="https://cdn.discordapp.com/attachments/766785755305213953/777596834734145546/ProfileFrameArtboard_1.png" width="100">

[![PkgGoDev](https://pkg.go.dev/badge/github.com/TimothyStiles/poly)](https://pkg.go.dev/github.com/TimothyStiles/poly)
[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/TimothyStiles/poly/blob/main/LICENSE)
![Tests](https://github.com/TimothyStiles/poly/workflows/Test/badge.svg)
![Test Coverage](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/TimothyStiles/e58f265655ac0acacdd1a38376ccd32a/raw/coverage.json)
[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/koeng101/poly/blob/main/LICENSE)
![Tests](https://github.com/koeng101/poly/workflows/Test/badge.svg)
![Test Coverage](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/koeng101/e58f265655ac0acacdd1a38376ccd32a/raw/coverage.json)

Poly is a Go package for engineering organisms.
Poly is a Go package for engineering organisms. This is a fork of the main poly project incorporating more features and bug fixes.

* **Fast:** Poly is fast and scalable.

* **Modern:** Poly tackles issues that other libraries and utilities just don't. From general codon optimization and primer design to circular sequence hashing. All written in a language that was designed to be fast, scalable, and easy to develop in and maintain. Did we say it was fast?

* **Reproducible:** Poly is well tested and designed to be used in industrial, academic, and hobbyist settings. No more copy and pasting strings into random websites to process the data you need.

* **Ambitious:** Poly's goal is to be the most complete, open, and well used collection of computational synthetic biology tools ever assembled. If you like our dream and want to support us please star this repo, request a feature, open a pull request, or [sponsor the project](https://github.com/sponsors/TimothyStiles).
* **Ambitious:** Poly's goal is to be the most complete, open, and well used collection of computational synthetic biology tools ever assembled. If you like our dream and want to support us please star this repo, request a feature, or open a pull request.


## Install

`go get github.com/TimothyStiles/poly@latest`
`go get github.com/koeng101/poly@latest`

## Documentation


* **[Library](https://pkg.go.dev/github.com/TimothyStiles/poly#pkg-examples)**
* **[Library](https://pkg.go.dev/github.com/koeng101/poly#pkg-examples)**

* **[Tutorials](https://github.com/TimothyStiles/poly/tree/main/tutorials): ([live](https://gitpod.io/#tutorial=true/https://github.com/TimothyStiles/poly) | [github](https://github.com/TimothyStiles/poly/tree/main/tutorials))**

* **[Learning Synbio](https://github.com/TimothyStiles/how-to-synbio)**

## Community

* **[Discord](https://discord.gg/Hc8Ncwt):** Chat about Poly and join us for game nights on our discord server!
* **[Tutorials](https://github.com/koeng101/poly/tree/main/tutorials)**

## Contributing

* **[Code of conduct](CODE_OF_CONDUCT.md):** Please read the full text so you can understand what we're all about and remember to be excellent to each other!

* **[Contributor's guide](CONTRIBUTING.md):** Please read through it before you start hacking away and pushing contributions to this fine codebase.

## Sponsor

* **[Sponsor](https://github.com/sponsors/TimothyStiles):** 🤘 Thanks for your support 🤘

## License

* [MIT](LICENSE)

* Copyright (c) 2023 Timothy Stiles
* Copyright (c) 2023 Keoni Gandall, Timothy Stiles
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