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https://github.com/rust-bio/rust-bio
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
https://github.com/rust-bio/rust-bio
Last synced: about 2 months ago
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This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
- Host: GitHub
- URL: https://github.com/rust-bio/rust-bio
- Owner: rust-bio
- License: mit
- Created: 2015-01-25T16:40:31.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2024-07-22T15:01:16.000Z (about 2 months ago)
- Last Synced: 2024-07-23T13:17:14.968Z (about 2 months ago)
- Language: Rust
- Homepage: https://rust-bio.github.io
- Size: 2.64 MB
- Stars: 1,548
- Watchers: 71
- Forks: 202
- Open Issues: 104
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.md
Awesome Lists containing this project
- Awesome-Bioinformatics - Rust-Bio - Rust implementations of algorithms and data structures useful for bioinformatics. [ [paper-2016](http://bioinformatics.oxfordjournals.org/content/early/2015/10/06/bioinformatics.btv573.short?rss=1) ] (Package suites)
README
[](https://crates.io/crates/bio)
[](https://crates.io/crates/bio)
[](https://crates.io/crates/bio)
[](https://github.com/rust-bio/rust-bio/actions/workflows/rust.yml)
[](https://coveralls.io/github/rust-bio/rust-bio)
[](https://zenodo.org/badge/latestdoi/29821195)
# 
Rust-Bio, a bioinformatics library for Rust.
This library provides [Rust](https://www.rust-lang.org) implementations of algorithms and data structures useful for bioinformatics.
All provided implementations are rigorously tested via continuous integration.
**Please see the [API documentation](https://docs.rs/bio) for available features and examples of how to use them.**
When using Rust-Bio, **please cite** the following article:
[Köster, J. (2016). Rust-Bio: a fast and safe bioinformatics library. Bioinformatics, 32(3), 444-446.](http://bioinformatics.oxfordjournals.org/content/early/2015/10/06/bioinformatics.btv573.short?rss=1)
Further, you can cite the used versions via DOIs:
Rust-Bio: [](https://zenodo.org/badge/latestdoi/29821195)
## Contribute
Any contributions are welcome, from a simple bug report to full-blown new modules:
If you **find a bug** and don't have the time or in-depth knowledge to fix it, just [check if you can add info to an existing issue](https://github.com/rust-bio/rust-bio/issues) and otherwise [file a bug report](https://github.com/rust-bio/rust-bio/issues/new/choose) with as many infos as possible.
Pull requests are welcome if you want to contribute fixes, documentation, or new code. Before making commits, it would be helpful to first install `pre-commit` to avoid failed continuous integration builds due to issues such as formatting:
1. Install `pre-commit` (see [pre-commit.com/#installation](https://pre-commit.com/#installation))
2. Run `pre-commit install` in the rust-bio base directory
Depending on your intended contribution frequency, you have two options for opening pull requests:
1. For one-time contributions, simply [fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the repository, apply your changes to a branch in your fork and then open a pull request.
2. If you plan on contributing more than once, become a contributor by saying hi [on the `rust-bio` Discord server](https://discord.gg/rssQABT),
Together with a short sentence saying who you are and mentioning what you want to contribute.
We'll add you to the team.
Then, you don't have to create a fork, but can simply push new branches into the main repository and open pull requests there.
If you want to contribute and don't know where to start, have a look at the [roadmap](https://github.com/rust-bio/rust-bio/issues/3).
### Documentation guidelines
Every public function and module should have [documentation comments](https://doc.rust-lang.org/stable/rust-by-example/meta/doc.html).
Check out [which types of comments to use where](https://doc.rust-lang.org/stable/reference/comments.html#doc-comments).
In `rust-bio`, documentation comments should:
* [explain functionality](https://doc.rust-lang.org/rustdoc/how-to-write-documentation.html)
* give at least one useful example of how to use it (best as [doctests](https://doc.rust-lang.org/rustdoc/documentation-tests.html),
that run during testing, and using descriptive [`expect()`](https://doc.rust-lang.org/std/result/enum.Result.html#method.expect)
statements for handling any `Err()`s that might occur)
* describe time and memory complexity listed (where applicable)
* cite and link sources and explanations for data structures, algorithms or code (where applicable)
For extra credit, feel free to familiarize yourself with:
* the Rust [documentation conventions](https://rust-lang.github.io/rfcs/1574-more-api-documentation-conventions.html#appendix-a-full-conventions-text)
* the Rust [API documentation guidelines](https://rust-lang.github.io/api-guidelines/documentation.html)
## Minimum supported Rust version
Currently the minimum supported Rust version is 1.65.0.
## License
Licensed under the MIT license http://opensource.org/licenses/MIT. This project may not be copied, modified, or distributed except according to those terms.