scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
We're very excited to announce scikit-bio 0.5.0. scikit-bio is no longer compatible with Python 2. scikit-bio is compatible with Python 3.4 and later. This is a maintenance release containing a number of bug fixes and minor improvements.
You can review the CHANGELOG.md for a complete description of the changes in this release. To learn about what you can do with scikit-bio, you should browse our (awesome!) API documentation.
Be sure to follow @scikitbio on twitter for project updates, and as always, thanks for your interest in scikit-bio!
We're very excited to announce scikit-bio 0.4.2. This is the last Python 2.7 compatible release. Future scikit-bio releases will only support Python 3. This is a maintenance release containing a number of bug fixes, as well as support for reading and writing Stockholm files.
You can review the CHANGELOG.md for a complete description of the changes in this release. To learn about what you can do with scikit-bio, you should browse our (awesome!) API documentation.
Be sure to follow @scikitbio on twitter for project updates, and as always, thanks for your interest in scikit-bio!
We're very excited to announce scikit-bio 0.4.1. This release introduces several big new features, including the new TablularMSA object which has replaced the Alignment object, the addition of phylogenetic diversity metrics (unweighted UniFrac, weighted UniFrac, and Faith's Phylogenetic Diversity), and a lot more.
You can review the CHANGELOG.md for a complete description of the changes in this release. To learn about what you can do with scikit-bio, you should browse our (awesome!) API documentation.
We expect that scikit-bio 0.4.1 will be the last release that includes Python 2.7 support. In our next release we'll be transitioning to Python 3 only, as discussed in RFC 2.
Be sure to follow @scikitbio on twitter for project updates, and as always, thanks for your interest in scikit-bio!
We're extremely excited to announce the first beta release of scikit-bio, version 0.4.0, from SciPy 2015 in Austin, TX! This is a major release in which the following subpackages have been mostly or entirely rewritten:
skbio.sequence
skbio.io
These APIs have changed (and improved!) since 0.2.3, and are now considered stable. All other APIs are now considered experimental, and will be stabilizing in our upcoming releases.
Beginning with this release, all aspects of our public API are annotated to indicate their stability so our users are aware of what APIs can be relied on, and which might change. The new API stability docs contain more details, including what we mean by stable and experimental in this context.
We now have a dedicated scikit-bio twitter account, which will be the primary way that we share news about scikit-bio. You should follow @scikitbio on twitter for project updates.
We're also excited to have had some new contributors in this development cycle. Check out our contributors page to see who's involved (and get in touch if you want to get involved - we're interested in working with developers of all skill levels!).
You can review our CHANGELOG.md for a more detailed description of the changes since 0.2.3. To learn about what you can do with scikit-bio, you can browse our (awesome!) documentation or learn some new bioinformatics recipes with the scikit-bio cookbook.
Thanks for your interest in scikit-bio!
This is a minor maintenance release with several important bug fixes affecting:
Alignment.position_frequencies
Alignment.position_entropies
Alignment.omit_gap_positions
Alignment.omit_gap_sequences
BiologicalSequence.k_word_frequencies
SequenceCollection.k_word_frequencies
Please review the CHANGELOG.md for a complete description of these bug fixes and other changes in the release, including a few minor features and usability enhancements.
We're excited to announce the release of scikit-bio 0.2.2. You can review our CHANGELOG.md for a description of the changes since 0.2.1. To learn about what you can do with scikit-bio, you can browse our (awesome!) documentation, watch @gregcaporaso's SciPy 2014 presentation (or just look at the slides), or learn some new bioinformatics recipes with the scikit-bio cookbook.
This is a minor maintenance release to report deprecations via DeprecationWarning instead of UserWarning (see #774). Previously, scikit-bio reported deprecation warnings to users, which wasn't appropriate because these warnings were intended for developers (see Python's deprecation warning docs for more details). Since scikit-bio is still in alpha and the API is in flux, reporting deprecations using DeprecationWarning will (by default) hide these warnings from users, allowing developers more time to update their software to the latest scikit-bio API.
There are also several new features in scikit-bio 0.2.2:
DissimilarityMatrix/DistanceMatrix objects can now be plotted as heatmaps via DissimilarityMatrix.plot (this is the default representation in the IPython Notebook)As this is an alpha release, major backwards-incompatible API changes can and will happen. We are committed to fully documenting all API changes in CHANGELOG.md, and we will attempt to provide deprecation warnings in advance for all API changes.
If you're looking for updates on scikit-bio, you can follow @gregcaporaso on twitter or look for the #skbio hashtag (though unfortunately that's not unique to us). If you have technical support questions, please post them on Stack Overflow and tag as skbio. Before posting on Stack Overflow for the first time, you should be sure to review their guidelines for asking a question. If you have features requests, please post them as issues on our issue tracker.
We're also excited to have had some new contributors in this development cycle. Check out our contributors page to see who's involved (and get in touch if you want to get involved - we're interested in working with developers of all skill levels!).
Thanks for your interest in scikit-bio!
We're excited to announce the release of scikit-bio 0.2.1. You can review our CHANGELOG.md for a description of the changes since 0.2.0. To learn about what you can do with scikit-bio, you can browse our (awesome!) documentation, watch @gregcaporaso's SciPy 2014 presentation (or just look at the slides), or learn some new bioinformatics recipes with the scikit-bio cookbook.
Our main focus in this release is unified input and output (I/O) via an I/O registry system. Previously, there were many ways to read and write various file formats into and out of scikit-bio objects. The scikit-bio I/O registry provides a single entry point to all I/O using a simple procedural interface. Additionally, the registry dynamically generates an equivalent object-oriented API for any scikit-bio object that can be serialized or deserialized. Finally, the registry supports automatic file format detection via file sniffers. See the skbio.io docs for more details on the I/O registry and the benefits it provides. Thanks to the astropy project for the inspiration!
As this is an alpha release, major backwards-incompatible API changes can and will happen. We are committed to fully documenting all API changes in CHANGELOG.md, and we will attempt to provide deprecation warnings in advance for all API changes.
If you're looking for updates on scikit-bio, you can follow @gregcaporaso on twitter or look for the #skbio hashtag (though unfortunately that's not unique to us). If you have technical support questions, please post them on Stack Overflow and tag as skbio. Before posting on Stack Overflow for the first time, you should be sure to review their guidelines for asking a question. If you have features requests, please post them as issues on our issue tracker.
We're also excited to have had some new contributors in this development cycle. Check out our contributors page to see who's involved (and get in touch if you want to get involved - we're interested in working with developers of all skill levels!).
Thanks for your interest in scikit-bio!
We're very excited to present the first alpha release of scikit-bio. You can review our CHANGELOG.md for a description of the changes since 0.1.4. To learn about what you can do with scikit-bio, you can browse our (awesome!) documentation or watch @gregcaporaso's SciPy 2014 presentation (or just look at the slides).
Our main focus in this release was re-organization of a lot of the codebase to make it simpler for our users to work with. As a result, there are many (documented) API changes. We think that these changes make the scikit-bio codebase and documentation much easier to navigate.
As this is an alpha release, major backwards-incompatible API changes can and will happen. We are now committed to fully documenting all API changes in CHANGELOG.md, and we will attempt to provide deprecation warnings in advance for all API changes.
If you're looking for updates on scikit-bio, you can follow @gregcaporaso on twitter or look for the #skbio hashtag (though unfortunately that's not unique to us). If you have technical support questions, please post them on Stack Overflow and tag as skbio. Before posting on Stack Overflow for the first time, you should be sure to review their guidelines for asking a question. If you have features requests, please post them as issues on our issue tracker.
We're also excited to have had some new contributors in this development cycle. Check out our contributors page to see who's involved (and get in touch if you want to get involved - we're interested in working with developers of all skill levels!).
Thanks for your interest in scikit-bio!
This is a candidate alpha release of scikit-bio. You likely do not want to be using this specific release: it is an internal test.
This is another minor, incremental update to the scikit-bio pre-alpha release. You can review our CHANGELOG.md for a description of the changes since 0.1.3.
Please keep in mind that scikit-bio is still a pre-alpha release and that major backwards-incompatible API changes can and will happen. That said, we're excited to have people start using scikit-bio. See our (awesome!) documentation if you're looking to get started with scikit-bio. If you have bug reports or features requests please post them on our issue tracker.
We also now have an skbio tag on Stack Overflow. If you have technical support questions, please post them on Stack Overflow and tag as skbio. Before posting on Stack Overflow for the first time, you should be sure to review their guidelines for asking a question.
Some of the developers (@gregcaporaso, @ElBrogrammer, @adamrp, @ebolyen, and @ElDeveloper) will be attending SciPy 2014 this summer, and @gregcaporaso will be presenting on scikit-bio. Come find us if you're interested!