unifrac - Add unweighted_unnormalized method and dense pair interface

What's Changed

• Add support for unweighted_unnormalized by @sfiligoi in https://github.com/biocore/unifrac/pull/164
• Add support for the dense pair interface by @sfiligoi in https://github.com/biocore/unifrac/pull/166
• It now properly builds on ARM-based MacOS

Full Changelog: https://github.com/biocore/unifrac/compare/1.3.2...1.5

- Python
Published by sfiligoi 10 months ago

unifrac - Minor, release automation

What's Changed

• add release automation by @wasade in https://github.com/biocore/unifrac/pull/163

Full Changelog: https://github.com/biocore/unifrac/compare/1.3.1...1.3.2

- Python
Published by wasade 11 months ago

unifrac - Maintenance

What's Changed

• Switch h5unifrac_all to lazy load semantics by @sfiligoi in https://github.com/biocore/unifrac/pull/155
• Remove extraneous str casts by @wasade in https://github.com/biocore/unifrac/pull/159
• Update arguments name used in beta_diversity in tests by @eamanu in https://github.com/biocore/unifrac/pull/160
• unifrac.faith_pd now accepts in memory objects by @wasade in https://github.com/biocore/unifrac/pull/162
• CSC representation bug fixed by @wasade in https://github.com/biocore/unifrac/pull/162, see also https://github.com/biocore/unifrac/issues/161
• Additional table validations by @wasade in https://github.com/biocore/unifrac/pull/162, see also https://github.com/biocore/unifrac/issues/34
• Test on OSX Intel (macos-13) and OSX Arm64 (macos-14) in GitHub Actions, deprecate Python 3.8, add Python 3.12, switch from nose to pytest, by @wasade in https://github.com/biocore/unifrac/pull/162

New Contributors

• @eamanu made their first contribution in https://github.com/biocore/unifrac/pull/160

Full Changelog: https://github.com/biocore/unifrac/compare/1.3...1.3.1

- Python
Published by wasade 11 months ago

unifrac - Add support for subsampling, PERMANOVA and multi-unifrac

What's Changed

• Add support for multi unifrac to file by @sfiligoi in https://github.com/biocore/unifrac/pull/151 and https://github.com/biocore/unifrac/pull/152
• Add PERMANOVA and multi-object h5 reads by @sfiligoi in https://github.com/biocore/unifrac/pull/150 and https://github.com/biocore/unifrac/pull/153

Full Changelog: https://github.com/biocore/unifrac/compare/1.2...1.3

- Python
Published by sfiligoi almost 3 years ago

unifrac - Change default precision and deprecate the threads argument

What's Changed

• Deprecate threads and add n_substeps by @sfiligoi in https://github.com/biocore/unifrac/pull/146
• Switch from condensed to matrix API calls by @sfiligoi in https://github.com/biocore/unifrac/pull/147
• Change default precision to fp32 and add explicit fp64 functions by @sfiligoi in https://github.com/biocore/unifrac/pull/148

Full Changelog: https://github.com/biocore/unifrac/compare/1.1.1...1.2

- Python
Published by sfiligoi about 3 years ago

unifrac - Bug fix for compatibility with biom-format 2.1.12

What's Changed

• Expand build matrix by @wasade in https://github.com/biocore/unifrac/pull/144

Full Changelog: https://github.com/biocore/unifrac/compare/1.1.0...1.1.1

- Python
Published by wasade almost 4 years ago

unifrac - Provide in-memory support against unifrac-binaries

What's Changed

• Support for passing biom and the tree in memory by @wasade in https://github.com/biocore/unifrac/pull/142

Full Changelog: https://github.com/biocore/unifrac/compare/1.0.0...1.1.0

- Python
Published by wasade almost 4 years ago

unifrac - Release associated with manuscript describing OpenACC improvements

This is a historical release documenting the code used for benchmarking the OpenACC release. We advise using the latest version of this software. Details for install, including a functional example, can be found here.

- Python
Published by wasade about 4 years ago

unifrac - Python-only repo, depends on unifrac-binaries

Since the python binding and the backend implementation evolve independently, the sucpp code was moved into an independent repo (unifrac-binaries). This repo now only contains the python bindings.

- Python
Published by sfiligoi about 4 years ago

unifrac - Bug fix for massive PCoA and simplified build

As the title says, thanks @sfiligoi!!

- Python
Published by wasade over 4 years ago

unifrac - Automatic PCoA compute

This release improves documentation and automatic PCoA computation

- Python
Published by wasade about 5 years ago

unifrac - Cache locality, and other performance improvements

This release brings substantial performance improvements to UniFrac for CPUs and GPUs thanks to @sfiligoi's incredible rework of the underlying algorithms and implementations, as well as a few minor bug fixes.

- Python
Published by wasade over 5 years ago

unifrac - GPU optimization, performance improvements, binary output

With this release, we expose the ability to apply UniFrac to GPUs with upwards of 500x performance gains. More detail on the optimization can be found in an arXiv post, made possible thanks to the incredible efforts from @sfiligoi! While the primary focus was the adaption to GPUs, many of the improvements extend to CPUs as well.

Thank you as well to @gwarmstrong and @ChrisKeefe for contributions and testing over the past year since the last release!

- Python
Published by wasade over 5 years ago

unifrac - 0.10.0: Faith's PD and bug fixes

New Features:

• High-performance calculation of Faith's PD. See PR's #65, #70 and #93.

Bug fixes:

• Segmentation faults were occuring in ssu depending upon the order that threads started execution. See #63. This issue has been fixed.

- Python
Published by ElDeveloper over 6 years ago

unifrac - 0.9.3 checkpoint release

Incorporating API examples, and improved error checking.

- Python
Published by wasade over 7 years ago

unifrac - 0.9.2 conda build support

- Python
Published by ElDeveloper over 8 years ago

unifrac - 0.9.1, conda-build support

- Python
Published by wasade over 8 years ago

unifrac - 0.9.0 UniFrac release

- Python
Published by ElDeveloper over 8 years ago

unifrac - state UniFrac

- Python
Published by ElDeveloper over 8 years ago