skan v0.10.0#

This is a major release of skan that changes, removes, or deprecates much functionality. As skan has grown in popularity, we’ve been working hard to clean out the warts and kinks in the API, improve compatibility with libraries such as dask, and fix several bugs reported by users. This has brought one major change in how skan computes branch lengths (#135): junctions are now cleaned up by computing their minimum spanning tree rather than by computing their centroid (see the FAQ). This change can be reverted with a keyword argument in this version (junction_mode='centroid'), but will be mandatory in upcoming versions. If you need to preserve the old results, pin skan to <v0.11.

Thanks to Genevieve Buckley, Marianne Corvellec, Zoltan Csati, Marlene da Vitoria Lobo, and Kevin Yamauchi for their contributions!

API changes#

  • #135: the unique_junctions keyword argument to the Skeleton class is deprecated. Use instead junction_mode. Note however that this option will be removed in 0.11, so you should pin your skan dependency if you need this behavior.

  • #139: the skan GUI and corresponding skan.gui module and skan command have all been removed. A new, much more sophisticated napari plugin is in development at https://github.com/kevinyamauchi/napari-skeleton-curator and will be folded into a future version of skan (probably v0.11).

Improvements#

  • skan tests now pass on GitHub Actions on all platforms (#139).

  • skan documentation is now built and deployed on GitHub Actions (#140).

  • skan releases are created using GitHub Actions (#141).

  • the skan code base is now formatted by yapf (#136).

  • skan is now easier to adapt for dask arrays (though there is still much work to be done here) ((#107, #112 and #123).