numpy 2.0-compatible skan package not on PyPI

[GuillaumeLeGoc]

Hi,
First and foremost, thanks a lot for this package.

I just got a bunch of errors with numpy 2.0 with skan 0.11.1. I see that numpy 2 compatibility was added in #229, but it seems it was not published on PyPI.
I'm working on something that will require skan as a dependency and was wondering if you were planning to make a release, and if so, with what timeline ? To see if I need to pin numpy to <2 in my project.

Cheers,
Guillaume

[GuillaumeLeGoc]

Additional note :
I installed the current git version with pip install git+https://github.com/jni/skan.git, using Skeleton and summarize (with separator="_" to avoid warnings) worked as intended 😄

[jni]

Ach, yeah, sorry @GuillaumeLeGoc, I have been trying to get #214 past the finish line, but it's stuck on a bug I couldn't figure out, and haven't had time to revisit since the last time I played with it.

I'll just push out a release tomorrow without it, and pruning will have to wait for the next one.

Thanks for the prod, sorry for the wait, and thank you for your interest in skan! 😊

[GuillaumeLeGoc]

Alright, thanks for your reply. And good luck for the iterative pruning !

[jni]

Ach, sorry, I'm travelling and this once again fell off the plate 😅, thanks for the prod, will push ASAP!

[jni]

@GuillaumeLeGoc the pre-release version 0.12.0rc2 is out on PyPI for testing. You can test it with pip install skan==0.12.0rc2 or pip install -U --pre skan. The release notes are at https://skeleton-analysis.org/dev/misc/release-notes/release-v0.12.html. Please let me know if it's all working for you and I'll push the actual release!

[GuillaumeLeGoc]

Hi, thanks for the RC !
My usage is fairly simple, I skeletonize a binary image with scikit-image morphology.skeletonize, remove small objects with morphology.remove_small_objects, and instantiate skan.Skeleton. Then, from skan.summarize(skeleton, separator="_"), I collect each branches path_coordinates in shapely.LineString objects, to finally store them with geojson.Feature and geojson.FeatureCollection.

With skan 0.12.0rc2, I was able to generate identical geojson files as with the previous version, so all is good for me, cheers !
Let me know if you want me to run other tests.

[jni]

Let me know if you want me to run other tests.

Nope, that's all good, with smaller projects I go with just-in-time user testing, meaning as long as it works for you I'm happy to push, and if anything else is broken I'll fix as other users complain. 😅

0.12 is out now on PyPI, and should be out on conda-forge in ~24h. Happy coding, and do let me know if you run into other issues!

[GuillaumeLeGoc]

Nice philosophy 😄
Thanks a lot for your responsiveness, cheers !