Update Echoshader for newer NumPy and Zarr (GSoC 2026)

[LOCEANlloydizard]

Currently, zarr and numpy are pinned to older major versions (zarr>=2,<3 and numpy<2). It would be useful to unpin these and test Echoshader’s notebooks, updating the code where necessary to ensure compatibility with newer versions.

[LOCEANlloydizard]

Hi @Safwannn89, we ran into an error while installing echoshader on the cloud due to dependency issues!
The problem is related to #221, because that PR pins zarr==2.16.1. Sorry that’s my fault, I missed that.

The best approach now would be to align with echopype current dependencies (i.e., zarr>=3 and no pinning on numpy), so that everything remains compatible moving forward.

Would you be happy to make that change and check that the notebooks still run? Sorry again, missed that!

[Safwannn89]

Hi @LOCEANlloydizard, no worries at all! It happens. I will get this updated right away. I'll align the dependencies with echopype by setting zarr>=3 and ensuring numpy is completely unpinned. I will run through all the tutorial notebooks locally to verify everything is fully compatible and stable, and then I'll open a new PR with the fix!

[Safwannn89]

Hi @LOCEANlloydizard! I know you have a very busy schedule right now, so absolutely no rush, but I just wanted to gently ping this PR #242 for whenever you have a free moment. I also sent you a quick email last week with a little more context. Let me know if you need me to adjust anything once you get a chance to review it!

Thanks.