Review dependencies in setup.cfg

[imagejan]

This commit tries to list all direct dependencies explicitly.

This is what running pixi x pipreqs .\src produces:

dask==2025.3.0
magicgui==0.10.0
multiscale_spatial_image==2.0.2
multiview_stitcher==0.1.23
napari==0.5.6
networkx==3.4.2
numpy==2.2.4
pytest==8.3.5
qtpy==2.4.3
spatial_image==1.2.1
tifffile==2025.3.30
tqdm==4.67.1
xarray==2025.3.1

The multiview-stitcher[aicsimageio] dependency moves to the test dependencies, as it's only required to load test data.

[m-albert]

Thanks a lot for this @imagejan!

Cleaning the dependencies and making them more explicit is definitely needed here. I'll have a look at the CI errors, most likely towards end of the week.

[imagejan]

Hi @m-albert,

sorry, the previous commit had a typo in aicsimageio and didn't install the required test dependency. If you approve again, I can see if my changes pass now.

I was digging into it because I had issues installing napari-stitcher in a pixi project where I couldn't find versions of aicsimageio compatible with the requirements of other packages, hence this pull request trying to improve the situation. (I guess in the long term, multiview-stitcher might want to switch to bioio as a dependency for test data.)

[imagejan]

Great, all tests still pass 🙂

@m-albert would you be willing to merge this and then cut and deploy a patch release? This would simplify installation on our end..

[m-albert]

sorry, the previous commit had a typo in aicsimageio and didn't install the required test dependency. If you approve again, I can see if my changes pass now.

I changed the settings so that your PRs shouldn't need approval anymore.

I was digging into it because I had issues installing napari-stitcher in a pixi project where I couldn't find versions of aicsimageio compatible with the requirements of other packages, hence this pull request trying to improve the situation. (I guess in the long term, multiview-stitcher might want to switch to bioio as a dependency for test data.)

Interesting. I agree that bioio would be preferable and we had already migrated to it (with the help of @joshua-gould here), however there had been dependency resolution problems (which unfortunately I can't reconstruct anymore, I wonder whether they're similar to the ones you're experiencing right now with aicsimageio). Probably the best will be to move reading of czi files outside of multiview-stitcher and napari-stitcher (and convert example data to a different format, e.g. OME-Zarr v4 as the only directly supported file format).

[m-albert]

Great, all tests still pass 🙂

Nice!

@m-albert would you be willing to merge this and then cut and deploy a patch release? This would simplify installation on our end..

Definitely! I'd only change one thing, namely to remove napari from the install_requires (it's only needed in testing).

[imagejan]

We have:

napari-stitcher/src/napari_stitcher/_mosaic_widget.py

Line 14 in 1c0f2dc

from napari.utils import notifications

napari-stitcher/src/napari_stitcher/_stitcher_widget.py

Line 15 in 1c0f2dc

from napari.utils import notifications

napari-stitcher/src/napari_stitcher/_stitcher_widget.py

Line 27 in 1c0f2dc

from napari.layers import Image, Labels

napari-stitcher/src/napari_stitcher/_utils.py

Line 8 in 1c0f2dc

from napari.utils import progress

napari-stitcher/src/napari_stitcher/viewer_utils.py

Lines 15 to 16 in 1c0f2dc

	from napari.experimental import link_layers
	from napari.utils import notifications

... so we indeed require napari (but not pyqt or any other UI package) to be present.

[m-albert]

I'd only change one thing, namely to remove napari from the install_requires (it's only needed in testing).

Sorry I got confused, this is wrong! Merging and creating a patch release.

[m-albert]

Yes you are completely right, thanks for showing the occurrences.

[imagejan]

Thank you for the super fast response! 🚀

[m-albert]

Release is out, thank you for contributing :)

[m-albert]

I was digging into it because I had issues installing napari-stitcher in a pixi project where I couldn't find versions of aicsimageio compatible with the requirements of other packages, hence this pull request trying to improve the situation. (I guess in the long term, multiview-stitcher might want to switch to bioio as a dependency for test data.)

Actually I recently stumbled upon the same issue. FYI the aicsimageio dependency is now entirely optional (and not required for testing) both in multiview-stitcher>=0.1.24 and napari-stitcher>=0.1.2.