Fix unet loading issue - Githubissues

AbigailMcGovern / iterseg

napari plugin for iteratively improving 3D instance segmentation of cells (u-net x watershed)

BSD 3-Clause "New" or "Revised" License

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Fix unet loading issue #14

Closed AbigailMcGovern closed 9 months ago

AbigailMcGovern commented 9 months ago

Changes:

Upload newest version of unet
changed options.package data in setup.cfg to include unet in distribution

AbigailMcGovern commented 9 months ago

ping @jni

jni commented 9 months ago

Gah, still getting the error. For reference here's what I'm doing to test it:

build this package with python -m build .
install the built package (not in-place) with pip install dist/iterseg-0.0.10-py3-none-any.whl
launch napari with napari --plugin napari-ome-zarr path/to/platelets-image.zarr
launch iterseg / segment platelets
click run

Also .whl's are just zip files so after the build step you can just cd dist; unzip iterseg-0.0.10-py3-none-any.whl and see whether the unet is there...

Got a meeting now but will look again later... I don't know off the top of my head why it's still not getting packaged.

jni commented 9 months ago

Ok this commit seems informative 🤣

https://github.com/jni/platelet-unet-watershed/commit/66aab7620d2e1646e3d4d33fe85c1691c63353cb

tldr make sure you have a MANIFEST.in file and include the data directory there.

You are probably wondering why you need to specify to include this thing in so many places, and you would be right to wonder that. 🤣 I have no earthly idea.

jni commented 9 months ago

(And make sure you include the LICENSE file as well.)

jni commented 9 months ago

btw this is reasonably urgent because the reviewers at some point will be testing the package and it should work! 😬

jni commented 9 months ago

@AbigailMcGovern I don't want to merge this until the zarrs are gone. 😅

btw am I to understand that your unet is numbered YYDDMM? Because that is crazy 😂