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AllenCell / napari-allencell-segmenter

A plugin that enables image segmentation provided by Allen Institute for Cell Science
BSD 3-Clause "New" or "Revised" License
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Need to support aicsimageio v4 #117

Closed schoinh closed 3 years ago

schoinh commented 3 years ago

Description

At the end of June, the aicsimageio napari plugin (napari-aicsimageio) started to use aicsimageio v4 under the hood, but the aicsimageio version we use for this segmenter plugin is pinned to <4. This makes the napari plugins napari-aicsimageio and napari-allencell-segmenter incompatible to use together.

Fixing this bug might also resolve #116

Expected Behavior

napari-allencell-segmenter needs to support aicsimageio v4

Reproduction

  1. Install and open napari in a fresh virtual environment
  2. Install the napari-aicsimageio plugin
  3. Install the napari-allencell-segmenter plugin
  4. Open the "Show status" button in the napari plugin installation window. Error message as follows: 
    ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
napari-aicsimageio 0.3.5 requires aicsimageio[all]~=4.0.2, but you have aicsimageio 3.3.7 which is incompatible.
Successfully installed aicsimageio-3.3.7 aicspylibczi-2.8.0 napari-allencell-segmenter-1.0.3 readlif-0.3.1

    You can see above that installing napari-allencell-segmenter downgrades aicsimageio in the virtual environment from v4 to v3.3.7.

Environment

Reproduced on Mac/Python 3.9 and Windows

Originally posted by @schoinh in https://github.com/AllenCell/napari-allencell-segmenter/issues/116#issuecomment-897887946

yrkim98 commented 3 years ago

This is fixed if we unpin the <4 version on aicsimageio in the napari-aicssegmentation repo

schoinh commented 3 years ago

Great. I'll close this issue then!