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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
16 stars 6 forks source link

Cannot install napari-allencell-segmenter through napari menu #156

Open Nadalyn-CZI opened 1 year ago

Nadalyn-CZI commented 1 year ago

I am a technical writer working on the documentation for a segmentation tutorial that uses napari-allencell-segmenter.

Description

A clear description of the bug When I try to install napari-allencell-segmenter through the napari menu (plugins>Install/Uninstall), I cannot get it to install. I can install it using pip install and then use it through the menu. One of the developers told me that the plugin tries to downgrade napari to 0.4.15 and this may be causing the problem. I have been using it with 0.4.15 after pip installing it and there don't seem to be any problems with using it, just with installing it.

Error message

There is no error message, the plugin just doesn't install through the napari menu.

Expected Behavior

What did you expect to happen instead? That the plugin would be installed.

Reproduction

Please list the exact steps we can take to reproduce this bug.

  1. Open napari on a Windows machine (I am using Windows 10 Enterprise, Version 10.0.19045, Build 19045).
  2. Go to plugins>install/uninstall and search on allencell.
  3. Select napari-allencell-segmenter.
  4. Click the install button on the right end of the line.
  5. Check for installation. (It never installs.)
  6. Open an Anaconda prompt and use this command: python -m pip install napari==0.4.14
  7. Go back to napari and check for installation.

Environment

yrkim98 commented 1 year ago

Thanks for the report! We're looking into this now and I'll report back soon.

Nadalyn-CZI commented 1 year ago

Thanks for letting me know!

On Mon, May 1, 2023 at 4:30 PM Brian Kim @.***> wrote:

Thanks for the report! We're looking into this now and I'll report back soon.

— Reply to this email directly, view it on GitHub https://github.com/AllenCell/napari-allencell-segmenter/issues/156#issuecomment-1530322557, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3CMNTH4G5QXPB4AI62O6V3XEATPTANCNFSM6AAAAAAXM62BC4 . You are receiving this because you authored the thread.Message ID: @.***>

-- Nadalyn Miller 214-906-5489 personal cell

yrkim98 commented 1 year ago

Caused by this conflict 

The conflict is caused by:
    aicssegmentation 0.5.0 depends on scikit-image<0.19.0 and >=0.18.0
    napari 0.4.17 depends on scikit-image>=0.19.1
    aicssegmentation 0.5.0 depends on scikit-image<0.19.0 and >=0.18.0
    napari 0.4.16 depends on scikit-image>=0.19.1

Resolving this over in aics-segmentation

Nadalyn-CZI commented 1 year ago

Thanks!

On Thu, May 4, 2023 at 11:32 AM Brian Kim @.***> wrote:

Caused by this conflict

The conflict is caused by: aicssegmentation 0.5.0 depends on scikit-image<0.19.0 and >=0.18.0 napari 0.4.17 depends on scikit-image>=0.19.1 aicssegmentation 0.5.0 depends on scikit-image<0.19.0 and >=0.18.0 napari 0.4.16 depends on scikit-image>=0.19.1

Resolving this over in aics-segmentation https://github.com/AllenCell/aics-segmentation

— Reply to this email directly, view it on GitHub https://github.com/AllenCell/napari-allencell-segmenter/issues/156#issuecomment-1535049915, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3CMNTHFTGAA4ZGQCZLYSNTXEPKYZANCNFSM6AAAAAAXM62BC4 . You are receiving this because you authored the thread.Message ID: @.***>

-- Nadalyn Miller 214-906-5489 personal cell

camisap commented 1 month ago

I am seeing the same behavior with pip installing the app. No error is raised with running pip install napari-allencell-segmenter, but when I open the napari app, the plugin is not listed under the Plugins tab. From reading the issue above, I thought I'd share the versions of packages in my environment:

scikit-image 0.24.0 napari 0.5.1
napari-base 0.5.1
napari-console 0.0.9
napari-plugin-engine 0.2.0
napari-plugin-manager 0.1.0
napari-svg 0.2.0

Operating system (ex. MacOS Big Sur): MacOS Sonoma 14.4.1 Python version (ex. 3.8): Python 3.11.9 napari version (ex. 0.4.1): napari 0.5.1
How did you install the napari viewer (as a bundled app or through command line with pip)?: command line with a conda environment