brainglobe / cellfinder

Automated 3D cell detection in very large images

Home Page:https://brainglobe.info/documentation/cellfinder/index.html

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[BUG] CLI scripts raise errors due to missing functions.

willGraham01 opened this issue · comments

Describe the bug

The cellfinder_curate_new and cellfinder_curate CLI options that come with the package raise errors when invoked, due to missing functions.

To Reproduce
Install the package into a clean environment, then (to circumnavigate #245) install napari and brainreg-segment.
Then run

$ cellfinder_curate_new
Traceback (most recent call last):
  File "/home/ccaegra/mambaforge/envs/test/bin/cellfinder_curate_new", line 5, in <module>
    from cellfinder.train.curation import main
  File "/home/ccaegra/mambaforge/envs/test/lib/python3.9/site-packages/cellfinder/train/curation.py", line 12, in <module>
    from napari.utils.io import magic_imread
ImportError: cannot import name 'magic_imread' from 'napari.utils.io' (/home/ccaegra/mambaforge/envs/test/lib/python3.9/site-packages/napari/utils/io.py)

There is an additional issue with the fact that the same script(s) also attempt to import

napari_cellfinder.cellfinder

which doesn't exist. Presumably this should be cellfinder-napari or cellfinder-core.

Expected behaviour
No error should be produced - the missing import must be resolved.