[BUG] CLI scripts raise errors due to missing functions.
willGraham01 opened this issue · 1 comments
willGraham01 commented
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.
adamltyson commented
See #245 (comment)