Error while trying to open GUI in the latest PlantSeg version

[adkrishnan]

Hello,
Facing an issue while trying to open the GUI for the latest version of PlantSeg 1.8.1 after an install in a fresh environment
ModuleNotFoundError: No module named 'bioimage.io'
(same error even on trying to open Napari GUI)

Even on installing bioimage.core separately
displays an error in the legacy_gui/gui_widgets.py
KeyError: 'is_segmentation'

[qin-yu]

Hi @adkrishnan thanks for reporting this issue!

Legacy GUI is now not the main focus, but is still very useful. When it launches, it checks this template file and it's configs:

plant-seg/plantseg/resources/config_gui_template.yaml

Line 84 in aece266

is_segmentation: True

unless there is already a config file before the installation of PlantSeg in ~/.plantseg_models/configs/ (because you had previous versions of PlantSeg). So if you try to delete the files there, the KeyError may be fixed.

[qin-yu]

This has been documented before but I know the docs are hard to find when you actually need it:

https://kreshuklab.github.io/plant-seg/chapters/getting_started/troubleshooting/#missing-configuration-key-errors

[qin-yu]

Hey @adkrishnan Athul says you tried deleting the folder but still has KeyError, in this case I recommend you to try and see what does this give:

(plant-seg) [qyu@kreshuk configs]$ python
Python 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from plantseg import PATH_CONFIGS
>>> PATH_CONFIGS
PosixPath('/home/qyu/.plantseg_models/configs')

So basically you need to remove everything inside the PATH_CONFIGS to update to the latest config.

[adkrishnan]

I deleted everything and installed bioimageio.core using mamba install -c conda-forge bioimageio.core separately along with PlantSeg
Its working now
Thankyou very much

[qin-yu]

For the missing package it is very strange because I did include it in the config:

plant-seg/conda-recipe/meta.yaml

Line 34 in aece266

- bioimageio.core>=0.6.5

But since PlantSeg works for you know I'll leave this issue open and come back later to see if anything is wrong with the environment.

Thanks again for reporting!

[lorenzocerrone]

I get the same issue on my machine

[qin-yu]

I get the same issue on my machine

Do you know what conda uses for checking the requirements? I have bioimageio.core all three configs:

plant-seg/conda-recipe/meta.yaml

Line 34 in aece266

- bioimageio.core>=0.6.5

plant-seg/environment-dev.yaml

Line 27 in aece266

- bioimageio.core>=0.6.5

plant-seg/environment.yaml

Line 20 in aece266

- bioimageio.core>=0.6.5

[lorenzocerrone]

Only meta.yaml counts. It is strange that the deps are not built into the package dependencies by Conda, but I have seen it in the past. As a short-term solution, let's add it to the installation instructions.

[qin-yu]

Only meta.yaml counts. It is strange that the deps are not built into the package dependencies by Conda, but I have seen it in the past.

Ohhh I never imagined Conda would do that because it feels like a major bug of it.

As a short-term solution, let's add it to the installation instructions.

Do you have time for the docs? Otherwise I can add it after our meeting.