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kreshuklab / plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images
https://kreshuklab.github.io/plant-seg/
MIT License
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fix(docs): teach Qt to find napari icons #271

Closed qin-yu closed 1 month ago

qin-yu commented 1 month ago

This PR fixes a rabbit-hole issue that I encountered when trying to run the PlantSeg documentation build.

Issue

Qt wasn't able to find the icons napari build.

WARNING: Cannot open file '/yu/repositories/plant-seg/theme_light:/minus_50.svg', because: No such file or directory
WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_light:/minus_50.svg', because: No such file or directory
WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory
WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory
WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/plus_50.svg', because: No such file or directory
WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/plus_50.svg', because: No such file or directory

Solution

To resolve the issue, simply add the following line to set the search path for Qt:

PyQt5.QtCore.QDir.addSearchPath(f'theme_{name}', str(_theme_path(name)))

Cause

The reason why Qt inside magicgui widgets couldn’t locate the SVG file built by Napari is that QApplication never initializes in the context of an MkDocs build using markdown-exec.

Under normal usage, napari._qt.qt_event_loop.get_app() gets the singleton Napari app, and the line PyQt5.QtCore.QDir.addSearchPath(f'theme_{name}', str(_theme_path(name))) within this context allows Qt to recognize the temporary path for all SVGs, such as:

/home/qyu/.cache/napari/plant-seg_1bbf9c2c85c974192c72e305681854d064a243cf/_themes/dark

To verify this, you can simply instantiate a Napari viewer with viewer = napari.Viewer() before calling .setStyleSheet(), which also resolves the problem.

Discussion

Logs before this PR ### Logs before this PR ```pytb (plant-seg) [qyu@kreshuk-gpu1 plant-seg]$ mkdocs serve INFO - Building documentation... INFO - git-committers plugin ENABLED INFO - git-committers: found page authors cache file - loading it INFO - Cleaning site directory INFO - The following pages exist in the docs directory, but are not included in the "nav" configuration: - snippets/napari/dataprocessing/rescale.md INFO - DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs given by the platformdirs library. To remove this warning and see the appropriate new directories, set the environment variable `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. The use of platformdirs will be the default in `jupyter_core` v6 File "/yu/miniconda3/envs/plant-seg/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 90, in deprecation warnings.warn(message, DeprecationWarning, stacklevel=stacklevel + 1) File "/yu/miniconda3/envs/plant-seg/lib/python3.11/site-packages/jupyter_client/connect.py", line 22, in from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write WARNING: Qt: Session management error: Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed WARNING:vispy:Qt: Session management error: Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed 2024-06-05 19:37:06,242 [MainThread] INFO PlantSeg Zoo - Fetching BioImage.IO Model Zoo collection from https://raw.githubusercontent.com/bioimage-io/collection-bioimage-io/gh-pages/collection.json INFO:PlantSeg Zoo:Fetching BioImage.IO Model Zoo collection from https://raw.githubusercontent.com/bioimage-io/collection-bioimage-io/gh-pages/collection.json 2024-06-05 19:37:06,249 [MainThread] INFO PlantSeg Zoo - Loaded model from PlantSeg zoo: generic_confocal_3D_unet INFO:PlantSeg Zoo:Loaded model from PlantSeg zoo: generic_confocal_3D_unet 2024-06-05 19:37:06,304 [MainThread] INFO PlantSeg Zoo - Loaded model from user specified weights: /home/qyu/.plantseg_models/generic_confocal_3D_unet/best_checkpoint.pytorch INFO:PlantSeg Zoo:Loaded model from user specified weights: /home/qyu/.plantseg_models/generic_confocal_3D_unet/best_checkpoint.pytorch WARNING: Cannot open file '/yu/repositories/plant-seg/theme_light:/drop_down_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_light:/drop_down_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_light:/drop_down_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_light:/drop_down_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_light:/drop_down_50.svg', because: No such file or directory ... ... WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/plus_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/plus_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/plus_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/plus_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/minus_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/minus_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/minus_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/minus_50.svg', because: No such file or directory INFO - Doc file 'chapters/getting_started/troubleshooting.md' contains a link '#problems-with---headless-and-daskdistributed', but there is no such anchor on this page. INFO - git-committers: saving page authors cache file INFO - Documentation built in 45.24 seconds INFO - [19:37:29] Watching paths for changes: 'docs', 'mkdocs.yml' INFO - [19:37:29] Serving on http://127.0.0.1:8000/plant-seg/ WARNING - [19:37:29] "GET /plant-seg/images/favicon.ico HTTP/1.1" code 404 INFO - [19:37:29] Browser connected: http://127.0.0.1:8000/plant-seg/chapters/plantseg_interactive_napari/data_processing/ INFO - [19:37:36] Detected file changes INFO - Building documentation... INFO - git-committers plugin ENABLED INFO - git-committers: found page authors cache file - loading it INFO - The following pages exist in the docs directory, but are not included in the "nav" configuration: - snippets/napari/dataprocessing/rescale.md WARNING: Cannot open file '/yu/repositories/plant-seg/theme_light:/drop_down_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_light:/drop_down_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_light:/drop_down_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_light:/drop_down_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_light:/drop_down_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_light:/drop_down_50.svg', because: No such file or directory ... ... WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/drop_down_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/plus_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/plus_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/plus_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/plus_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/minus_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/minus_50.svg', because: No such file or directory WARNING: Cannot open file '/yu/repositories/plant-seg/theme_dark:/minus_50.svg', because: No such file or directory WARNING:vispy:Cannot open file '/yu/repositories/plant-seg/theme_dark:/minus_50.svg', because: No such file or directory INFO - Doc file 'chapters/getting_started/troubleshooting.md' contains a link '#problems-with---headless-and-daskdistributed', but there is no such anchor on this page. INFO - git-committers: saving page authors cache file INFO - Documentation built in 32.14 seconds INFO - [19:38:08] Reloading browsers INFO - [19:38:09] Browser connected: http://127.0.0.1:8000/plant-seg/chapters/plantseg_interactive_napari/data_processing/ ```
Logs after this PR ### Logs after this PR ```pytb (plant-seg) [qyu@kreshuk-gpu1 plant-seg]$ mkdocs serve INFO - Building documentation... INFO - git-committers plugin ENABLED INFO - git-committers: found page authors cache file - loading it INFO - Cleaning site directory INFO - The following pages exist in the docs directory, but are not included in the "nav" configuration: - snippets/napari/dataprocessing/rescale.md INFO - DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs given by the platformdirs library. To remove this warning and see the appropriate new directories, set the environment variable `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. The use of platformdirs will be the default in `jupyter_core` v6 File "/yu/miniconda3/envs/plant-seg/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 90, in deprecation warnings.warn(message, DeprecationWarning, stacklevel=stacklevel + 1) File "/yu/miniconda3/envs/plant-seg/lib/python3.11/site-packages/jupyter_client/connect.py", line 22, in from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write WARNING: Qt: Session management error: Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed WARNING:vispy:Qt: Session management error: Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed 2024-06-05 19:43:23,834 [MainThread] INFO PlantSeg Zoo - Fetching BioImage.IO Model Zoo collection from https://raw.githubusercontent.com/bioimage-io/collection-bioimage-io/gh-pages/collection.json INFO:PlantSeg Zoo:Fetching BioImage.IO Model Zoo collection from https://raw.githubusercontent.com/bioimage-io/collection-bioimage-io/gh-pages/collection.json 2024-06-05 19:43:24,152 [MainThread] INFO PlantSeg Zoo - Loaded model from PlantSeg zoo: generic_confocal_3D_unet INFO:PlantSeg Zoo:Loaded model from PlantSeg zoo: generic_confocal_3D_unet 2024-06-05 19:43:24,198 [MainThread] INFO PlantSeg Zoo - Loaded model from user specified weights: /home/qyu/.plantseg_models/generic_confocal_3D_unet/best_checkpoint.pytorch INFO:PlantSeg Zoo:Loaded model from user specified weights: /home/qyu/.plantseg_models/generic_confocal_3D_unet/best_checkpoint.pytorch INFO - Doc file 'chapters/getting_started/troubleshooting.md' contains a link '#problems-with---headless-and-daskdistributed', but there is no such anchor on this page. INFO - git-committers: saving page authors cache file INFO - Documentation built in 45.88 seconds INFO - [19:43:47] Watching paths for changes: 'docs', 'mkdocs.yml' INFO - [19:43:47] Serving on http://127.0.0.1:8000/plant-seg/ INFO - [19:43:47] Browser connected: http://127.0.0.1:8000/plant-seg/chapters/plantseg_interactive_napari/data_processing/ ```