KitwareMedical / KitwareMedical/vpaw

Linking with pediatric_airway_atlas will cause `typing_extensions` error

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Dominant language
Python
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Description

Linking with pediatric_airway_atlas will cause `typing_extensions` error as shown below:
```
Traceback (most recent call last):
File "/home/vncuser/workdir/vpaw2-r1/Slicer-build/bin/Python/slicer/util.py", line 3295, in tryWithErrorDisplay
yield
File "/home/vncuser/workdir/vpaw2-r1/Slicer-build/lib/vpaw-5.7/qt-scripted-modules/VPAWModel.py", line 362, in onLinkPediatricAirwayAtlasButton
self.logic.linkPediatricAirwayAtlas(
File "/home/vncuser/workdir/vpaw2-r1/Slicer-build/lib/vpaw-5.7/qt-scripted-modules/VPAWModel.py", line 459, in linkPediatricAirwayAtlas
response = self.installAndImportDependencies() and self.ensureModulePath(
File "/home/vncuser/workdir/vpaw2-r1/Slicer-build/lib/vpaw-5.7/qt-scripted-modules/VPAWModel.py", line 552, in installAndImportDependencies
installed_modules = [
File "/home/vncuser/workdir/vpaw2-r1/Slicer-build/lib/vpaw-5.7/qt-scripted-modules/VPAWModel.py", line 556, in
importlib.import_module(import_name),
File "/home/vncuser/workdir/vpaw2-r1/python-install/lib/python3.9/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1030, in _gcd_import
File "", line 1007, in _find_and_load
File "", line 986, in _find_and_load_unlocked
File "", line 680, in _load_unlocked
File "", line 850, in exec_module
File "", line 228, in _call_with_frames_removed
File "/home/vncuser/workdir/vpaw2-r1/python-install/lib/python3.9/site-packages/monai/__init__.py", line 83, in
from .utils.module import load_submodules # noqa: E402
File "/home/vncuser/workdir/vpaw2-r1/python-install/lib/python3.9/site-packages/monai/utils/__init__.py", line 16, in
from .deprecate_utils import DeprecatedError, deprecated, deprecated_arg, deprecated_arg_default
File "/home/vncuser/workdir/vpaw2-r1/python-install/lib/python3.9/site-packages/monai/utils/deprecate_utils.py", line 22, in
from monai.utils.module import version_leq
File "/home/vncuser/workdir/vpaw2-r1/python-install/lib/python3.9/site-packages/monai/utils/module.py", line 30, in
import torch
File "/home/vncuser/workdir/vpaw2-r1/python-install/lib/python3.9/site-packages/torch/__init__.py", line 73, in
from typing_extensions import TypeIs as _TypeIs
ImportError: cannot import name 'TypeIs' from 'typing_extensions' (/home/vncuser/workdir/vpaw2-r1/python-install/lib/python3.9/site-packages/typing_extensions.py)

```

Current work around is to open python console within Slicer and run the following:
```
slicer.util.pip_install("typing_extensions --upgrade")
```
Then restart the VPAW application and try linking again.

Contributor guide

Open the contributing guide

Research direction

Start in qt-scripted-modules/VPAWModel.py, especially installAndImportDependencies and linkPediatricAirwayAtlas, then reproduce the pediatric_airway_atlas linking flow in Slicer. Check how typing_extensions and the MONAI/PyTorch imports are installed and imported; done means linking succeeds without manually running slicer.util.pip_install("typing_extensions --upgrade") and restarting.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
tooling
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
55/100

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