Quote $PY_EXE variable to deal with Python path that contain spaces in Bash

[ytl0623]

Fixes #5857.

Description

When dealing with paths that contain spaces in Bash, it's important to properly quote the variables to ensure that spaces are handled correctly. So, maybe we can replace all $PY_EXE variables to "$PY_EXE" in the runtests.sh file.

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).
• Breaking change (fix or new feature that would cause existing functionality to change).
• New tests added to cover the changes.
• Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
• Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[ericspod]

Hi @ytl0623 thanks for the contribution. Could you please remove the changes to the source files that have been introduced? These are unrelated to the runtests.sh script file. Once that's done we can check that the script still works manually.

[ytl0623]

Hi @ericspod, I've removed other unrelated changes to the runtests.sh script file. Could you please help me review it again?

Thanks in advance!

[dzenanz]

LGTM, I have not tried it yet.

[ericspod]

Looks good now, thanks!

[KumoLiu]

/build

[dzenanz]

This partly works:

Dzenan@Ryzenator MINGW64 /m/Dev/MONAI (dev)
$ ./runtests.sh --quick --unittests  --disttests
Run tests under /m/Dev/MONAI
PYTHONPATH: /m/Dev/MONAI:
Python: /c/Program Files/Python39/python
MONAI version: 1.3.0+38.gac6bd5dd
Numpy version: 1.22.4
Pytorch version: 2.0.1+cu117
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: ac6bd5dd4ccd6c1e19c259dc93e1eb61610c7876
MONAI __file__: M:\Dev\MONAI\monai\__init__.py

Optional dependencies:
Pytorch Ignite version: 0.4.11
ITK version: 5.3.0
Nibabel version: 3.2.1
scikit-image version: 0.22.0
scipy version: 1.11.4
Pillow version: 9.2.0
Tensorboard version: 2.6.0
gdown version: 4.7.1
TorchVision version: 0.15.2+cu117
tqdm version: 4.62.2
lmdb version: 1.4.1
psutil version: 5.8.0
pandas version: 1.3.2
einops version: 0.7.0
transformers version: 4.21.3
mlflow version: 2.8.1
pynrrd version: 1.0.0
clearml version: 1.13.2

For details about installing the optional dependencies, please visit:
    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies

--------------------------------------------------------------------------------
quick
--------------------------------------------------------------------------------
coverage
--------------------------------------------------------------------------------
unittests
2.0.1+cu117
tensor([[0.3538, 0.6480, 0.5858],
        [0.6119, 0.5092, 0.2991],
        [0.1511, 0.2344, 0.4977],
        [0.5254, 0.6991, 0.4507],
        [0.0519, 0.8435, 0.1419]])
./runtests.sh: line 723: /c/Program: No such file or directory

[ericspod]

Yes it looks like we missed a few places, wherever ${cmd} occurs it needs to be quoted as well. @ytl0623 could you do that fix and propose a new PR? Thanks!

[dzenanz]

I could give it a try.

[dzenanz]

Uh-oh, a few quick tries all failed. The closest I got was: ./runtests.sh: line 723: /c/Program Files/Python39/python -m coverage run --append ./tests/runner.py -p "^(?!test_integration).*(?<!_dist)$": No such file or directory. I will leave this to someone more familiar with bash syntax.

[ytl0623]

Hi, @dzenanz @ericspod, maybe you can try ${cmdPrefix}"${cmd}" ./tests/runner.py -p "^(?!test_integration).*(?<!_dist)$" in runtests.sh file.

This works for me.

unittests
Running tests in folder: '.'
With file pattern: '^(?!test_integration).*(?<!_dist)$'
monai test runner: excluding tests.test_rankfilter_dist
monai test runner: excluding tests.test_integration_determinism
monai test runner: excluding tests.test_integration_autorunner
monai test runner: excluding tests.test_integration_fast_train
monai test runner: excluding tests.test_integration_gpu_customization
monai test runner: excluding tests.test_call_dist
monai test runner: excluding tests.test_integration_stn
monai test runner: excluding tests.test_cumulative_average_dist
monai test runner: excluding tests.test_sampler_dist
monai test runner: excluding tests.test_integration_bundle_run
monai test runner: excluding tests.test_integration_segmentation_3d
monai test runner: excluding tests.test_integration_workers
monai test runner: excluding tests.test_timedcall_dist
monai test runner: excluding tests.test_handler_metrics_saver_dist
monai test runner: excluding tests.test_integration_nnunetv2_runner
monai test runner: excluding tests.test_handler_confusion_matrix_dist
monai test runner: excluding tests.test_integration_unet_2d
monai test runner: excluding tests.test_integration_lazy_samples
monai test runner: excluding tests.test_integration_workflows_gan
monai test runner: excluding tests.test_persistentdataset_dist
monai test runner: excluding tests.test_weighted_random_sampler_dist
monai test runner: excluding tests.test_lmdbdataset_dist
monai test runner: excluding tests.test_handler_rocauc_dist
monai test runner: excluding tests.test_handler_classification_saver_dist
monai test runner: excluding tests.test_prepare_batch_default_dist
monai test runner: excluding tests.test_handler_regression_metrics_dist
monai test runner: excluding tests.test_evenly_divisible_all_gather_dist
monai test runner: excluding tests.test_integration_workflows
monai test runner: excluding tests.test_integration_sliding_window
monai test runner: excluding tests.test_integration_classification_2d
monai test runner: excluding tests.test_fl_monai_algo_dist
monai test runner: excluding tests.test_cv2_dist

[dzenanz]

That's one of the first things I tried. That gives me: ./runtests.sh: line 723: /c/Program Files/Python39/python -m coverage run --append: No such file or directory