⚗️✨♻️ Support bundled transforms

[dyollb]

What do these changes do?

This PR implements

• loading pre-processing transforms from the config file (using monai.bundle)
• implements loading yml (and json) config files
• adds tests to check/understand behavior of bundle.ConfigParser
• removes save_nifti branch during training, i.e. automatic predicting based on validation data
• default pre-processing/augmentation now moves data to GPU after CropForegroundd

Related issue/s

• use bundle approach to make pre-processing transforms flexible #34
• Use YML instead (or in addition to) to JSON for config files #31

How to test

Checklist

• 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).
• Unit tests for the changes and run locally with the command pytest tests
• Documentation reflects the changes

[codecov]

Codecov Report

Merging #36 (0a67c03) into main (5d0b862) will increase coverage by 1.16%.
The diff coverage is 50.00%.

@@            Coverage Diff             @@
##             main      #36      +/-   ##
==========================================
+ Coverage   17.32%   18.48%   +1.16%     
==========================================
  Files          44       45       +1     
  Lines        2211     2229      +18     
  Branches      365      366       +1     
==========================================
+ Hits          383      412      +29     
+ Misses       1805     1794      -11     
  Partials       23       23              

Flag	Coverage Δ
unittests	18.48% <50.00%> (+1.16%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/segmantic/util/json.py	71.42% <ø> (ø)
src/segmantic/seg/monai_unet.py	23.58% <14.81%> (+1.69%)	⬆️
src/segmantic/commands/monai_unet_cli.py	67.56% <66.66%> (+9.67%)	⬆️
src/segmantic/prepro/labels.py	88.88% <88.88%> (+0.17%)	⬆️
src/segmantic/__init__.py	100.00% <100.00%> (ø)
src/segmantic/seg/dataset.py	83.87% <100.00%> (ø)
src/segmantic/util/cli.py	100.00% <100.00%> (ø)

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[pcrespov]

• Interesting the validation of path
• I did not know about the warnings with codecov 👍 . You will achieve 100% coverage in no time :-)

[pcrespov]

Nice!
Why dont' you parametrize these?
When you have to test more variants it will be difficult to check whichone failed

https://docs.pytest.org/en/6.2.x/example/parametrize.html#paramexamples

Something like (please double check) ...

params_data = {
 "args1_skip_default": ({"file_path": "/path/file.txt", "arg_int": 10}, False), 
  "args1_wrong_type": ({"file_path": 23, "arg_int": 10, "arg_float": 5}, True)
}

@pytest.mark.parametrize(
   "arguments,expected_failure", list(params_data.values()), ids=list(params_data.keys())
def test_validate_args(arguments, expected_failure):
   ...

[dyollb]

nice!

[dyollb]

Thanks @pcrespov for your review!