New command line API functionality

[sarthakpati]

Fixes #ISSUE_NUMBER

Major Changes

• Usability updates
  • new CLI functionality to make it standardized using click, and related changes to workflows and tests
  • standardized logging (Add logging final version #893)
  • torch version update (Update PyTorch dependency #857)
  • workflows updated to use specific pip versions (Hardcoding pip version for workflows #887)
  • single function to get all augmentations (Adding function to get augmentation transforms #889)
  • allow metrics functionality to use separate target and prediction inputs (Metrics library updated to support comma separate inputs #900)
  • trigger CI tests for all branches (Trigger tests for pull requests to all branches #855)
  • added check for case-insensitive headers for metrics (22ee9bd)
• New features
  • new segmentation architecture (Add dynunet model #873)
  • new metrics (Added metrics for BraTS Path challenge #885)

Checklist

• CONTRIBUTING guide has been followed.
• PR is based on the current GaNDLF master .
• Non-breaking change (does not break existing functionality): provide as many details as possible for any breaking change.
• Function/class source code documentation added/updated (ensure typing is used to provide type hints, including and not limited to using Optional if a variable has a pre-defined value).
• Code has been blacked for style consistency and linting.
• If applicable, version information has been updated in GANDLF/version.py.
• If adding a git submodule, add to list of exceptions for black styling in pyproject.toml file.
• Usage documentation has been updated, if appropriate.
• Tests added or modified to cover the changes; if coverage is reduced, please give explanation.
• If customized dependency installation is required (i.e., a separate pip install step is needed for PR to be functional), please ensure it is reflected in all the files that control the CI, namely: python-test.yml, and all docker files [1,2,3].

[github-actions]

MLCommons CLA bot All contributors have signed the MLCommons CLA ✍️ ✅

[codecov]

Codecov Report

Attention: Patch coverage is 94.25386% with 67 lines in your changes missing coverage. Please review.

Project coverage is 94.61%. Comparing base (5e43783) to head (5652542).

Files	Patch %	Lines
testing/entrypoints/__init__.py	84.72%	22 Missing ⚠️
GANDLF/entrypoints/collect_stats.py	77.50%	9 Missing ⚠️
update_version.py	57.14%	9 Missing ⚠️
GANDLF/config_manager.py	64.70%	6 Missing ⚠️
GANDLF/data/augmentation/__init__.py	73.33%	4 Missing ⚠️
GANDLF/entrypoints/verify_install.py	86.95%	3 Missing ⚠️
GANDLF/entrypoints/construct_csv.py	96.49%	2 Missing ⚠️
GANDLF/entrypoints/optimize_model.py	93.10%	2 Missing ⚠️
GANDLF/cli/deploy.py	0.00%	1 Missing ⚠️
GANDLF/entrypoints/anonymizer.py	97.95%	1 Missing ⚠️
... and 8 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #845      +/-   ##
==========================================
- Coverage   95.04%   94.61%   -0.44%     
==========================================
  Files         122      160      +38     
  Lines        8297     9450    +1153     
==========================================
+ Hits         7886     8941    +1055     
- Misses        411      509      +98     

Flag	Coverage Δ
unittests	94.61% <94.25%> (-0.44%)	⬇️

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[sarthakpati]

@szmazurek I should have addressed all comments...

[szmazurek]

Super minor thing regarding logging levels and imo good to go

[szmazurek]

Another remark regarding logging