Metrics library updated to support comma separate inputs

[scap3yvt]

Fixes #N.A.

Proposed Changes

• input csv can now be split into target and prediction csvs
• multiple sanity checks to ensure coherence

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]

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[sarthakpati]

Marking this as draft until this gets checked by @vpchung.

[scap3yvt]

Hi @sarthakpati @VukW - the entrypoint tests are failing with this error:

2024-07-11T18:00:00.8453595Z testing/entrypoints/__init__.py:288: AssertionError
2024-07-11T18:00:00.8454648Z ----------------------------- Captured stdout call -----------------------------
2024-07-11T18:00:00.8455623Z Test failed on the new case: -i path_na -o output.json -c config.yaml

I am sure why this is the case. Could one of you please help?

[sarthakpati]

I believe this is happening because of this change, which allows a generic string to be passed:

This specific case: "-i path_na -o output.json -c config.yaml" needs to be removed from the tests because this will actually fail, since click is no longer checking for the validity of the input to -i.

[vpchung]

LGTM. I have a couple of suggestions, but they're minor.

[vpchung]

This assumes that the second column is always the one that contains the target or prediction values. Perhaps an assertion can be added before this to ensure that the first column is "SubjectID" before renaming the second column (on the off-chance that "SubjectID" is second column instead of the first).

[scap3yvt]

Should be addressed - can you please check?

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.45%. Comparing base (c331503) to head (5832c03).
Report is 62 commits behind head on new-apis_v0.1.0-dev.

Additional details and impacted files

@@                   Coverage Diff                   @@
##           new-apis_v0.1.0-dev     #900      +/-   ##
=======================================================
+ Coverage                94.40%   94.45%   +0.04%     
=======================================================
  Files                      158      159       +1     
  Lines                     9314     9391      +77     
=======================================================
+ Hits                      8793     8870      +77     
  Misses                     521      521              

Flag	Coverage Δ
unittests	94.45% <100.00%> (+0.04%)	⬆️

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[sarthakpati]

Minor changes in wording