[ENH] More user-friendly handling of input decoding/reading errors

[alyssadai]

• Closes [BUG] TSV file with non-utf-8 encoding produces cryptic UnicodeDecodeError #314
• Closes Make ValueError raised when jsonschema validation fails more informative #167

Changes proposed in this pull request:

• Explicitly require UTF-8 encoding of inputs for the bagel pheno command
• Print informative error message (without a traceback!) when a UnicodeDecodeError or JSONDecodeError are encountered
• Return more details about offending entry in data dict when jsonschema validation fails

For reviewer: Any thoughts on whether this should have the pr-patch or pr-bug-fix label?

Checklist

This section is for the PR reviewer

• PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines for more info)
• PR has a label for the release changelog or skip-release (to be applied by maintainers only)
• PR links to GitHub issue with mention Closes #XXXX
• Tests pass
• Checks pass

For new features:

• Tests have been added

For bug fixes:

• There is at least one test that would fail under the original bug conditions.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.06%. Comparing base (5813406) to head (3ade62c).
Report is 21 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #337      +/-   ##
==========================================
+ Coverage   97.98%   98.06%   +0.07%     
==========================================
  Files          13       13              
  Lines         746      775      +29     
==========================================
+ Hits          731      760      +29     
  Misses         15       15              

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[coveralls]

Pull Request Test Coverage Report for Build 10423411977

Details

• 35 of 35 (100.0%) changed or added relevant lines in 3 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.08%) to 98.065%

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Totals
Change from base Build 10379234725:	0.08%
Covered Lines:	760
Relevant Lines:	775

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💛 - Coveralls

[surchs]

Very cool PR, thanks @alyssadai!

I didn't try it out locally, I'm assuming this PR does not change the long stacktraces that typer is printing to the terminal on an error. I left a comment inline about whether our nicely formatted error messages would be hidden by the long stacktraces.

Also some 🍒, take a look.

🧑‍🍳

[neurobagel-bot]

🚀 PR was released in v0.3.0 🚀