[FIX] Package pipeline-catalog as data files in CLI installation

[alyssadai]

• Fixes [BUG] Pipeline catalog is now inside the container but still not found by the CLI #375
• Fixes CI should not install in dev mode #376

Changes proposed in this pull request:

• pipeline-catalog submodule moved into bagel module so that it ends up inside the package directory after installation
  • pipeline-catalog wouldn't be automatically included in the installation since it's not a module (no __init__.py), so we additionally must update the package config file to include this subdirectory as additional package data
• for separation of concerns, test suite moved out of bagel module, and test data submodules (neurobagel_examples, bids-examples) moved under tests/
• for CI tests, CLI is no longer installed in editable mode to more closely replicate production env

Checklist

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• 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 98.37%. Comparing base (e4897ba) to head (a436386).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #379      +/-   ##
==========================================
- Coverage   98.37%   98.37%   -0.01%     
==========================================
  Files          16       16              
  Lines         983      982       -1     
==========================================
- Hits          967      966       -1     
  Misses         16       16              

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[coveralls]

Pull Request Test Coverage Report for Build 11709023670

Details

• 5 of 5 (100.0%) changed or added relevant lines in 2 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage decreased (-0.001%) to 98.371%

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Totals
Change from base Build 11691648696:	-0.001%
Covered Lines:	966
Relevant Lines:	982

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💛 - Coveralls

[surchs]

Thanks @alyssadai for fixing this.

I understand that my guess of dev-mode install didn't fix it, so having a test here that would have caught the original bug is tricky. So let's do this: let's merge the fix without the test, but please create an issue to find a way to run the tests on the installed package. My guess is that the CLIRunner we use to "call" the CLI as if we used it from the command line is the limitation here, but I'm sure there is a way to force it to run on the installed CLI (even something silly like making an actual system call with subprocess or something - but I'm sure something smarter must exist too).

In any case: thanks for the fix 🧑‍🍳

[neurobagel-bot]

🚀 PR was released in v0.3.3 🚀