[FIX] Make pipeline-catalog submodule available to built Docker image

[alyssadai]

• Fixes [BUG] Unrecognized pipelines when adding imaging derivatives #372

Changes proposed in this PR:

• Fixes our GH actions workflows for building + pushing images to DockerHub to check out submodules

Checklist

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• PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines for more info)
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• 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 98.37%. Comparing base (282cc7d) to head (8676d0c).
Report is 4 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #373   +/-   ##
=======================================
  Coverage   98.37%   98.37%           
=======================================
  Files          16       16           
  Lines         983      983           
=======================================
  Hits          967      967           
  Misses         16       16           

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[coveralls]

Pull Request Test Coverage Report for Build 11676619270

Details

• 0 of 0 changed or added relevant lines in 0 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage remained the same at 98.372%

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Totals
Change from base Build 11672898473:	0.0%
Covered Lines:	967
Relevant Lines:	983

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💛 - Coveralls

[surchs]

looks mostly good, just a 🍒 note on inflated image size

🧑‍🍳

[alyssadai]

Hey Seb, re-requesting your review here for an extra pair of eyes on the Dockerfile changes.

Agree with your suggestion to only copy in required files. As part of maybe #350, I think we can also move the test suite out of the bagel directory for the same reason, since we don't need to copy the tests into the image (and it's best practice to keep them separate from the main program code, like how we're doing in the API repos).

[neurobagel-bot]

🚀 PR was released in v0.3.2 🚀