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Implement a registry for cellfinder test data #1

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wants to merge 4 commits into from
Closed

Implement a registry for cellfinder test data #1

wants to merge 4 commits into from

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alessandrofelder
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@alessandrofelder alessandrofelder commented Jun 10, 2024 •
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Description

What is this PR

  • Bug fix
  • Addition of a new feature
  • Other

Why is this PR needed?

We'd like to keep test data on GIN and access it easily across BrainGlobe repos

What does this PR do?

  • Implements fixtures to get data from GIN through a pooch registry
  • includes a utility fixture to fetch all files that match the registry entries and are in a specific subfolder from GIN
  • adds an example test for use of these fixture

(also currently contains some changes related to this fork not being synced with the BrainGlobe one yet)

References

At least an initial attempt at brainglobe#439

How has this PR been tested?

new example test and manual inspection of my local .cache folder

Is this a breaking change?

Don't think so

Does this PR require an update to the documentation?

No, this is already in line with our developer docs (but we could expand on them there, I guess).

Checklist:

  • The code has been tested locally
  • Tests have been added to cover all new functionality (unit & integration)
  • The documentation has been updated to reflect any changes
  • The code has been formatted with pre-commit

adamltyson and others added 4 commits June 7, 2024 12:38
@adamltyson
Add citation to readme (#438)
95cee20 
Just to make it more obvious (i.e. not just the citation.cff file).
@matham @alessandrofelder
Prevent zero underflow in volume (#437)
352aa40 
* Prevent zero underflow in volume.

* Update tests/core/test_integration/test_detection_structure_splitting.py

Co-authored-by: Alessandro Felder <[email protected]>

* Now that point is fully inside, it'll all shifted upward by one.

---------

Co-authored-by: Alessandro Felder <[email protected]>
@alessandrofelder
add registry.txt for GIN cellfinder/
1f62c92
@alessandrofelder
implement fixtures and example test for registry
130f330
@alessandrofelder alessandrofelder marked this pull request as ready for review June 10, 2024 13:49
@alessandrofelder
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Closing as already implemented here and in brainglobe#440

@alessandrofelder alessandrofelder deleted the pooch-registry branch August 5, 2024 15:34
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3 participants
@alessandrofelder @adamltyson @matham