[ENH]: Move data downloading/handling to junifer-data package.

[synchon]

Are you requiring a new dataset or marker?

• I understand this is not a marker or dataset request

Which feature do you want to include?

Currently, Junifer is handling the data, downloading from various sources. Ideally, this should be centralized and versiones.

How do you imagine this integrated in junifer?

1. Junifer uses the junifer-data API.
2. junifer-data keeps a datalad dataset with all data objects, including externals. Each commit to this datasets has a tag.
3. junifer knows exactly which is the tag that we are dealing with, so each junifer version will always work with the same data files.
4. We have a command download or similar that makes junifer download all (or the requested) files to be used later on with the run command.

Do you have a sample code that implements this outside of junifer?

No response

Anything else to say?

No response

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.67%. Comparing base (b39d56b) to head (700aa5f).
Report is 14 commits behind head on main.

❌ Your project status has failed because the head coverage (85.67%) is below the target coverage (90.00%). You can increase the head coverage or adjust the target coverage.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #363      +/-   ##
==========================================
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==========================================
  Files         133      133              
  Lines        5652     5633      -19     
  Branches      958      954       -4     
==========================================
- Hits         4837     4826      -11     
+ Misses        624      618       -6     
+ Partials      191      189       -2     

Flag	Coverage Δ
junifer	85.67% <100.00%> (+0.09%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
junifer/data/coordinates/_coordinates.py	79.71% <100.00%> (+0.29%)	⬆️
junifer/data/masks/_masks.py	68.57% <100.00%> (ø)
junifer/data/parcellations/_parcellations.py	92.12% <100.00%> (+0.17%)	⬆️
junifer/data/template_spaces.py	81.81% <100.00%> (+0.42%)	⬆️
junifer/data/utils.py	62.50% <100.00%> (-4.17%)	⬇️
junifer/typing/_typing.py	100.00% <100.00%> (ø)

[synchon]

4. We have a command download or similar that makes junifer download all (or the requested) files to be used later on with the run command.

This is not yet implemented and would depend on junifer-data API. Will implement after the necessary API is available from junifer-data.

[github-actions]

PR Preview Action v1.6.0
🚀 View preview at https://juaml.github.io/junifer/pr-preview/pr-363/
Built to branch gh-pages at 2025-01-27 11:23 UTC. Preview will be ready when the GitHub Pages deployment is complete.

[synchon]

4. We have a command download or similar that makes junifer download all (or the requested) files to be used later on with the run command.

This is not yet implemented and would depend on junifer-data API. Will implement after the necessary API is available from junifer-data.

junifer-data-client v1.1.0 now has a download command to do this via CLI only.

[fraimondo]

CI is not green though

[synchon]

CI is not green though

It's a new problem with gh-action where numpy is not getting built for the docs. Will take care of it after getting the important stuff in.