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ENH: Implement X5 representation and output to filesystem #241

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oesteban
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@oesteban oesteban commented Jul 17, 2025

Building on top of #213 and #241, this PR adds a baseline implementation for BIDS' X5.

@sgiavasis, @jmarabotto: I tried to cherry-pick everything you did within the other PR, and pushed your branch for reference to the upstream repository. In a second pass after this PR, I want to review how much from outside nitransforms.io needs to be picked up back.

Julien Marabotto and others added 9 commits July 16, 2025 16:37
(cherry picked from commit 49bf4c3)
(cherry picked from commit 74090ac)
(cherry picked from commit ba8a389)
(cherry picked from commit e4e3f44)
…s to the future. Started the beginning of some xfm_utils for quicker testing and validation.

(cherry picked from commit 7ba96c3)
(cherry picked from commit 0e213cb)
(cherry picked from commit 3d263bb)
(cherry picked from commit a102f1e)
(cherry picked from commit e465332)
@oesteban oesteban marked this pull request as draft July 17, 2025 07:51
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codecov bot commented Jul 17, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.55%. Comparing base (eff0b71) to head (ce1083c).
Report is 19 commits behind head on master.

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #241      +/-   ##
==========================================
+ Coverage   95.38%   95.55%   +0.17%     
==========================================
  Files          28       30       +2     
  Lines        2948     3063     +115     
==========================================
+ Hits         2812     2927     +115     
  Misses        136      136              
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unittests 95.33% <100.00%> (+0.18%) ⬆️

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@oesteban oesteban force-pushed the codex/create-x5transform-dataclass-in-nitransforms.io.x5 branch from 5dc7281 to bcbadda Compare July 17, 2025 09:22
@oesteban oesteban changed the title Add basic X5 writer ENH: Implement BIDS X5 io module Jul 17, 2025
@oesteban oesteban force-pushed the codex/create-x5transform-dataclass-in-nitransforms.io.x5 branch from 6ffc445 to 740a0c4 Compare July 17, 2025 10:33
@oesteban oesteban changed the title ENH: Implement BIDS X5 io module ENH: Implement X5 representation and output to filesystem Jul 17, 2025
@oesteban oesteban added the enhancement New feature or request label Jul 17, 2025
@oesteban oesteban force-pushed the codex/create-x5transform-dataclass-in-nitransforms.io.x5 branch 3 times, most recently from de96326 to 6ec566f Compare July 17, 2025 13:25
@oesteban oesteban marked this pull request as ready for review July 17, 2025 13:26
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I'm going to misbehave and merge this without the necessary review, in part to be respectful of the well-deserved break some are taking.

This is relatively safe (in that it only adds support for X5 and removes brittle code), and it builds upon prior work within #213. I've tried to credit that work by manually setting co-authorship of commits :)

@oesteban oesteban force-pushed the codex/create-x5transform-dataclass-in-nitransforms.io.x5 branch 3 times, most recently from 22490db to d9dbd6f Compare July 17, 2025 14:18
oesteban and others added 3 commits July 17, 2025 16:27
Resolves: #111.

Co-authored-by: Julien Marabotto <166002186+jmarabotto@users.noreply.github.com>
Co-authored-by: sgiavasis <sgiava77@gmail.com>
@oesteban oesteban force-pushed the codex/create-x5transform-dataclass-in-nitransforms.io.x5 branch from d9dbd6f to ce1083c Compare July 17, 2025 14:29
Co-authored-by: Julien Marabotto <166002186+jmarabotto@users.noreply.github.com>
Co-authored-by: sgiavasis <sgiava77@gmail.com>
@oesteban oesteban merged commit 2e73ee9 into master Jul 17, 2025
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@oesteban oesteban deleted the codex/create-x5transform-dataclass-in-nitransforms.io.x5 branch July 17, 2025 15:06
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Design and implementation of an X5 internal representation of transforms
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