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Consistently use acres like other BIDS Apps - #1060

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tsalo merged 2 commits into
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use-acres
Jun 11, 2026
Merged

Consistently use acres like other BIDS Apps#1060
tsalo merged 2 commits into
mainfrom
use-acres

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@tsalo tsalo commented Jun 11, 2026

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Closes #904.

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Codecov Report

❌ Patch coverage is 83.87097% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 47.33%. Comparing base (4428d00) to head (7e6739f).
⚠️ Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
qsiprep/interfaces/eddy.py 50.00% 1 Missing ⚠️
qsiprep/workflows/anatomical/volume.py 85.71% 1 Missing ⚠️
qsiprep/workflows/dwi/intramodal_template.py 50.00% 1 Missing ⚠️
qsiprep/workflows/dwi/util.py 0.00% 1 Missing ⚠️
qsiprep/workflows/fieldmap/pepolar.py 50.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1060      +/-   ##
==========================================
- Coverage   47.41%   47.33%   -0.08%     
==========================================
  Files          66       66              
  Lines        9888     9877      -11     
  Branches     1096     1096              
==========================================
- Hits         4688     4675      -13     
- Misses       4970     4973       +3     
+ Partials      230      229       -1     

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Pull request overview

This PR standardizes access to packaged static resources (JSON configs, LUTs, templates, etc.) by switching workflow/interface code from importlib.resources + as_path to the qsiprep.data loader (backed by acres), aligning QSIPrep with other BIDS Apps and addressing #904.

Changes:

  • Replaced importlib.resources.files(...)/as_path(...) resource lookups with qsiprep.data.load(...) across fieldmap, DWI, anatomical workflows, and an interface.
  • Updated CLI boilerplate/NOTICE loading to use qsiprep.data.
  • Minor cleanup: removed a large commented-out block and modernized a string type check.

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated no comments.

Show a summary per file
File Description
qsiprep/workflows/fieldmap/unwarp.py Load ANTs registration settings via qsiprep.data.load.
qsiprep/workflows/fieldmap/syn.py Load atlas and transform JSONs via qsiprep.data.load.
qsiprep/workflows/fieldmap/pepolar.py Load ANTs translation/rigid settings via qsiprep.data.load.
qsiprep/workflows/dwi/util.py Remove dead commented code; use isinstance(..., str) in _list_squeeze.
qsiprep/workflows/dwi/registration.py Load intermodal ACPC registration settings via qsiprep.data.load.
qsiprep/workflows/dwi/intramodal_template.py Load intramodal nonlinear settings via qsiprep.data.load.
qsiprep/workflows/dwi/hmc.py Load SHORELine registration presets via qsiprep.data.load.
qsiprep/workflows/dwi/fsl.py Load default eddy params via qsiprep.data.load.
qsiprep/workflows/anatomical/volume.py Load FreeSurfer LUT/config, affine, identity transform, QuickSyN settings via qsiprep.data.load.
qsiprep/interfaces/eddy.py Load b02b0_1.cnf via qsiprep.data.load when needed.
qsiprep/cli/workflow.py Load NOTICE and boilerplate.bib via qsiprep.data.load.

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@tsalo
tsalo merged commit 0fb1eac into main Jun 11, 2026
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@tsalo
tsalo deleted the use-acres branch June 11, 2026 16:26
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Replace pkg_resources with qsiprep.data

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