Adopt NiPreps-style packaging

[tsalo]

Closes none.

Changes proposed in this pull request

• Move FSL and Connectome Workbench requirements into Dockerfile.
• Add Dockerfile.base with non-Python, non-conda requirements. This still builds off of the package-wise Docker images in qsiprep_build, except for the main Dockerfile there.
• Add pixi.lock file.
• Add pixi-lock GitHub Action.
• Stop using pkg_resources, which is no longer supported. Use importlib.resources instead.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 59.49367% with 32 lines in your changes missing coverage. Please review.
✅ Project coverage is 47.13%. Comparing base (4f38efc) to head (af97b4a).

Files with missing lines	Patch %	Lines
qsiprep/interfaces/ants.py	7.14%	13 Missing ⚠️
qsiprep/interfaces/itk.py	9.09%	10 Missing ⚠️
qsiprep/utils/resources.py	40.00%	2 Missing and 1 partial ⚠️
qsiprep/interfaces/gradients.py	75.00%	1 Missing and 1 partial ⚠️
qsiprep/interfaces/eddy.py	66.66%	1 Missing ⚠️
qsiprep/workflows/anatomical/volume.py	88.88%	1 Missing ⚠️
qsiprep/workflows/dwi/intramodal_template.py	66.66%	1 Missing ⚠️
qsiprep/workflows/fieldmap/pepolar.py	66.66%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1028      +/-   ##
==========================================
+ Coverage   46.28%   47.13%   +0.85%     
==========================================
  Files          65       66       +1     
  Lines        9814     9836      +22     
  Branches     1088     1084       -4     
==========================================
+ Hits         4542     4636      +94     
+ Misses       5036     4979      -57     
+ Partials      236      221      -15     

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[tsalo]

It's finally ready!!!!

[Copilot]

Pull request overview

This PR modernizes QSIPrep’s packaging/build/CI to align with NiPreps-style workflows, including moving away from pkg_resources, adopting pixi environments for container builds, and reworking CI to build/test via Docker images.

Changes:

• Replace pkg_resources.resource_filename(...) with importlib.resources.files(...)-based resource resolution across workflows/interfaces.
• Introduce pixi-based build/test Docker images (plus a new Dockerfile.base) and update CircleCI to build/test using those images and cached datasets.
• Add lockfile automation (pixi-lock.yml), new maintenance docs, and expand test coverage (incl. a new gradients unit test).

Reviewed changes

Copilot reviewed 29 out of 31 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
qsiprep/workflows/fieldmap/unwarp.py	Switch resource file lookup away from pkg_resources.
qsiprep/workflows/fieldmap/syn.py	Switch atlas/transform resource lookup away from pkg_resources.
qsiprep/workflows/fieldmap/pepolar.py	Switch ANTs settings JSON resource lookup away from pkg_resources.
qsiprep/workflows/dwi/util.py	Update commented resource lookup example to new files()/as_path() pattern.
qsiprep/workflows/dwi/registration.py	Replace pkg_resources resource lookup with files()/as_path().
qsiprep/workflows/dwi/intramodal_template.py	Replace pkg_resources resource lookup with files()/as_path().
qsiprep/workflows/dwi/hmc.py	Replace pkg_resources resource lookup with files()/as_path().
qsiprep/workflows/dwi/fsl.py	Replace pkg_resources lookup for eddy config JSON with files()/as_path().
qsiprep/workflows/anatomical/volume.py	Replace pkg_resources lookups for LUT/config/JSON/identity transform resources.
qsiprep/utils/resources.py	Add as_path() helper to adapt importlib.resources.files() results into filesystem paths.
qsiprep/tests/test_interfaces_gradients.py	Add an end-to-end unit test for get_fsl_motion_params().
qsiprep/tests/test_cli.py	Adjust integration tests (dataset choice, sloppy mode, and add “unbiased” anat-only run).
qsiprep/tests/run_local_tests.py	Update local docker test runner to match pixi-based image layout.
qsiprep/tests/data/intramodal_template_outputs.txt	Update expected outputs list for intramodal template integration test.
qsiprep/interfaces/itk.py	Make composite transform disassembly more robust across ANTs/ITK naming conventions.
qsiprep/interfaces/gradients.py	Harden ITK→FSL conversion by using subprocess.run and text ITK transforms to avoid segfaults.
qsiprep/interfaces/eddy.py	Replace pkg_resources lookup for b02b0_1.cnf with files()/as_path().
qsiprep/interfaces/ants.py	Make output transform discovery more robust across ANTs naming/location conventions.
qsiprep/cli/workflow.py	Replace pkg_resources lookups; update pandoc invocation to use --citeproc.
pyproject.toml	Update key dependencies; add pixi workspace configuration; move codespell config into pyproject.toml.
Dockerfile.base	Add new “base” image Dockerfile for non-Python runtime dependencies.
Dockerfile	Switch to pixi-based environment build; produce test and qsiprep image targets.
.maint/INSTRUCTIONS.md	Add maintainer docs for Docker/pixi/tag bump workflows.
.gitignore	Ignore pixi environments and Cursor env file.
.github/workflows/pixi-lock.yml	Add a lockfile-update workflow for PRs.
.gitattributes	Treat pixi.lock as generated/binary for merges and linguist.
.dockerignore	Ensure .pixi is excluded from docker build context.
.cursor/rules/cursorenv.mdc	Add Cursor editor rule for conda environment activation.
.codespellrc	Remove standalone codespell config (now in pyproject.toml).
.circleci/config.yml	Major CI refactor: build images + run tests inside docker with cached data/registry and combined coverage.

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[Copilot]

PATH references $FSFAST_HOME, but that variable is never set in this Dockerfile, so the value will expand to empty at build time (and triggers the UndefinedVar warning noted in the PR description). Either define FSFAST_HOME explicitly or remove it from PATH if it’s not required.

[mattcieslak]

Amazing, this looks great

[mattcieslak]

I don't think we actually use freesurfer's robust template anymore

[tsalo]

I think a lot of the docstrings for the integration tests are outdated/incorrect. We should probably update them at some point.

[tsalo]

@mattcieslak since you've approved, I'll merge this once CI passes. That alright?

[mattcieslak]

Sounds great! I think we may want to switch the main branch to main at some point too, since all the other apps use it