chore: Replace conda with pixi and lock #3503
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #3503 +/- ##
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+ Coverage 73.63% 73.64% +0.01%
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Files 60 60
Lines 4612 4618 +6
Branches 586 586
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+ Hits 3396 3401 +5
- Misses 1087 1088 +1
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effigies
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Sep 4, 2025
effigies
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Sep 4, 2025
mgxd
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Big fan of having a single tool handle dependency resolution / environment freezing - just a few questions:
- how would upgrading
pixi.locklook when cutting a new release? - is the size difference of the test image just due to lack of metadata? https://circleci.com/api/v1.1/project/github/nipreps/fmriprep/14338/output/110/0?file=true&allocation-id=68bb5934b822b028391d9507-0-build%2FABCDEFGH
If you're going for a minimal update (e.g., nipreps fixes only): Update your dependencies in If you're looking to do general upgrades, use There's also a
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@mgxd I cancelled the docker build on GHA after FreeSurfer took 2 hours. If you're good with this, we can merge and the next one will actually go into the cache and save us time in the future... |
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Let's do it |
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Sep 11, 2025
Not sure how we missed this in #3503, but we need to use a downloaded image to avoid reading stdin in fmriprep-docker.
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25.2.0 (October 01, 2025) New feature release in the 25.2.x series. This release is an *fMRIPrep Long-Term Support (LTS)* release. The planned support window is 4 years, until October 2029. This release is an incremental improvement over 25.1.x, but includes some fixes and improvements that do not fit within our `bug-fix policy <https://www.nipreps.org/devs/releases/#bug-fix-releases>`__. Importantly, the change in interpolation in 25.1.0 introduced artifacts for some datasets. This release changes the default interpolation mode to ``grid-constant``, which resolves those problems while not reintroducing the issue the previous release sought to fix. This release also (finally) introduces per-session processing. The ``--session-label`` flag selects the sessions to process, and the ``--subject-anatomical-reference`` flag indicates whether and how to combine across sessions. Existing filters passed via ``--bids-filter-file`` may need to be updated or removed in favor of using these flags to achieve the desired behavior. We would like to thank the AMP-SCZ and ENIGMA consortia for testing out and providing feedback on this release. * FIX: Clean up output report language (#3529) * FIX: Default to grid-constant interpolation mode (#3516) * FIX: Adapt to transposed ndcoords in nitransforms (#3517) * FIX: Write out Freesurfer-derived outputs (#3512) * FIX: Add kwargs to _warnings.py (#3483) * ENH: Resample BOLD data to any surface template space using the Connectome Workbench (#3461) * ENH: Add boldref / sbref to source metadata (#3532) * ENH: Add dedicated session filtering, alternative anatomical template options (#3495) * ENH: Write out goodvoxels mask (#3513) * ENH: Add registration metadata to boldref-to-anat transforms (#3500) * ENH: Write out cortex mask GIFTIs (#3491) * ENH: Update transforms.py according to new transform chain of nitransforms (#3494) * RF/DOC: Improve and document command-line parser defaults (#3487) * DOC: Explain better SDC and B0FieldSource requirement (#2768) * DOC: Document `freesurfer` parameter in BOLD confound workflow init (#3504) * DOC: Add myself to contributor list (#3506) * DOC: Fix non-standard Input/Output docstring section management (#3505) * MNT: Split Dockerfile into base and pixi layers (#3521) * MNT: Replace conda with pixi and lock (#3503) * MNT: Update license metadata using SPDX expression (#3486) * MNT: no need to re-run `ruff check` after `ruff format` (#3480) * MNT: Update pre-commit ruff legacy alias (#3479)
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This PR replaces the conda+pip locks with pixi, which allows us to have a single lockfile.
In passing, I also started installing AFNI tools from their Docker builds, moved the template fetch and MSM download into their own layers. Since this somehow caused me to re-fetch FreeSurfer, I went ahead and updated the base image.