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@dependabot dependabot bot commented on behalf of github Dec 23, 2024

Bumps astral-sh/setup-uv from 4 to 5.

Release notes

Sourced from astral-sh/setup-uv's releases.

v5.0.0 🎄 Merry Christmas - Help fastly and users by default

Changes

This christmans 🎄 release is a bit early bit still full of presents 🎁 Since we are changing some of the defaults this can lead to breaking changes, thus the major version increase.

Here are the highlights:

Default to enable-cache: true on GitHub hosted runners

Did you know that that Fastly, the company hosting PyPI, theoretically has to pay $12.5 million per month and so far have served more than 2.41 exabytes of data? image

This is why they asked us to turn on caching by default. After weighting the pros and cons we decided to automatically upload the cache to the GitHub Actions cache when running on GitHub hosted runners. You can still disable that with enable-cache: false.

I remember when I first got into actions and didn't understand all the magic. I was baffled that some actions did something behind the scenes to make everything faster. I hope with this change we help a lot of users who are don't want to or are afraid to understand what enable-cache does.

Add **/requirements*.txt to default cache-dependency-glob

If caching is enabled we automatically searched for a uv.lock file and when this changed we knew we had to refresh the cache. A lot of projects don't use this but rather the good old requirements.txt. We now automatically search for both uv.lockand requirements*.txt (this means also requirements-test.txt, requirements-dev.txt, ...) files. You can change this with cache-dependency-glob

Auto activate venv when python-version is set

Some workflows install packages on the fly. This automatically works when using a python version that is already present on the runner. But if uv installs the version, e.g. because it is a free-threaded version or an old one, it is a standalone-build and installing packages "into the system" is not possible.

We now automatically create a new virtual environment with uv venv and activate it for the rest of the workflow if python-version is used. This means you can now do

- name: Install uv
  uses: astral-sh/setup-uv@auto-environment
  with:
    python-version: 3.13t
- run: uv pip install -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython

🚨 Breaking changes

🐛 Bug fixes

🚀 Enhancements

... (truncated)

Commits

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Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 4 to 5.
- [Release notes](https://github.com/astral-sh/setup-uv/releases)
- [Commits](astral-sh/setup-uv@v4...v5)

---
updated-dependencies:
- dependency-name: astral-sh/setup-uv
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code labels Dec 23, 2024
@effigies effigies merged commit fe6bfa0 into master Dec 23, 2024
19 checks passed
@effigies effigies deleted the dependabot/github_actions/astral-sh/setup-uv-5 branch December 23, 2024 12:56
@effigies effigies added this to the 25.0.0 milestone Mar 19, 2025
effigies added a commit that referenced this pull request Mar 25, 2025
25.0.0 (March 25, 2025)

New feature release in the 25.0.x series.

This release substantially improves support for pre-computed derivatives.
Previous releases would miss some derivatives and rerun the computations.
Note that derivatives from previous versions will be accepted,
so it should not be necessary to recompute derivatives from previous versions.
The recommended command line is::

    fmriprep BIDS_DIR OUT_DIR participant --derivatives fmriprep=PRECOMP_DIR

Note that multiple derivatives can be specified, for example::

    fmriprep BIDS_DIR OUT_DIR participant \
      anat=PRECOMPUTED_ANATOMICAL_DIR \
      func=PRECOMPUTED_FUNCTIONAL_DIR

When the same file is found in multiple derivatives, the last one found takes precedence.

Additionally, `--force-*` flags have been consolidated into a single
`--force` flag that can take multiple, space-separated arguments.

Structural processing changes
-----------------------------
We now output white, pial and midthickness fsLR meshes on the subject surface.
Look for `sub-<subject>_hemi-<L|R>_space-fsLR_*_<surf>.surf.gii` files.

Brain extraction has been modified slightly to more closely match the
`antsBrainExtraction.sh` workflow distributed by ANTs.
The impact should be minimal, but in rare cases this fixes a crash.

Fieldmap processing changes
---------------------------
SyN-SDC fieldmap filtering is now single-level, following the improvements
for gradient-echo fieldmaps in 24.1.

Jacobian-weighting during fieldmap unwarping is now on by default *only*
for PEPolar fieldmaps.
To enable for other fieldmap types, use `--force fieldmap-jacobian`.

All merged pull requests
------------------------

* FIX: Detect and apply precomputed fieldmaps (#3439)
* FIX: Calculate bold mask and dummy scans in transform-only runs (#3428)
* FIX: Use consistent skull-stripping pre- and post- SDC (#3415)
* FIX: Use removeprefix instead of lstrip or ternary operator (#3409)
* FIX: Listify sessions when generating reports (#3408)
* FIX: Ensure fieldmap is resampled correctly in report (#3387)
* FIX: Stop excluding FS minc_modify_header used during fallback registration (#3372)
* FIX: Repair and test query for precalculated baseline/boldref files (#3370)
* FIX: Repair search for precomputed transforms (#3369)
* ENH: Enable Jacobians only for PEPOLAR by default, allow forcing (#3443)
* ENH: Create `--force` flag that accepts a list, replacing individual `--force-*` flags (#3442)
* ENH: Output fsLR meshes on subject surfaces (#3411)
* ENH: Flexibilize "sophisticated" pepolar to allow monomodal execution (#3393)
* ENH: Update FSL packages for reported bug fixes (#3374)
* RF: Calculate RMSD from motion transforms (#3427)
* RF: Reconstruct motion confounds from minimal derivatives (#3424)
* RF: Replace deprecated pkgutil.find_loader (#3384)
* RF: Upgrade nitransforms and remove workarounds (#3378)
* DOC: Fix xfm extension in the outputs docs (#3435)
* DOC: Mention fMRIPost-AROMA in parser documentation (#3356)
* MNT: Remove CLI flags with expired deprecation periods (#3445)
* MNT: Update pinned environment (#3440)
* MNT: Bump pins, update RTD config (#3425)
* MNT: Declare linux/amd64 platform during Docker build (#3422)
* MNT: Bump astral-sh/setup-uv from 4 to 5 (#3417)
* MNT: Test support for Python 3.13 (#3416)
* MNT: Install Workbench CLI via conda (#3410)
* MNT: Update minimum dependencies, test with tox-uv (#3412)
* MNT: Install c3d through conda (#3382)
* CI: Fetch tags and 200 commits to support describe (#3381)
* CI: Build docker images in GHA, store cache inline and push to GHCR (#3380)
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