MAINT: Move CI to GHA and fix stale niworkflows imports#248
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MAINT: Move CI to GHA and fix stale niworkflows imports#248
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…ycle Address several compatibility issues with current niworkflows/nipype versions that surfaced when building documentation (workflow graphs): - Move ``ValidateImage`` import from ``niworkflows.interfaces.images`` to ``niworkflows.interfaces.header`` (reorganized upstream). - Map ``dwi2anat_init`` vocabulary for ``init_bbreg_wf``: niworkflows now expects ``'register'``/``'header'`` instead of ``'t1w'``/``'header'``. - Update BBR output field names: ``itk_epi2t1`` → ``itk_epi_to_t1w``, ``itk_t1_to_epi`` → ``itk_t1w_to_epi``. - Replace removed ``PatchedMRICoreg`` with ``nipype.interfaces.freesurfer.MRICoreg``. - Remove ``LTAConvert`` inversion step (removed from nipype; output was unused). - Split ``hmc_buffer`` into ``hmc_buffer`` + ``mask_buffer`` to break the ``hmc_buffer ↔ brainextraction_wf`` graph cycle that prevented ``topological_sort`` (and thus doc-build workflow plotting). - Fix ``init_dwi_fit_wf`` docstring example to query the actual DWI file from the mock BIDS layout instead of a hardcoded dummy path. - Remove unsupported ``.. footbibliography::`` directive (no ``sphinxcontrib-bibtex`` configured). - Update ``CLAUDE.md`` with doc-build instructions. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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Load each 3D volume's data into memory before concatenation to prevent `indexed_gzip` `ZranError` when many gzipped NIfTI files are open simultaneously. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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Summary
This PR migrates dMRIPrep's CI/CD from CircleCI to GitHub Actions (tests, style checks, and PyPI publishing) and fixes several stale imports and workflow bugs that surfaced when testing against current versions of niworkflows and nipype.
CircleCI is retained only for Docker image builds; all other CI responsibilities now live in GHA with proper matrix testing, trusted publisher PyPI deployment, and pull request triggers.
Changes
CI/CD
.github/workflows/test.ymlwith matrix testing across Python 3.10--3.13 and three dependency strategies (latest, pre-release, minimum supported). Includes style checks and Codecov upload..github/workflows/pypi-package.ymlimplementing the build-package, TestPyPI, and PyPI deployment pipeline with aReleaseenvironment gate for production uploads.pull_requesttriggers to docs and pypi-package workflows; restrictedpushtriggers intest.ymltomasteronly to prevent double-triggering on PRs.test_deploy_pypi,deploy_pypi, anddeployablejobs from the CircleCI configuration. CircleCI now handles Docker builds exclusively.Workflow fixes
from niworkflows.interfaces.images import ValidateImagewithfrom niworkflows.interfaces.header import ValidateImageto match the current niworkflows API.epi2t1w_initvalue changed from't1w'to'register'and corresponding BBR output field names updated to match current niworkflows conventions.hmc_buffernode to resolve a graph cycle in the DWI fit workflow that caused Nipype to fail at execution time.PatchedMRICoregwith the upstreamMRICoreginterface and removed the unavailableLTAConvertimport.footbibliographySphinx directive.Style
Post-merge admin
Before the PyPI workflow can publish:
nipreps/dmriprepon test.pypi.org (workflow:pypi-package.yml, environment: none for TestPyPI).nipreps/dmriprepon pypi.org (workflow:pypi-package.yml, environment:Release).Releasemust be created in the repository settings with appropriate protection rules (e.g., manual approval, restricted tomasterbranch tags).Test plan
pypi-package.ymlsuccessfully builds the sdist and wheel (the "build-package" job)ImportErrorat import time)🤖 Generated with Claude Code