Fix Cubed workflow: Python 3.12 and dict chunks - #1345
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cubed and cubed-xarray now require Python >=3.12, so the install step
has been failing with:
ERROR: Package 'cubed' requires a different Python: 3.11.16 not in '>=3.12'
With xarray installed from main, the Cubed workflow fails because
warnings are treated as errors and DataArray.chunk() now warns when
given a dimension-ordered tuple:
FutureWarning: Supplying chunks as dimension-order tuples is
deprecated. It will raise an error in the future. Instead use a
dict with dimension names as keys.
Spell out the dimension names in the test parametrizations instead,
and update the hint in pca.py to match.
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Billyzhang1229
marked this pull request as ready for review
September 3, 2026 16:22
jeromekelleher
approved these changes
Sep 4, 2026
jeromekelleher
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This seems like a clear win too. Would you like to take a look @tomwhite?
tomwhite
approved these changes
Sep 4, 2026
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The Cubed workflow has been red for a while. Two independent problems:
cubedandcubed-xarraynow require Python >= 3.12, so the install step failed:First commit bumps the job to 3.12.
With that fixed, 10 tests failed because xarray main now warns on tuple chunks and warnings are errors:
Second commit rewrites the test parametrizations to use dimension names (
{"variants": 100, "samples": 10, "ploidy": -1}instead of(100, 10, -1)), so the call sites stay as they were. Also updates the rechunking hint inpca.pyto the dict form. Tests pass locally against both the pinned xarray 2025.3.0 and xarray main.Verified green on my fork: https://github.com/Billyzhang1229/sgkit/actions/runs/33771138386