feat: support Python 3.13 and drop the upper Python cap (cyvcf2 >=0.32)#283
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nh13 wants to merge 1 commit into
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feat: support Python 3.13 and drop the upper Python cap (cyvcf2 >=0.32)#283nh13 wants to merge 1 commit into
nh13 wants to merge 1 commit into
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The previous cyvcf2~=0.31.4 pin blocked Python 3.13: cyvcf2 0.31.x ships no cp313 build, which forced requires-python to cap at <3.13. cyvcf2 0.32+ adds 3.13 support with an unchanged API, so relax the pin to >=0.32 and widen requires-python to >=3.10 (and the pixi dev env to <3.14). Verified cyvcf2 0.33.0 against permutect's actual read/write usage (encode_variant, overlapping_filters, find_variant_type, and the filter_variants Writer/header path) and ran the unit suite on Python 3.13.14: all green.
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@davidbenjamin once this merges, could we cut a new release (e.g. v0.7.2)? It drops the upper Python cap ( |
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cyvcf2~=0.31.4pin was the blocker for Python 3.13: cyvcf2 0.31.x shipped nocp313build, which forcedrequires-pythonto cap at<3.13. cyvcf2 0.32+ adds 3.13 support with an unchanged API, so this relaxes the pin to>=0.32and drops the upper Python cap entirely —requires-pythonis now>=3.10(unbounded).Because the cap is removed (not merely raised to 3.13), the package is forward-compatible with Python 3.14+ as soon as the dependency builds exist — no further permutect change required. On the conda side that is already true (conda-forge ships
pytorch/cyvcf2py314builds), so the Bioconda recipe will be able to enable 3.14 directly.Verified on Python 3.13.14: exercised cyvcf2 0.33.0 against permutect's actual usage (
encode_variant,overlapping_filters,find_variant_type, and thefilter_variantsWriter/header/round-trip path) and ran the unit suite — all green.3.14 is permitted by
requires-pythonbut is not dev-tested here: the pixi dev env can't resolve torch 2.10's macOS-arm64cp314wheel (a pytorch wheel-tagging detail, unrelated to permutect), so the pixi dev environment stays capped at<3.14.Follow-up: once released, the Bioconda recipe can drop its
cyvcf2 <0.32andpython <3.13caps and add py314.