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Align minimum supported dependencies with SPEC 0 - #454

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@Zethson Zethson commented Sep 6, 2026

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Applies the SPEC 0 drop schedule as of 2026 Q3, raising the floors to Python 3.12, numpy 2.2, scipy 1.15, pandas 2.3, scikit-learn 1.6 and matplotlib 3.10, and drops Python 3.11 from the CI matrix.
The test suite passes on Python 3.12 both at the new floors and against current releases of every dependency; anndata, formulaic and formulaic-contrasts are not SPEC 0 core packages so their floors are untouched.

SPEC 0 recommends dropping support for Python versions 3 years after their
initial release and for core scientific Python packages 2 years after theirs.
Applying that schedule as of 2026 Q3 raises the floors to Python 3.12, numpy
2.2, scipy 1.15, pandas 2.3, scikit-learn 1.6 and matplotlib 3.10.

Python 3.11 was released in October 2022 and is dropped from the metadata and
from the CI matrix. anndata, formulaic and formulaic-contrasts are not SPEC 0
core packages, so their floors are left alone.

The requirements page still pointed at setup.py for the dependency list; it now
points at pyproject.toml and states the support policy rather than the one-off
note about Python 3.10.

The test suite passes on Python 3.12 both at the new floors and against current
releases of every dependency.

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
@Zethson Zethson closed this by deleting the head repository Sep 6, 2026
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