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See https://scientific-python.org/specs/spec-0000/ for more info. The concerning part is
image

which means we can't have both 1.13 scipy and 2.0 numpy simultaneously 1.13 scipy doesn't support 2.0 numpy.

Few options:

  1. Manually "edit" min job to either downgrade numpy or upgrade scipy if we change the pyproject.toml to reflect spec0 properly
  2. Add more min jobs that have different dependency chains (i.e., do both of the above separately)
  3. Leave as-is with the non spec0 deps in the pyproject.toml
  • Closes #
  • Tests added
  • Release note added (or unnecessary)

@ilan-gold ilan-gold added this to the 0.13.0 milestone Oct 2, 2025
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codecov bot commented Oct 2, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.76%. Comparing base (390ad29) to head (26ce950).

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #2143   +/-   ##
=======================================
  Coverage   85.76%   85.76%           
=======================================
  Files          46       46           
  Lines        7081     7081           
=======================================
  Hits         6073     6073           
  Misses       1008     1008           
Files with missing lines Coverage Δ
src/anndata/_core/aligned_mapping.py 95.10% <100.00%> (ø)
src/anndata/_core/extensions.py 96.25% <100.00%> (ø)
src/anndata/_core/merge.py 85.11% <100.00%> (ø)
src/anndata/_io/specs/lazy_methods.py 96.15% <100.00%> (ø)
src/anndata/_io/specs/registry.py 94.50% <100.00%> (ø)
src/anndata/_settings.py 94.33% <100.00%> (ø)
src/anndata/_types.py 100.00% <100.00%> (ø)
src/anndata/compat/__init__.py 85.18% <100.00%> (ø)
src/anndata/experimental/backed/_lazy_arrays.py 91.59% <100.00%> (ø)
src/anndata/experimental/pytorch/_annloader.py 23.30% <ø> (ø)
... and 1 more

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