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fix: Pin numpy<2 to fix CI test failures#501

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Alpaca233 merged 2 commits into
Cephla-Lab:masterfrom
Alpaca233:fix/pin-numpy-version
Feb 27, 2026
Merged

fix: Pin numpy<2 to fix CI test failures#501
Alpaca233 merged 2 commits into
Cephla-Lab:masterfrom
Alpaca233:fix/pin-numpy-version

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@Alpaca233 Alpaca233 commented Feb 27, 2026

This is temporary. We'll start using numpy 2 after moving to napari 0.6.

Summary

  • Pin numpy to <2 in setup_22.04.sh to fix CI test failures
  • scipy/napari/cupyx packages are compiled against NumPy 1.x and crash with NumPy 2.x due to binary ABI incompatibility

Context

CI started failing because pip now installs NumPy 2.x by default, but dependencies like scipy 1.12.0 were compiled against NumPy 1.x.

Error message:

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash.

Future work

To upgrade to NumPy 2, we would need to:

  • Upgrade scipy to >=1.13
  • Possibly upgrade napari to 0.5.5+
  • Test for any NumPy 2 API breaking changes in the codebase

🤖 Generated with Claude Code

Alpaca233 and others added 2 commits February 27, 2026 13:08
scipy/napari/cupyx packages in CI are compiled against NumPy 1.x and
crash with NumPy 2.x due to binary ABI incompatibility.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@Alpaca233 Alpaca233 merged commit 5e5fb92 into Cephla-Lab:master Feb 27, 2026
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