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TileDB-Inc / TileDB-VCF

Efficient variant-call data storage and retrieval library using the TileDB storage library.
https://tiledb-inc.github.io/TileDB-VCF/
MIT License
82 stars 13 forks source link

Hotfix: pin numpy < 2 #734

Closed jdblischak closed 1 week ago

jdblischak commented 1 week ago

Both the nightlies in this repo (#730) and my centralized nightlies (https://github.com/jdblischak/centralized-tiledb-nightlies/issues/12#issuecomment-2176240410) have been failing for a week due to the release of numpy 2. PRs #731 and #732 have the numpy<2 pin, but they are still undergoing review. To fix the nightly builds, I cherry-picked @awenocur's commit to pin numpy<2.

jdblischak commented 1 week ago

Fun. The macos-11 jobs were immediately canceled due to a scheduled brownout.

This is a scheduled macOS-11 brownout. The macOS-11 environment is deprecated and will be removed on June 28th, 2024.

Recall that we are stuck on macos-11 because of htslib:

https://github.com/TileDB-Inc/TileDB-VCF/blob/7ff0bacababf61ffff6d94ba2f3e3d447557b20e/.github/workflows/macos.yml#L21-L23

jdblischak commented 1 week ago

I started a centralized nightly run using the branch adamwenocur/sc-49903/update (ie PR #732) (can't use my PR branch because it is on a fork)

jdblischak commented 1 week ago

The centralized nightly passed. I'm addressing the macos-11 problem in a followup PR (#735)