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fix scanpy version #251

Merged
merged 10 commits into from
Apr 22, 2024
Merged

fix scanpy version #251

merged 10 commits into from
Apr 22, 2024

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SarahOuologuem
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@SarahOuologuem SarahOuologuem linked an issue Apr 9, 2024 that may be closed by this pull request
@SarahOuologuem SarahOuologuem requested a review from bio-la April 9, 2024 10:52
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bio-la commented Apr 9, 2024

scverse/muon#135

@SarahOuologuem
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@bio-la Unpinning the scanpy and scipy versions doesn't work for the spatial workflows, e.g. see here
Scipy version 1.13.0 throws errors in the spatial workflows. The workflows work with a pinned version of scipy to 1.12.0 instead of 1.13.0. Or should i rather pin scipy eg to < 1.13.0?

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bio-la commented Apr 17, 2024

Ok let's roll with it for now. My guess is all of those pins for scvi and Jax are the issues but let's keep a working env for spatial and I'll take a look at versions later! Should I add my review and merge now?

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okay, thank you! yes, i would say so

@bio-la bio-la merged commit 78e62f2 into main Apr 22, 2024
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@SarahOuologuem SarahOuologuem deleted the sarah_scanpy_version branch April 27, 2024 13:01
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all our code is failing for muon's import
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