Scipy upperbounding removed in version 1.11.4

[ddemaeyer]

Loading version 1.11.4 without overrulling the scipy version results in a scipy clash. Used to be fixed in version 1.11.3, but not in 1.11.4

scanpy/pyproject.toml

Line 53 in 2ecd869

"scipy>=1.8.1",

[flying-sheep]

Hi, please use the bug report template to file bug reports, it’s important for us to have a stack trace and so on. We can’t act if we don’t know what you mean!

https://github.com/scverse/scanpy/issues/new?template=bug-report.yml

you can edit this issue to include the requested information or close it and file a new one, up to you!

[ddemaeyer]

Due to a version upgrade of scipy from 1.15 to 1.16 there is api incompatibility when installing scanpy 1.11.4. Performing a fresh install of version 1.11.4 will pull scipy 1.16.1. ''' Import scanpy ''' results in an error during loading. The tagged line contained in pyproject contained a upperbounding on scipy in version 1.11.3 of scanpy to prevent this issue. Seems to be removed in 1.11.4 which does not seem to work for me.

…

On Wed, Aug 6, 2025, 15:14 Philipp A. ***@***.***> wrote: *flying-sheep* left a comment (scverse/scanpy#3759) <#3759 (comment)> Hi, please use the bug report template to file bug reports, it’s important for us to have a stack trace and so on. We can’t act if we don’t know what you mean! https://github.com/scverse/scanpy/issues/new?template=bug-report.yml — Reply to this email directly, view it on GitHub <#3759 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AANRED6ZF2FPGQ3QVUKGVRD3MH5UVAVCNFSM6AAAAACDEXMMA6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTCNRQGEZTEMRUGY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[flying-sheep]

I can’t reproduce, everything works fine for me. Please post a stack trace in a code block