Update to numpy>=2

[nrontsis]

As described in the title; numpy>=2 is required for some projects I am working with, and is becoming the standard in many projects.

[nrontsis]

Hi @clami66 any thoughts on this? Happy to work to address any concerns.

Thanks!

[nrontsis]

Until this gets merged, here's how I generate wheels from this branch:

• start from a clean repo state
• add .python-version file with your desired python version
• change pyproject.toml to reflect desired package name and version.
• change run_test.sh to prepend uv run in the binary variables
• run ./run_test.sh
• run uv build

[loodvn]

Would be great if dockq could merge this in - thanks for the interim fix suggestion!

[clami66]

Sorry for the late response.

But to explain the delay in merging: there are some differences between results compared to the previous version, so CI tests are failing. We need to look more in detail at what's changed and run a more extensive test before we can merge.

Thanks for contributing to DockQ!

[ddelalamo-takeda]

Hi @clami66 any update on this? Is there anything someone in the community can do to move this along? Asking because I'm defaulting to using the branch from @nrontsis in cases where DockQ needs to be in the same container as, for example, modern structure prediction methods reliant on numpy≥2, such as Protenix. The changes in this PR seem fairly innocuous, so just curious if there is any way I or someone else can help get this merged into main