feat: support numpy 2.0

[martinkim0]

closes #2390

[martinkim0]

this is currently blocked by the following upstream dependencies not supporting numpy 2.0:

• loompy
• pymde

[codecov]

Codecov Report

Attention: Patch coverage is 25.00000% with 3 lines in your changes missing coverage. Please review.

Project coverage is 85.21%. Comparing base (30337b7) to head (302ae54).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2842      +/-   ##
==========================================
- Coverage   85.22%   85.21%   -0.01%     
==========================================
  Files         166      166              
  Lines       14229    14228       -1     
==========================================
- Hits        12126    12125       -1     
  Misses       2103     2103              

Files	Coverage Δ
src/scvi/train/_callbacks.py	86.02% <25.00%> (ø)

... and 2 files with indirect coverage changes

[Zethson]

The last release of pymde was in 2022 and the last commit a year ago. I am not sure how sustainable it is to keep depending on it...

[canergen]

Agreed seems like lowly maintained. I am then also against keeping it optional and we should just highlight it in some tutorial. With RAPIDS UMAP the need is also much smaller now. Loompy still doesn't support >2.0 based on a quick check though. So let's wait until they have figured things out and drop pyMDE then.

[canergen]

@ori-kron-wis Can you switch loom to anndata.io (https://anndata.readthedocs.io/en/latest/generated/anndata.io.read_loom.html)? I assume we then support numpy>2.0. We should for now make pyMDE optional and set an optional requirement to numpy<2.0 for this dependency. We should drop it for the 1.3 release.