[python] Support NumPy 2

[johnkerl]

Issue and/or context: #2536

Changes:

Notes for Reviewer:

Main thing to watch for: NumPy 2.0 does not support Python 3.8, while we have not yet dropped support for Python 3.8 (#2141).

Per https://github.com/numpy/numpy/releases/tag/v2.0.0:

The Python versions supported by this release are 3.9-3.12.

I thought we'd need a bit in setup.py like

        # There is no Python 3.8 support for NumPy 2
        "numpy<2; python_version<'3.9'",
        "numpy; python_version>='3.9'",

but in hindsight it seems not -- a Python 3.8 asking to get NumPy will simply not be offered version 2 in the first place 😎

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.33%. Comparing base (2942ea2) to head (03eb9a8).
Report is 47 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2934      +/-   ##
==========================================
+ Coverage   83.22%   83.33%   +0.10%     
==========================================
  Files          51       51              
  Lines        5462     5462              
==========================================
+ Hits         4546     4552       +6     
+ Misses        916      910       -6     

Flag	Coverage Δ
python	83.33% <ø> (+0.10%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
python_api	83.33% <ø> (+0.10%)	⬆️
libtiledbsoma	∅ <ø> (∅)

[johnkerl]

Oddly, the "Show package versions" bit in
https://github.com/single-cell-data/TileDB-SOMA/actions/runs/10585607673/job/29332572332?pr=2934
is showing even for Python 3.11

Run python scripts/show-versions.py
tiledbsoma.__version__    1.12.0rc0.post106.dev3370075614
tiledb.version()          0.31.1
core version              2.25.0
anndata.__version__  (ad) 0.10.8
numpy.__version__    (np) 1.26.4 <--------------- we are not getting numpy 2.1 installed :(
pandas.__version__   (pd) 2.2.2
pyarrow.__version__  (pa) 17.0.0
scanpy.__version__   (sc) 1.10.2
scipy.__version__    (sp) 1.14.1
python__version__         3.[11](https://github.com/single-cell-data/TileDB-SOMA/actions/runs/10585607673/job/29332572332?pr=2934#step:9:12).9

🤔

[johnkerl]

I just pushed a rebase. Good news: this time (unlike before) we do get numpy 2
https://github.com/single-cell-data/TileDB-SOMA/actions/runs/11347335957/job/31558479564?pr=2934

python scripts/show-versions.py
  shell: /usr/bin/bash -e {0}
  env:
    pythonLocation: /opt/hostedtoolcache/Python/[3](https://github.com/single-cell-data/TileDB-SOMA/actions/runs/11347335957/job/31558479564?pr=2934#step:9:3).9.20/x64
    PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.9.20/x6[4](https://github.com/single-cell-data/TileDB-SOMA/actions/runs/11347335957/job/31558479564?pr=2934#step:9:4)/lib/pkgconfig
    Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.9.20/x64
    Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.9.20/x64
    Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.9.20/x64
    LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.9.20/x64/lib
tiledbsoma.__version__    1.1[5](https://github.com/single-cell-data/TileDB-SOMA/actions/runs/11347335957/job/31558479564?pr=2934#step:9:5).0rc0.post28.dev4289275158
tiledb.version()          0.32.3
core version              2.2[6](https://github.com/single-cell-data/TileDB-SOMA/actions/runs/11347335957/job/31558479564?pr=2934#step:9:6).2
anndata.__version__  (ad) 0.10.9
numpy.__version__    (np) 2.0.2
pandas.__version__   (pd) 2.2.3
pyarrow.__version__  (pa) 1[7](https://github.com/single-cell-data/TileDB-SOMA/actions/runs/11347335957/job/31558479564?pr=2934#step:9:7).0.0
scanpy.__version__   (sc) 1.10.3
scipy.__version__    (sp) 1.13.1
python__version__         3.9.20

[johnkerl]

Trying to add @kounelisagis as a reviewer ...

[kounelisagis]

Thanks!