Add support for numpy 2, update all deps

[rly]

Motivation

Fix #1106. Fix #1130.

Checklist

• [x] Did you update CHANGELOG.md with your changes?
• [x] Does the PR clearly describe the problem and the solution?
• [x] Have you reviewed our Contributing Guide?
• [x] Does the PR use "Fix #XXX" notation to tell GitHub to close the relevant issue numbered XXX when the PR is merged?

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 88.77%. Comparing base (5e13d64) to head (871625e).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #1139 +/- ## ========================================== - Coverage 88.78% 88.77% -0.01% ========================================== Files 45 45 Lines 9782 9774 -8 Branches 2778 2777 -1 ========================================== - Hits 8685 8677 -8 Misses 780 780 Partials 317 317 ```

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