[staging-next] sage: numpy/scipy upgrade patches

[collares]

Description of changes

One Sage doctest triggers a deprecation warning with NumPy 1.25.0. It is a code example from the Computational Mathematics with SageMath book, and for this reason I am still deciding what is the "most upstreamable" fix. I've asked about it at sagemath/sage#35826 (comment), but I'd like to get Nixpkgs patched sooner rather than later because of the upcoming staging-next cycle at #245935.

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 23.11 Release Notes (or backporting 23.05 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md.