[staging-next] sage: unpin python, adapt to scipy 1.16 update

[collares]

Revert #418009, since the relevant CPython 3.13 bug was fixed in 3.13.5. We also update the expectations for some numerical optimization tests due to the SciPy update.

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
  • sandbox = relaxed
  • sandbox = true
• 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/)
• Nixpkgs 25.11 Release Notes (or backporting 25.05 Nixpkgs Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
• NixOS 25.11 Release Notes (or backporting 25.05 NixOS Release notes)
  • (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, pkgs/README.md, maintainers/README.md and other contributing documentation in corresponding paths.

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[collares]

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 423832
Commit: 739a7b4848c875e333d47ab55b48ca30657baa7b

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x86_64-linux

❌ 1 package failed to build:

• labplot

✅ 3 packages built:

• cantor (libsForQt5.cantor, plasma5Packages.cantor)
• sage
• sageWithDoc

[collares]

The labplot failure is unrelated. It happens because readstat is broken (cc @swflint):

configure.ac:43: warning: macro 'AM_ICONV' not found in library
autoreconf: running: /nix/store/0qmqybsb86p5g6vqxj992grj9hyh72wa-autoconf-2.72/bin/autoconf --force
configure.ac:43: error: possibly undefined macro: AM_ICONV
      If this token and others are legitimate, please use m4_pattern_allow.
      See the Autoconf documentation.

A fix similar to #421040 needs to be applied to readstat.

[AndrewKvalheim]

A fix similar to #421040 needs to be applied to readstat.

Completed in #425879