cypari2, cysignals: updates

[collares]

Motivation for this change

Some Sage-related package updates that didn't make it into #114881. For future PRs, the following still needs to be done (after Sage 9.3, probably):

• The eclib update requires Sage patches that change the public API (https://trac.sagemath.org/ticket/31443), so I think we should just wait until Sage 9.3 to upgrade it.
• The pari update is still not ready upstream (https://trac.sagemath.org/ticket/30801).
• gap needs to be updated to 4.11.1.

Closes #103810.

Things done

• Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
• Built on platform(s)
  • NixOS
  • macOS
  • other Linux distributions
• Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
• Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
• Tested execution of all binary files (usually in ./result/bin/)
• Determined the impact on package closure size (by running nix path-info -S before and after)
• Ensured that relevant documentation is up to date
• Fits CONTRIBUTING.md.

[r-rmcgibbo]

Result of nixpkgs-review pr 117123 at 305874ad run on aarch64-linux 1

8 packages built successfully:

• python38Packages.cypari2
• python38Packages.cysignals
• python38Packages.fpylll
• python38Packages.pplpy
• python39Packages.cypari2
• python39Packages.cysignals
• python39Packages.fpylll
• python39Packages.pplpy

2 suggestions:

• warning: unclear-gpl

  gpl2 is a deprecated license, check if project uses gpl2Plus or gpl2Only and change meta.license accordingly.

  Near pkgs/development/python-modules/cypari2/default.nix:62:5:

     |
  62 |     license = licenses.gpl2;
     |     ^
  

• warning: unused-argument

  Unused argument: fetchpatch.
  Near pkgs/development/python-modules/cysignals/default.nix:2:3:

    |
  2 | , fetchpatch
    |   ^
  

---

Result of nixpkgs-review pr 117123 at 305874ad run on x86_64-linux 1

2 packages skipped due to time constraints:

• sage
• sageWithDoc

8 packages built successfully:

• python38Packages.cypari2
• python38Packages.cysignals
• python38Packages.fpylll
• python38Packages.pplpy
• python39Packages.cypari2
• python39Packages.cysignals
• python39Packages.fpylll
• python39Packages.pplpy

2 suggestions:

• warning: unclear-gpl

  gpl2 is a deprecated license, check if project uses gpl2Plus or gpl2Only and change meta.license accordingly.

  Near pkgs/development/python-modules/cypari2/default.nix:62:5:

     |
  62 |     license = licenses.gpl2;
     |     ^
  

• warning: unused-argument

  Unused argument: fetchpatch.
  Near pkgs/development/python-modules/cysignals/default.nix:2:3:

    |
  2 | , fetchpatch
    |   ^
  

[omasanori]

Thank you for continued work on updating dependencies! I will look into this.

Regarding unclear-gpl, cypari2 is gpl2Plus (source).

[collares]

Thank you @omasanori! Changed cypari2 to reflect that.

[collares]

Tests are failing on aarch64, but they were already failing before (see the testrun on #117017 for example). Any ideas?

@ofborg build sage

[timokau]

If the failure is unrelated I think the fix is out of scope for this PR. You could mark sage as broken on that platform for now to reduce the time hydra and others waste trying to build it and increase the "signal to noise ratio" of the CI.

Is this PR still a work in progress?

[collares]

@timokau I was doing some more investigation on the aarch64 failures (every test that uses Jmol hangs, apparently), but as you said this is out of scope for the current PR. So this PR is ready now.

[collares]

As for marking sage as broken on aarch64, I am debugging the jmol hangs at #117465. If I can't find a cause, I'll mark it as broken there.

[timokau]

Thank you for working on this.

[collares]

Thanks for the review and for merging!