sage: 10.0 -> 10.2

[collares]

Description of changes

Surprisingly painless upgrade. I'm using an autogenerated tarball containing some configuration files (e.g., Pipfile, setup.cfg, requirements.txt) which are generated upstream from Sage-the-distribution files (build/pkgs/) via the bootstrap script. I'm glad I found this tarball, because I like the idea of being isolated from Sage-the-distro files.

An alternative would be to pass spkg arguments to the bootstrap script as in sagemath/sage#35950, but we'd need to solve issues like ./bootstrap: line 50: /build/sage-src-10.2/build/bin/sage-package: cannot execute: required file not found due to the use of #!/usr/bin/env sage-bootstrap-python as a shebang in some dependencies of the bootstrap script. There are several ways around that, but all feel kind of hacky given our current package split, so the configure tarball seems best for now.

Fixes #282383. Please check ofBorg likes the upgrade before merging.

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/)
• 24.05 Release Notes (or backporting 23.05 and 23.11 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.

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[collares]

@ofborg build sageWithDoc

[collares]

Docbuilding failure:

[tutorial ] Extension error:
[tutorial ] Notebook execution failed (exception: [Errno 2] No such file or directory: '/nix/store/1dv5m71dgl6n8dxd7riqjz094vqmyws8-python3-3.11.7/bin/sage')

sagelib installs a Jupyter kernel definition at share/jupyter/kernels/sagemath/kernel.json and it points to the wrong Python environment. We do have our own kernel definition, so ideally Sage would just not install this. It shouldn't matter because we set JUPYTER_PATH in relevant places, but sage --docbuild unsets it; we had a workaround for it, but recent Sage changes bypass it.

There is also a weird pplpy test failure because exception messages don't get printed, but only on x86_64-darwin.

[timokau]

Thank you for your continued maintenance of sage! I know that this is a lot of work.

[collares]

Sage tests pass now. pplpy fails on x86_64-darwin, but that is also the case on Nixpkgs master.

[collares]

Rebased on top of the fpylll update. This should be good to go.

@timokau @7c6f434c @omasanori are you happy with merging this? It fixes a build failure on master.

[7c6f434c]

Looks good!

[timokau]

Yes, fine by me :)

[collares]

Thank you!

[hellwolf]

wonderful! thank you!

[hellwolf]

I still have problem building sage from unstable:

$ nix build .#sage
error: builder for '/nix/store/dqs8zz45330l72r9y3kimnny070wj4gr-python3.11-primecountpy-0.1.0.drv' failed with exit code 1;
       last 10 log lines:
       > checking for references to /build/ in /nix/store/dhf01bl49dmqj6bwdaw82nz585xyh1fy-python3.11-primecountpy-0.1.0-dist...
       > patching script interpreter paths in /nix/store/dhf01bl49dmqj6bwdaw82nz585xyh1fy-python3.11-primecountpy-0.1.0-dist
       > Executing pythonRemoveTestsDir
       > Finished executing pythonRemoveTestsDir
       > Running phase: pythonCatchConflictsPhase
       > Found duplicated packages in closure for dependency 'cython':
       >  cython 0.29.36 (/nix/store/hn15nr4k2zk2akfyv0szcwg21zdnds6k-python3.11-cython-0.29.36/lib/python3.11/site-packages/Cython-0.29.36.dist-info)
       >   cython 3.0.6 (/nix/store/xx59gyk65a4s5vrmql8dyddx69dbvwfi-python3.11-cython-3.0.6/lib/python3.11/site-packages/Cython-3.0.6.dist-info)
       >
       > Package duplicates found in closure, see above. Usually this happens if two packages depend on different version of the same dependency.
       For full logs, run 'nix log /nix/store/dqs8zz45330l72r9y3kimnny070wj4gr-python3.11-primecountpy-0.1.0.drv'.
error: 1 dependencies of derivation '/nix/store/kd6ig9860k1lvls641zznvs0616k8sf5-python3-3.11.7-env.drv' failed to build
error: 1 dependencies of derivation '/nix/store/rw9412qz125d7h1wfdsdzzl6vjkm3r8b-python3.11-sagelib-10.0.drv' failed to build
error: 1 dependencies of derivation '/nix/store/hlcszwgsclllah0cjfmz6jkkvpy2vy43-sage-with-env-10.0.drv' failed to build
error: 1 dependencies of derivation '/nix/store/l7arwkx6f3hq8i5llyzdisr4qj827335-sage-10.0.drv' failed to build

[7c6f434c]

. is a checkout? What revision?

[collares]

Cross-referencing #282383 (comment); it seems to be working now.