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python3Packages.gensim: fix build with scipy 1.13 #308620

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@ghpzin ghpzin commented May 2, 2024

Description of changes

python3Packages.scipy update to 1.13.0 removed deprecated scipy.linalg.triu.
This PR adds patch from upstream commit that replaces it with numpy.triu if import from scipy.linalg.triu fails.
Currently there is no release tag with that fix.

See:
piskvorky/gensim#3524
scipy/scipy#19674

Fixes current build on unstable with python 3.11 (python311Packages.gensim):
https://hydra.nixos.org/build/256674931

Currently does not fix build with python 3.12, as it fails on building dependency - python312Packages.smart-open:
https://hydra.nixos.org/build/256692770

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:
  • 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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python3Packages.scipy update to 1.13.0 removed triu.
Patch from upstream commit replaces it with numpy.triu
if import from scipy.linalg.triu fails.

piskvorky/gensim#3524
scipy/scipy#19674
@ghpzin
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ghpzin commented May 3, 2024

Result of nixpkgs-review pr 308620 run on x86_64-linux 1

12 packages failed to build:
  • python312Packages.bpemb
  • python312Packages.bpemb.dist
  • python312Packages.fuzzytm
  • python312Packages.fuzzytm.dist
  • python312Packages.gensim
  • python312Packages.gensim.dist
  • python312Packages.natasha
  • python312Packages.natasha.dist
  • python312Packages.navec
  • python312Packages.navec.dist
  • python312Packages.slovnet
  • python312Packages.slovnet.dist
12 packages built:
  • python311Packages.bpemb
  • python311Packages.bpemb.dist
  • python311Packages.fuzzytm
  • python311Packages.fuzzytm.dist
  • python311Packages.gensim
  • python311Packages.gensim.dist
  • python311Packages.natasha
  • python311Packages.natasha.dist
  • python311Packages.navec
  • python311Packages.navec.dist
  • python311Packages.slovnet
  • python311Packages.slovnet.dist

@ghpzin ghpzin marked this pull request as ready for review May 3, 2024 17:25
@ghpzin ghpzin closed this May 7, 2024
@ghpzin ghpzin deleted the gensim-fix-scipy-triu branch August 10, 2024 08:51
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2 participants