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cytoscape: bump 3.6.1 -> 3.7.1 #56498

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merged 1 commit into from Mar 11, 2019
Merged

cytoscape: bump 3.6.1 -> 3.7.1 #56498

merged 1 commit into from Mar 11, 2019

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ariutta
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@ariutta ariutta commented Feb 28, 2019

Needed to update URL, because wget "http://chianti.ucsd.edu/cytoscape-3.7.1/cytoscape-3.7.1.tar.gz" returns 404.

Motivation for this change

Update to latest version, bumping from 3.6.1 -> 3.7.1.

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
  • 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 nox --run "nox-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)
  • Assured whether relevant documentation is up to date
  • Fits CONTRIBUTING.md.

@peterhoeg
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Please use fetchFromGitHub instead of fetchurl when fetching from GH.

@ariutta
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ariutta commented Mar 8, 2019

@peterhoeg, I would normally use fetchFromGitHub, but this is a special case. The current Nix package doesn't compile from source. Rather, it just downloads a gzipped tarball from this URL:

http://chianti.ucsd.edu/${name}/${name}.tar.gz

That URL works for version 3.6.1, but it doesn't work for version 3.7.1. The equivalent working URL is this:

https://github.com/cytoscape/cytoscape/releases/download/${version}/${name}.tar.gz

My update is very conservative, containing the minimal changes required to bump from 3.6.1 to 3.7.1.

If someone has time, it would definitely be better to get the code like this:

  src = fetchFromGitHub {
    owner = "cytoscape";
    repo = "cytoscape";
    rev = "${version}";
    sha256 = "0jqg3mxvgh9w4h9npbzql78ki03ypa5b3pjgwhivlqwwa60sxnn2";
  };

And then build from source. But I can't guarantee when I'll be able to make that happen, because it'll mean completely rewriting the package.

@peterhoeg
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Makes sense.

@peterhoeg peterhoeg merged commit 136126c into NixOS:master Mar 11, 2019
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3 participants