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Itk: 5.0.1 -> 5.1.0 #86142

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merged 5 commits into from May 9, 2020
Merged

Itk: 5.0.1 -> 5.1.0 #86142

merged 5 commits into from May 9, 2020

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bcdarwin
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Motivation for this change
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
  • [NA] 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.

@ofborg ofborg bot requested a review from viric April 27, 2020 19:16
@bcdarwin bcdarwin mentioned this pull request Apr 28, 2020
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@ofborg ofborg bot requested a review from knedlsepp April 28, 2020 00:10
@bcdarwin bcdarwin force-pushed the itk-5.1.0 branch 2 times, most recently from fd36929 to 82c095a Compare April 28, 2020 03:32
veprbl
veprbl reviewed Apr 28, 2020
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pkgs/development/libraries/science/biology/elastix/default.nix
nativeBuildInputs = [ cmake python3 ];
buildInputs = [ itk ];

doCheck = true;
doCheck = !stdenv.isDarwin; # usual dynamic linker issues
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What do you mean by usual issues? Can we resolve with preCheck = "export DYLD_LIBRARY_PATH ...?

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I tried doing something naive similar to what is done with LD_LIBRARY_PATH already but that didn't work. I don't really do much development on OS X so don't mind disabling this package if you prefer.

@veprbl
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veprbl commented Apr 28, 2020

@GrahamcOfBorg build elastix ezminc simpleitk vtk itk4

jonringer
jonringer reviewed Apr 28, 2020
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looks like h5c++ want's pkg-config to be available at runtime:

/nix/store/qvb7wnswcaqspp7k6v8ak18llfx89gw0-itk-5.1.0/h5c++
dir is /nix/store/qvb7wnswcaqspp7k6v8ak18llfx89gw0-itk-5.1.0
./results/itk/bin/h5c++: line 32: pkg-config: command not found

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@jonringer -- pkgconfig now propagated.

@bcdarwin bcdarwin requested a review from jonringer April 28, 2020 14:30
@knedlsepp
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@jonringer -- pkgconfig now propagated.

Hm. This means it will only be available to all nix-builds depending on it, but not at runtime when using nix run nixpkgs.itk. If we want the latter we probably will need to add the pkg-config PATH to the makeWrapperArgs, right?

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@knedlsepp -- h5cc and h5c++ are compiler wrappers so most likely they would be used by other derivations, although it's a bit unseemly to have them fail at runtime. Not sure what the best solution is here -- these are somewhat incidental programs built by the ITKHDF5 module which aren't needed to compile most programs using ITK (including all reverse deps in the Nixpkgs tree such as ANTs). Is it worth it to create a wrapper for them?

@bcdarwin bcdarwin force-pushed the itk-5.1.0 branch 2 times, most recently from 73b960d to 28d4943 Compare May 4, 2020 16:01
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bcdarwin commented May 4, 2020 •
edited

@knedlsepp @jonringer I've wrapped h5c++ with pkgconfig.

@bcdarwin bcdarwin requested a review from veprbl May 4, 2020 16:02
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veprbl commented May 4, 2020

@GrahamcOfBorg build elastix ezminc simpleitk vtk itk4

@bcdarwin
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bcdarwin commented May 5, 2020 •
edited

@GrahamcOfBorg build elastix ezminc simpleitk vtk itk4

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veprbl commented May 5, 2020

@GrahamcOfBorg build elastix ezminc simpleitk vtk itk4

@bcdarwin
itk: 5.0.1 -> 5.1.0
4048343
@bcdarwin
simpleitk: itk -> itk4
20cf206 
- simpleitk 1.2.4 is incompatible with ITK 5.1, so this can be reverted when 2.x is released.
@bcdarwin
ezminc: switch from itk5 to itk4 branch
6f1430a 
- itk5 branch currently lacks support for itk 5.1
@bcdarwin
elastix: update for ITK 5.1.0
5caa767 
- fetch patches to build elastix 5.0 with ITK 5.1
- update 'platforms': builds on Darwin, fails on aarch64
@veprbl veprbl merged commit e80302d into NixOS:master May 9, 2020
@bcdarwin bcdarwin deleted the itk-5.1.0 branch May 9, 2020 19:45
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@veprbl veprbl veprbl approved these changes

@viric viric Awaiting requested review from viric

@knedlsepp knedlsepp Awaiting requested review from knedlsepp

@jonringer jonringer Awaiting requested review from jonringer

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8.has: clean-up 8.has: package (new) 10.rebuild-darwin: 11-100 10.rebuild-linux: 1-10
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