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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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bcdarwin commented Apr 27, 2020

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 Apr 27, 2020
@bcdarwin bcdarwin mentioned this pull request Apr 28, 2020
5 of 9 tasks complete
@bcdarwin bcdarwin force-pushed the bcdarwin:itk-5.1.0 branch from 813c946 to 6fc0283 Apr 28, 2020
@ofborg ofborg bot requested a review from knedlsepp Apr 28, 2020
@bcdarwin bcdarwin force-pushed the bcdarwin:itk-5.1.0 branch 2 times, most recently from fd36929 to 82c095a Apr 28, 2020
nativeBuildInputs = [ cmake python3 ];
buildInputs = [ itk ];

doCheck = true;
doCheck = !stdenv.isDarwin; # usual dynamic linker issues

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veprbl Apr 28, 2020

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What do you mean by usual issues? Can we resolve with preCheck = "export DYLD_LIBRARY_PATH ...?

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bcdarwin Apr 28, 2020

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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.

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veprbl commented Apr 28, 2020

@GrahamcOfBorg build elastix ezminc simpleitk vtk itk4

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jonringer left a comment

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
@bcdarwin bcdarwin force-pushed the bcdarwin:itk-5.1.0 branch from 82c095a to e2d6ec0 Apr 28, 2020
@bcdarwin bcdarwin force-pushed the bcdarwin:itk-5.1.0 branch from e2d6ec0 to 400cecb Apr 28, 2020
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bcdarwin commented Apr 28, 2020

@jonringer -- pkgconfig now propagated.

@bcdarwin bcdarwin requested a review from jonringer Apr 28, 2020
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knedlsepp commented Apr 28, 2020

@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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bcdarwin commented Apr 28, 2020

@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 bcdarwin:itk-5.1.0 branch 2 times, most recently from 73b960d to 28d4943 May 4, 2020
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bcdarwin commented May 4, 2020

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

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

@GrahamcOfBorg build elastix ezminc simpleitk vtk itk4

@bcdarwin bcdarwin force-pushed the bcdarwin:itk-5.1.0 branch from 28d4943 to 6ae233a May 5, 2020
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bcdarwin commented May 5, 2020

@GrahamcOfBorg build elastix ezminc simpleitk vtk itk4

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veprbl commented May 5, 2020

@GrahamcOfBorg build elastix ezminc simpleitk vtk itk4

bcdarwin added 4 commits Apr 27, 2020
- simpleitk 1.2.4 is incompatible with ITK 5.1, so this can be reverted when 2.x is released.
- itk5 branch currently lacks support for itk 5.1
- fetch patches to build elastix 5.0 with ITK 5.1
- update 'platforms': builds on Darwin, fails on aarch64
@bcdarwin bcdarwin force-pushed the bcdarwin:itk-5.1.0 branch from 6ae233a to 5caa767 May 5, 2020
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veprbl approved these changes May 5, 2020
@veprbl veprbl merged commit e80302d into NixOS:master May 9, 2020
18 checks passed
18 checks passed
Evaluation Performance Report Evaluator Performance Report
Details
elastix, elastix.passthru.tests, ezminc, ezminc.passthru.tests, itk, itk.passthru.tests, simpleitk, simpleitk.passthru.tests, vtk, vtk.passthru.tests on aarch64-linux Success
Details
elastix, elastix.passthru.tests, ezminc, ezminc.passthru.tests, itk, itk.passthru.tests, simpleitk, simpleitk.passthru.tests, vtk, vtk.passthru.tests on x86_64-linux Success
Details
elastix, ezminc, itk4, simpleitk, vtk on aarch64-linux Success
Details
elastix, ezminc, itk4, simpleitk, vtk on x86_64-linux Success
Details
grahamcofborg-eval ^.^!
Details
grahamcofborg-eval-check-maintainers matching changed paths to changed attrs...
Details
grahamcofborg-eval-check-meta config.nix: checkMeta = true
Details
grahamcofborg-eval-darwin nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="5caa767"; rev="5caa76705bd839fb6733f64740dec95d7b2fefc5"; } ./pkgs/t
Details
grahamcofborg-eval-lib-tests nix-build --arg pkgs import ./. {} ./lib/tests/release.nix
Details
grahamcofborg-eval-nixos nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="5caa767"; rev="5caa76705bd839fb6733f64740dec95d7b2fefc5"; } ./nixos/
Details
grahamcofborg-eval-nixos-manual nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="5caa767"; rev="5caa76705bd839fb6733f64740dec95d7b2fefc5"; } ./nixos/
Details
grahamcofborg-eval-nixos-options nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="5caa767"; rev="5caa76705bd839fb6733f64740dec95d7b2fefc5"; } ./nixos/
Details
grahamcofborg-eval-nixpkgs-manual nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="5caa767"; rev="5caa76705bd839fb6733f64740dec95d7b2fefc5"; } ./pkgs/t
Details
grahamcofborg-eval-nixpkgs-tarball nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="5caa767"; rev="5caa76705bd839fb6733f64740dec95d7b2fefc5"; } ./pkgs/t
Details
grahamcofborg-eval-nixpkgs-unstable-jobset nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="5caa767"; rev="5caa76705bd839fb6733f64740dec95d7b2fefc5"; } ./pkgs/t
Details
grahamcofborg-eval-package-list nix-env -qa --json --file .
Details
grahamcofborg-eval-package-list-no-aliases nix-env -qa --json --file . --arg config { allowAliases = false; }
Details
@bcdarwin bcdarwin deleted the bcdarwin:itk-5.1.0 branch May 9, 2020
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