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Merge pull request #189329 from bcdarwin/itk4-removal

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Sandro 2022-09-05 16:05:51 +02:00 committed by GitHub
commit ef987a9604
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GPG Key ID: 4AEE18F83AFDEB23
9 changed files with 27 additions and 88 deletions
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4
pkgs/applications/science/biology/EZminc/default.nix
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@ -1,4 +1,4 @@
{ lib, stdenv, fetchFromGitHub, cmake, pkg-config, libminc, bicpl, itk4, fftwFloat, gsl }:
{ lib, stdenv, fetchFromGitHub, cmake, pkg-config, libminc, bicpl, itk, fftwFloat, gsl }:
stdenv.mkDerivation rec {
pname = "EZminc";
@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
};
nativeBuildInputs = [ cmake pkg-config ];
buildInputs = [ itk4 libminc bicpl fftwFloat gsl ];
buildInputs = [ itk libminc bicpl fftwFloat gsl ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake"
"-DEZMINC_BUILD_TOOLS=TRUE"

18
pkgs/applications/science/biology/ants/default.nix
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@ -1,26 +1,18 @@
{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, itk4, vtk_7, Cocoa }:
{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper, itk-unstable, vtk_8, Cocoa }:
stdenv.mkDerivation rec {
pname = "ANTs";
version = "2.2.0";
version = "2.4.1";
src = fetchFromGitHub {
owner = "ANTsX";
repo = "ANTs";
rev = "37ad4e20be3a5ecd26c2e4e41b49e778a0246c3d";
sha256 = "1hrdwv3m9xh3yf7l0rm2ggxc2xzckfb8srs88g485ibfszx7i03q";
rev = "v${version}";
sha256 = "sha256-sRZwRRqqU0xiu4K6xlLQV4xzVNnzMlnRsk+TPiv0wD0=";
};
patches = [
# Fix build with gcc8
(fetchpatch {
url = "https://github.com/ANTsX/ANTs/commit/89af9b2694715bf8204993e032fa132f80cf37bd.patch";
sha256 = "1glkrwa1jmxxbmzihycxr576azjqby31jwpj165qc54c91pn0ams";
})
];
nativeBuildInputs = [ cmake makeWrapper ];
buildInputs = [ itk4 vtk_7 ] ++ lib.optionals stdenv.isDarwin [ Cocoa ];
buildInputs = [ itk-unstable vtk_8 ] ++ lib.optionals stdenv.isDarwin [ Cocoa ];
cmakeFlags = [ "-DANTS_SUPERBUILD=FALSE" "-DUSE_VTK=TRUE" ];

35
pkgs/development/libraries/itk/4.x.nix
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@ -1,35 +0,0 @@
{ lib, stdenv, fetchFromGitHub, cmake, libX11, libuuid, xz, vtk_7, Cocoa }:
stdenv.mkDerivation rec {
pname = "itk";
version = "4.13.3";
src = fetchFromGitHub {
owner = "InsightSoftwareConsortium";
repo = "ITK";
rev = "v${version}";
sha256 = "067vkh39jxcvyvn69qjh4vi3wa7vdvm9m6qsg3jmnmm7gzw0kjlm";
};
cmakeFlags = [
"-DBUILD_TESTING=OFF"
"-DBUILD_EXAMPLES=OFF"
"-DBUILD_SHARED_LIBS=ON"
"-DModule_ITKMINC=ON"
"-DModule_ITKIOMINC=ON"
"-DModule_ITKIOTransformMINC=ON"
"-DModule_ITKVtkGlue=ON"
"-DModule_ITKReview=ON"
];
nativeBuildInputs = [ cmake xz ];
buildInputs = [ libX11 libuuid vtk_7 ] ++ lib.optionals stdenv.isDarwin [ Cocoa ];
meta = {
description = "Insight Segmentation and Registration Toolkit";
homepage = "https://www.itk.org/";
license = lib.licenses.asl20;
maintainers = with lib.maintainers; [viric];
platforms = with lib.platforms; linux ++ darwin;
};
}

5
pkgs/development/libraries/itk/5.x.nix Normal file
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@ -0,0 +1,5 @@
import ./generic.nix rec {
version = "5.2.1";
rev = "v${version}";
sourceSha256 = "sha256-KaVe9FMGm4ZVMpwAT12fA67T0qZS3ZueiI8z85+xSwE=";
}

8
pkgs/development/libraries/itk/default.nix → pkgs/development/libraries/itk/generic.nix
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@ -1,9 +1,11 @@
{ version, rev, sourceSha256 }:
{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper
, pkg-config, libX11, libuuid, xz, vtk, Cocoa }:
stdenv.mkDerivation rec {
pname = "itk";
version = "5.2.1";
inherit version;
itkGenericLabelInterpolatorSrc = fetchFromGitHub {
owner = "InsightSoftwareConsortium";
@ -22,8 +24,8 @@ stdenv.mkDerivation rec {
src = fetchFromGitHub {
owner = "InsightSoftwareConsortium";
repo = "ITK";
rev = "v${version}";
sha256 = "sha256-KaVe9FMGm4ZVMpwAT12fA67T0qZS3ZueiI8z85+xSwE=";
inherit rev;
sha256 = sourceSha256;
};
postPatch = ''

5
pkgs/development/libraries/itk/unstable.nix Normal file
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@ -0,0 +1,5 @@
import ./generic.nix {
version = "unstable-2022-07-02";
rev = "5e7aea957c82b67d4364b2b88999805616e3b01d";
sourceSha256 = "sha256-tjkoaHCuVdvgE6X+7Kb8mt9oxINWs4R0xD9cxdEeYKk=";
}

22
pkgs/development/libraries/vtk/7.x.nix
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@ -1,22 +0,0 @@
import ./generic.nix {
majorVersion = "7.1";
minorVersion = "1";
sourceSha256 = "0nm7xwwj7rnsxjdv2ssviys8nhci4n9iiiqm2y14s520hl2dsp1d";
patchesToFetch = [
{
url = "https://gitlab.kitware.com/vtk/vtk/-/commit/706f1b397df09a27ab8981ab9464547028d0c322.diff";
sha256 = "1q3pi5h40g05pzpbqp75xlgzvbfvyw8raza51svmi7d8dlslqybx";
}
{
url = "https://gitweb.gentoo.org/repo/gentoo.git/plain/sci-libs/vtk/files/vtk-8.2.0-gcc-10.patch?id=c4256f68d3589570443075eccbbafacf661f785f";
sha256 = "sha256:0bpwrdfmi15grsg4jy7bzj2z6511a0c160cmw5lsi65aabyh7cl5";
}
# Add missing include required with recent Qt.
{
url = "https://gitlab.kitware.com/vtk/vtk/-/commit/797f28697d5ba50c1fa2bc5596af626a3c277826.diff";
sha256 = "BFjoKws1hVD3Ly9RS4lGN62J6RTyI1E8ATHrZdzg7ds=";
}
];
}

2
pkgs/development/libraries/vtk/generic.nix
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@ -96,6 +96,6 @@ in stdenv.mkDerivation rec {
maintainers = with maintainers; [ knedlsepp tfmoraes lheckemann ];
platforms = with platforms; unix;
# /nix/store/xxxxxxx-apple-framework-Security/Library/Frameworks/Security.framework/Headers/Authorization.h:192:7: error: variably modified 'bytes' at file scope
broken = stdenv.isDarwin && (lib.versions.major majorVersion == "7" || lib.versions.major majorVersion == "8");
broken = stdenv.isDarwin && (lib.versions.major majorVersion == "8");
};
}

16
pkgs/top-level/all-packages.nix
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@ -18873,15 +18873,16 @@ with pkgs;
nodejs = nodejs-14_x;
};
itk4 = callPackage ../development/libraries/itk/4.x.nix {
stdenv = if stdenv.cc.isGNU && stdenv.system == "x86_64-linux" then gcc10Stdenv else stdenv;
itk_5 = callPackage ../development/libraries/itk/5.x.nix {
inherit (darwin.apple_sdk.frameworks) Cocoa;
};
itk = callPackage ../development/libraries/itk {
itk-unstable = callPackage ../development/libraries/itk/unstable.nix {
inherit (darwin.apple_sdk.frameworks) Cocoa;
};
itk = itk_5;
jama = callPackage ../development/libraries/jama { };
jansson = callPackage ../development/libraries/jansson { };
@ -21941,14 +21942,6 @@ with pkgs;
vte_290 = callPackage ../development/libraries/vte/2.90.nix { };
vtk_7 = libsForQt515.callPackage ../development/libraries/vtk/7.x.nix {
stdenv = gcc9Stdenv;
inherit (darwin) libobjc;
inherit (darwin.apple_sdk.libs) xpc;
inherit (darwin.apple_sdk.frameworks) Cocoa CoreServices DiskArbitration
IOKit CFNetwork Security ApplicationServices
CoreText IOSurface ImageIO OpenGL GLUT;
};
vtk_8 = libsForQt515.callPackage ../development/libraries/vtk/8.x.nix {
stdenv = gcc9Stdenv;
inherit (darwin) libobjc;
@ -34033,7 +34026,6 @@ with pkgs;
angsd = callPackage ../applications/science/biology/angsd { };
ants = callPackage ../applications/science/biology/ants {
stdenv = if stdenv.cc.isGNU && stdenv.system == "x86_64-linux" then gcc10Stdenv else stdenv;
inherit (darwin.apple_sdk.frameworks) Cocoa;
};