diff --git a/pkgs/applications/science/biology/EZminc/default.nix b/pkgs/applications/science/biology/EZminc/default.nix index 6c140b03ee4b..a4bb8c62f1c4 100644 --- a/pkgs/applications/science/biology/EZminc/default.nix +++ b/pkgs/applications/science/biology/EZminc/default.nix @@ -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=${libminc}/lib/cmake" "-DEZMINC_BUILD_TOOLS=TRUE" diff --git a/pkgs/applications/science/biology/ants/default.nix b/pkgs/applications/science/biology/ants/default.nix index ac332f271662..873cb28b5161 100644 --- a/pkgs/applications/science/biology/ants/default.nix +++ b/pkgs/applications/science/biology/ants/default.nix @@ -1,26 +1,18 @@ -{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, itk4, vtk_7, Cocoa }: +{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper, itk-unstable, vtk_8, Cocoa }: stdenv.mkDerivation rec { pname = "ANTs"; - version = "2.2.0"; + version = "2.4.1"; src = fetchFromGitHub { owner = "ANTsX"; repo = "ANTs"; - rev = "37ad4e20be3a5ecd26c2e4e41b49e778a0246c3d"; - sha256 = "1hrdwv3m9xh3yf7l0rm2ggxc2xzckfb8srs88g485ibfszx7i03q"; + rev = "v${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" ]; diff --git a/pkgs/development/libraries/itk/4.x.nix b/pkgs/development/libraries/itk/4.x.nix deleted file mode 100644 index 54a3c33cd017..000000000000 --- a/pkgs/development/libraries/itk/4.x.nix +++ /dev/null @@ -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${version}"; - sha256 = "067vkh39jxcvyvn69qjh4vi3wa7vdvm9m6qsg3jmnmm7gzw0kjlm"; - }; - - cmakeFlags = [ - "-DBUILD_TESTING=OFF" - "-DBUILD_EXAMPLES=OFF" - "-DBUILD_SHARED_LIBS=ON" - "-DModule_ITKMINC=ON" - "-DModule_ITKIOMINC=ON" - "-DModule_ITKIOTransformMINC=ON" - "-DModule_ITKVtkGlue=ON" - "-DModule_ITKReview=ON" - ]; - - nativeBuildInputs = [ cmake xz ]; - buildInputs = [ libX11 libuuid vtk_7 ] ++ lib.optionals stdenv.isDarwin [ Cocoa ]; - - meta = { - description = "Insight Segmentation and Registration Toolkit"; - homepage = "https://www.itk.org/"; - license = lib.licenses.asl20; - maintainers = with lib.maintainers; [viric]; - platforms = with lib.platforms; linux ++ darwin; - }; -} diff --git a/pkgs/development/libraries/itk/5.x.nix b/pkgs/development/libraries/itk/5.x.nix new file mode 100644 index 000000000000..e50f2bbca494 --- /dev/null +++ b/pkgs/development/libraries/itk/5.x.nix @@ -0,0 +1,5 @@ +import ./generic.nix rec { + version = "5.2.1"; + rev = "v${version}"; + sourceSha256 = "sha256-KaVe9FMGm4ZVMpwAT12fA67T0qZS3ZueiI8z85+xSwE="; +} diff --git a/pkgs/development/libraries/itk/default.nix b/pkgs/development/libraries/itk/generic.nix similarity index 94% rename from pkgs/development/libraries/itk/default.nix rename to pkgs/development/libraries/itk/generic.nix index 6816c37b9be6..0d742b393b1d 100644 --- a/pkgs/development/libraries/itk/default.nix +++ b/pkgs/development/libraries/itk/generic.nix @@ -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 = '' diff --git a/pkgs/development/libraries/itk/unstable.nix b/pkgs/development/libraries/itk/unstable.nix new file mode 100644 index 000000000000..bb64d4afca9a --- /dev/null +++ b/pkgs/development/libraries/itk/unstable.nix @@ -0,0 +1,5 @@ +import ./generic.nix { + version = "unstable-2022-07-02"; + rev = "5e7aea957c82b67d4364b2b88999805616e3b01d"; + sourceSha256 = "sha256-tjkoaHCuVdvgE6X+7Kb8mt9oxINWs4R0xD9cxdEeYKk="; +} diff --git a/pkgs/development/libraries/vtk/7.x.nix b/pkgs/development/libraries/vtk/7.x.nix deleted file mode 100644 index 615553f80f22..000000000000 --- a/pkgs/development/libraries/vtk/7.x.nix +++ /dev/null @@ -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="; - } - ]; -} diff --git a/pkgs/development/libraries/vtk/generic.nix b/pkgs/development/libraries/vtk/generic.nix index 467abeead3e3..b88ddee6b249 100644 --- a/pkgs/development/libraries/vtk/generic.nix +++ b/pkgs/development/libraries/vtk/generic.nix @@ -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"); }; } diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 3f5e0d176b73..60c7c2598a39 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -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; };