Merge branch 'nixos-unstable' of https://github.com/NixOS/nixpkgs

Conflicts:
	nixpkgs/nixos/modules/config/console.nix
	nixpkgs/nixos/modules/services/mail/mailman.nix
	nixpkgs/nixos/modules/services/mail/public-inbox.nix
	nixpkgs/nixos/modules/services/mail/rss2email.nix
	nixpkgs/nixos/modules/services/networking/ssh/sshd.nix
	nixpkgs/pkgs/applications/networking/instant-messengers/dino/default.nix
	nixpkgs/pkgs/applications/networking/irc/weechat/default.nix
	nixpkgs/pkgs/applications/window-managers/sway/default.nix
	nixpkgs/pkgs/build-support/go/module.nix
	nixpkgs/pkgs/build-support/rust/build-rust-package/default.nix
	nixpkgs/pkgs/development/interpreters/python/default.nix
	nixpkgs/pkgs/development/node-packages/overrides.nix
	nixpkgs/pkgs/development/tools/b4/default.nix
	nixpkgs/pkgs/servers/dict/dictd-db.nix
	nixpkgs/pkgs/servers/mail/public-inbox/default.nix
	nixpkgs/pkgs/tools/security/pinentry/default.nix
	nixpkgs/pkgs/tools/text/unoconv/default.nix
	nixpkgs/pkgs/top-level/all-packages.nix

5 files changed, 97 insertions, 79 deletions

diff --git a/nixpkgs/pkgs/development/libraries/itk/4.x.nix b/nixpkgs/pkgs/development/libraries/itk/4.x.nix
deleted file mode 100644
index 54a3c33cd017..000000000000
--- a/nixpkgs/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${version}";
-    sha256 = "067vkh39jxcvyvn69qjh4vi3wa7vdvm9m6qsg3jmnmm7gzw0kjlm";
-  };
-
-  cmakeFlags = [
-    "-DBUILD_TESTING=OFF"
-    "-DBUILD_EXAMPLES=OFF"
-    "-DBUILD_SHARED_LIBS=ON"
-    "-DModule_ITKMINC=ON"
-    "-DModule_ITKIOMINC=ON"
-    "-DModule_ITKIOTransformMINC=ON"
-    "-DModule_ITKVtkGlue=ON"
-    "-DModule_ITKReview=ON"
-  ];
-
-  nativeBuildInputs = [ cmake xz ];
-  buildInputs = [ libX11 libuuid vtk_7 ] ++ lib.optionals stdenv.isDarwin [ Cocoa ];
-
-  meta = {
-    description = "Insight Segmentation and Registration Toolkit";
-    homepage = "https://www.itk.org/";
-    license = lib.licenses.asl20;
-    maintainers = with lib.maintainers; [viric];
-    platforms = with lib.platforms; linux ++ darwin;
-  };
-}
diff --git a/nixpkgs/pkgs/development/libraries/itk/5.2.x.nix b/nixpkgs/pkgs/development/libraries/itk/5.2.x.nix
new file mode 100644
index 000000000000..e50f2bbca494
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/itk/5.2.x.nix
@@ -0,0 +1,5 @@
+import ./generic.nix rec {
+  version = "5.2.1";
+  rev = "v${version}";
+  sourceSha256 = "sha256-KaVe9FMGm4ZVMpwAT12fA67T0qZS3ZueiI8z85+xSwE=";
+}
diff --git a/nixpkgs/pkgs/development/libraries/itk/5.x.nix b/nixpkgs/pkgs/development/libraries/itk/5.x.nix
new file mode 100644
index 000000000000..765b464e46a1
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/itk/5.x.nix
@@ -0,0 +1,5 @@
+import ./generic.nix rec {
+  version = "5.3.0";
+  rev = "v${version}";
+  sourceSha256 = "sha256-+qCd8Jzpl5fEPTUpLyjjFBkfgCn3+Lf4pi8QnjCwofs=";
+}
diff --git a/nixpkgs/pkgs/development/libraries/itk/default.nix b/nixpkgs/pkgs/development/libraries/itk/default.nix
deleted file mode 100644
index 08971c4c81c1..000000000000
--- a/nixpkgs/pkgs/development/libraries/itk/default.nix
+++ /dev/null
@@ -1,44 +0,0 @@
-{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper
-, pkg-config, libX11, libuuid, xz, vtk, Cocoa }:
-
-stdenv.mkDerivation rec {
-  pname = "itk";
-  version = "5.2.1";
-
-  src = fetchFromGitHub {
-    owner = "InsightSoftwareConsortium";
-    repo = "ITK";
-    rev = "v${version}";
-    sha256 = "sha256-KaVe9FMGm4ZVMpwAT12fA67T0qZS3ZueiI8z85+xSwE=";
-  };
-
-  postPatch = ''
-    substituteInPlace CMake/ITKSetStandardCompilerFlags.cmake  \
-      --replace "-march=corei7" ""  \
-      --replace "-mtune=native" ""
-  '';
-
-  cmakeFlags = [
-    "-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 makeWrapper ];
-  buildInputs = [ libX11 libuuid vtk ] ++ lib.optionals stdenv.isDarwin [ Cocoa ];
-
-  postInstall = ''
-    wrapProgram "$out/bin/h5c++" --prefix PATH ":" "${pkg-config}/bin"
-  '';
-
-  meta = {
-    description = "Insight Segmentation and Registration Toolkit";
-    homepage = "https://www.itk.org/";
-    license = lib.licenses.asl20;
-    maintainers = with lib.maintainers; [viric];
-  };
-}
diff --git a/nixpkgs/pkgs/development/libraries/itk/generic.nix b/nixpkgs/pkgs/development/libraries/itk/generic.nix
new file mode 100644
index 000000000000..3a6b2afee0d9
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/itk/generic.nix
@@ -0,0 +1,87 @@
+{ version, rev, sourceSha256 }:
+
+{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper
+, pkg-config, libX11, libuuid, xz, vtk, Cocoa }:
+
+let
+  itkGenericLabelInterpolatorSrc = fetchFromGitHub {
+    owner = "InsightSoftwareConsortium";
+    repo = "ITKGenericLabelInterpolator";
+    rev = "2f3768110ffe160c00c533a1450a49a16f4452d9";
+    hash = "sha256-Cm3jg14MMnbr/sP+gqR2Rh25xJjoRvpmY/jP/DKH978=";
+  };
+
+  itkAdaptiveDenoisingSrc = fetchFromGitHub {
+    owner = "ntustison";
+    repo = "ITKAdaptiveDenoising";
+    rev = "24825c8d246e941334f47968553f0ae388851f0c";
+    hash = "sha256-deJbza36c0Ohf9oKpO2T4po37pkyI+2wCSeGL4r17Go=";
+  };
+
+  itkSimpleITKFiltersSrc = fetchFromGitHub {
+    owner = "InsightSoftwareConsortium";
+    repo = "ITKSimpleITKFilters";
+    rev = "bb896868fc6480835495d0da4356d5db009592a6";
+    hash = "sha256-MfaIA0xxA/pzUBSwnAevr17iR23Bo5iQO2cSyknS3o4=";
+  };
+in
+
+stdenv.mkDerivation {
+  pname = "itk";
+  inherit version;
+
+  src = fetchFromGitHub {
+    owner = "InsightSoftwareConsortium";
+    repo = "ITK";
+    inherit rev;
+    sha256 = sourceSha256;
+  };
+
+  postPatch = ''
+    substituteInPlace CMake/ITKSetStandardCompilerFlags.cmake  \
+      --replace "-march=corei7" ""  \
+      --replace "-mtune=native" ""
+    substituteInPlace Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/libopenjp2.pc.cmake.in  \
+      --replace "@OPENJPEG_INSTALL_LIB_DIR@" "@OPENJPEG_INSTALL_FULL_LIB_DIR@"
+    ln -sr ${itkGenericLabelInterpolatorSrc} Modules/External/ITKGenericLabelInterpolator
+    ln -sr ${itkAdaptiveDenoisingSrc} Modules/External/ITKAdaptiveDenoising
+    ln -sr ${itkSimpleITKFiltersSrc} Modules/External/ITKSimpleITKFilters
+  '';
+
+  cmakeFlags = [
+    "-DBUILD_EXAMPLES=OFF"
+    "-DBUILD_SHARED_LIBS=ON"
+    "-DITK_FORBID_DOWNLOADS=ON"
+    "-DModule_ITKMINC=ON"
+    "-DModule_ITKIOMINC=ON"
+    "-DModule_ITKIOTransformMINC=ON"
+    "-DModule_SimpleITKFilters=ON"
+    "-DModule_ITKVtkGlue=ON"
+    "-DModule_ITKReview=ON"
+    "-DModule_MGHIO=ON"
+    "-DModule_AdaptiveDenoising=ON"
+    "-DModule_GenericLabelInterpolator=ON"
+  ];
+
+  nativeBuildInputs = [ cmake xz makeWrapper ];
+  buildInputs = [ libX11 libuuid vtk ] ++ lib.optionals stdenv.isDarwin [ Cocoa ];
+  # Due to ITKVtkGlue=ON and the additional dependencies needed to configure VTK 9
+  # (specifically libGL and libX11 on Linux),
+  # it's now seemingly necessary for packages that configure ITK to
+  # also include configuration deps of VTK, even if VTK is not required or available.
+  # These deps were propagated from VTK 9 in https://github.com/NixOS/nixpkgs/pull/206935,
+  # so we simply propagate them again from ITK.
+  # This admittedly is a hack and seems like an issue with VTK 9's CMake configuration.
+  propagatedBuildInputs = vtk.propagatedBuildInputs;
+
+  postInstall = ''
+    wrapProgram "$out/bin/h5c++" --prefix PATH ":" "${pkg-config}/bin"
+  '';
+
+  meta = {
+    description = "Insight Segmentation and Registration Toolkit";
+    homepage = "https://www.itk.org";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [viric];
+  };
+}