vtk_8: remove

pkgs/applications/science/physics/elmerfem/default.nix

@@ -1,14 +1,14 @@
-{ lib, stdenv, fetchFromGitHub, cmake, git, gfortran, mpi, blas, liblapack, pkg-config, libGL, libGLU, opencascade, libsForQt5, tbb, vtkWithQt5 }:
+{ lib, stdenv, fetchFromGitHub, cmake, git, gfortran, mpi, blas, liblapack, pkg-config, libGL, libGLU, opencascade-occt, libsForQt5, tbb, vtkWithQt5 }:
 
 stdenv.mkDerivation rec {
   pname = "elmerfem";
-  version = "unstable-2023-02-03";
+  version = "unstable-2023-09-18";
 
   src = fetchFromGitHub {
     owner = "elmercsc";
     repo = pname;
-    rev = "39c8784b6e4543a6bf560b5d597e0eec1eb06343";
-    hash = "sha256-yyxgFvlS+I4PouDL6eD4ZrXuONTDejCSYKq2AwQ0Iug=";
+    rev = "0fcced06f91c93f44557efd6a5f10b2da5c7066c";
+    hash = "sha256-UuARDYW7D3a4dB6I86s2Ed5ecQxc+Y/es3YIeF2VyTc=";
   };
 
   hardeningDisable = [ "format" ];
@@ -28,7 +28,7 @@ stdenv.mkDerivation rec {
     libsForQt5.qwt
     libGL
     libGLU
-    opencascade
+    opencascade-occt
     tbb
     vtkWithQt5
   ];

pkgs/development/libraries/opencv/3.x.nix

@@ -22,7 +22,6 @@
 , enablePython    ? false, pythonPackages ? null
 , enableGtk2      ? false, gtk2
 , enableGtk3      ? false, gtk3
-, enableVtk       ? false, vtk_8
 , enableFfmpeg    ? false, ffmpeg
 , enableGStreamer ? false, gst_all_1
 , enableTesseract ? false, tesseract, leptonica
@@ -191,7 +190,6 @@ stdenv.mkDerivation {
     ++ lib.optional enablePython pythonPackages.python
     ++ lib.optional enableGtk2 gtk2
     ++ lib.optional enableGtk3 gtk3
-    ++ lib.optional enableVtk vtk_8
     ++ lib.optional enableJPEG libjpeg
     ++ lib.optional enablePNG libpng
     ++ lib.optional enableTIFF libtiff

pkgs/development/libraries/openscenegraph/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, lib, fetchFromGitHub, cmake, pkg-config, doxygen,
+{ stdenv, lib, fetchFromGitHub, fetchpatch, cmake, pkg-config, doxygen,
   libX11, libXinerama, libXrandr, libGLU, libGL,
   glib, ilmbase, libxml2, pcre, zlib,
   AGL, Accelerate, Carbon, Cocoa, Foundation,
@@ -11,7 +11,7 @@
   gdalSupport ? false, gdal,
   curlSupport ? true, curl,
   colladaSupport ? false, collada-dom,
-  opencascadeSupport ? false, opencascade,
+  opencascadeSupport ? false, opencascade-occt,
   ffmpegSupport ? false, ffmpeg,
   nvttSupport ? false, nvidia-texture-tools,
   freetypeSupport ? true, freetype,
@@ -51,7 +51,7 @@ stdenv.mkDerivation rec {
     ++ lib.optional gdalSupport gdal
     ++ lib.optional curlSupport curl
     ++ lib.optional colladaSupport collada-dom
-    ++ lib.optional opencascadeSupport opencascade
+    ++ lib.optional opencascadeSupport opencascade-occt
     ++ lib.optional ffmpegSupport ffmpeg
     ++ lib.optional nvttSupport nvidia-texture-tools
     ++ lib.optional freetypeSupport freetype
@@ -66,7 +66,15 @@ stdenv.mkDerivation rec {
     ++ lib.optionals (!stdenv.isDarwin) [  ]
     ++ lib.optionals stdenv.isDarwin [ AGL Accelerate Carbon Cocoa Foundation ]
     ++ lib.optional (restSupport || colladaSupport) boost
-  ;
+    ;
+
+  patches = [
+    (fetchpatch {
+      name = "opencascade-api-patch";
+      url = "https://github.com/openscenegraph/OpenSceneGraph/commit/bc2daf9b3239c42d7e51ecd7947d31a92a7dc82b.patch";
+      hash = "sha256-VR8YKOV/YihB5eEGZOGaIfJNrig1EPS/PJmpKsK284c=";
+    })
+  ];
 
   cmakeFlags = lib.optional (!withApps) "-DBUILD_OSG_APPLICATIONS=OFF" ++ lib.optional withExamples "-DBUILD_OSG_EXAMPLES=ON";
 

pkgs/development/libraries/science/biology/mirtk/default.nix

@@ -1,38 +1,64 @@
-{ lib, stdenv, gtest, fetchFromGitHub, cmake, boost, eigen, python3, vtk_8, zlib, tbb }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+, python3
+, boost
+, eigen
+, libGLU
+, fltk
+, itk
+, vtk
+, zlib
+, tbb
+}:
 
 stdenv.mkDerivation rec {
-  version = "2.0.0";
   pname = "mirtk";
+  version = "unstable-2022-07-22";
 
   src = fetchFromGitHub {
     owner = "BioMedIA";
     repo = "MIRTK";
-    rev = "v${version}";
-    sha256 = "0i2v97m66ir5myvi5b123r7zcagwy551b73s984gk7lksl5yiqxk";
+    rev = "973ce2fe3f9508dec68892dbf97cca39067aa3d6";
+    hash = "sha256-vKgkDrbyGOcbaYlxys1duC8ZNG0Y2nqh3TtSQ06Ox0Q=";
     fetchSubmodules = true;
   };
 
   cmakeFlags = [
     "-DWITH_VTK=ON"
     "-DBUILD_ALL_MODULES=ON"
     "-DWITH_TBB=ON"
+    "-DWITH_ITK=ON"
+    "-DWITH_GIFTICLIB=ON"
+    "-DWITH_NIFTILIB=ON"
   ];
 
-  doCheck = true;
-
-  checkPhase = ''
-    ctest -E '(Polynomial|ConvolutionFunction|Downsampling|EdgeTable|InterpolateExtrapolateImage)'
+  # tries to download data during configuration
+  postPatch = ''
+    substituteInPlace Packages/DrawEM/CMakeLists.txt --replace "include(Atlases.cmake)" ""
   '';
-  # testPolynomial - segfaults for some reason
-  # testConvolutionFunction, testDownsampling - main not called correctly
-  # testEdgeTable, testInterpolateExtrapolateImageFunction - setup fails
+
+  # tests don't seem to be maintained and gtest fails to link with BUILD_TESTING=ON;
+  # unclear if specific to Nixpkgs
+  doCheck = false;
 
   postInstall = ''
     install -Dm644 -t "$out/share/bash-completion/completions/mirtk" share/completion/bash/mirtk
   '';
 
-  nativeBuildInputs = [ cmake gtest ];
-  buildInputs = [ boost eigen python3 vtk_8 zlib tbb ];
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [
+    boost
+    eigen
+    fltk
+    itk
+    libGLU.dev
+    python3
+    tbb
+    vtk
+    zlib
+  ];
 
   meta = with lib; {
     homepage = "https://github.com/BioMedIA/MIRTK";

pkgs/development/python-modules/cadquery/default.nix

@@ -5,12 +5,11 @@
 , pythonAtLeast
 , fetchFromGitHub
 , pyparsing
-, opencascade
+, opencascade-occt
 , stdenv
 , python
 , cmake
 , swig
-, smesh
 , freetype
 , libGL
 , libGLU
@@ -42,8 +41,7 @@ let
 
     buildInputs = [
       python
-      opencascade
-      smesh
+      opencascade-occt
       freetype
       libGL
       libGLU
@@ -57,9 +55,6 @@ let
     cmakeFlags = [
       "-Wno-dev"
       "-DPYTHONOCC_INSTALL_DIRECTORY=${placeholder "out"}/${python.sitePackages}/OCC"
-      "-DSMESH_INCLUDE_PATH=${smesh}/include/smesh"
-      "-DSMESH_LIB_PATH=${smesh}/lib"
-      "-DPYTHONOCC_WRAP_SMESH=TRUE"
     ];
   });
 
@@ -76,7 +71,7 @@ in
     };
 
     buildInputs = [
-      opencascade
+      opencascade-occt
     ];
 
     propagatedBuildInputs = [
@@ -99,5 +94,6 @@ in
       homepage = "https://github.com/CadQuery/cadquery";
       license = licenses.asl20;
       maintainers = with maintainers; [ marcus7070 ];
+      broken = true;
     };
   }

pkgs/development/python-modules/pythonocc-core/default.nix

@@ -1,4 +1,7 @@
-{ lib, stdenv, python, fetchFromGitHub
+{ lib
+, stdenv
+, python
+, fetchFromGitHub
 , cmake
 , Cocoa
 , fontconfig
@@ -11,7 +14,6 @@
 , libXmu
 , opencascade-occt
 , rapidjson
-, smesh
 , swig4
 }:
 
@@ -34,18 +36,14 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ cmake swig4 ];
   buildInputs = [
-    python opencascade-occt smesh
+    python opencascade-occt
     freetype libGL libGLU libX11 libXext libXmu libXi
     fontconfig rapidjson
   ] ++ lib.optionals stdenv.isDarwin [ Cocoa ];
 
   cmakeFlags = [
     "-Wno-dev"
     "-DPYTHONOCC_INSTALL_DIRECTORY=${placeholder "out"}/${python.sitePackages}/OCC"
-
-    "-DSMESH_INCLUDE_PATH=${smesh}/include/smesh"
-    "-DSMESH_LIB_PATH=${smesh}/lib"
-    "-DPYTHONOCC_WRAP_SMESH=TRUE"
   ];
 
   passthru = {
@@ -57,6 +55,7 @@ stdenv.mkDerivation rec {
   meta = with lib; {
     description = "Python wrapper for the OpenCASCADE 3D modeling kernel";
     homepage = "https://github.com/tpaviot/pythonocc-core";
+    changelog = "https://github.com/tpaviot/pythonocc-core/releases/tag/${version}";
     license = licenses.lgpl3;
     platforms = platforms.unix;
     maintainers = with maintainers; [ gebner ];

pkgs/top-level/aliases.nix

@@ -1261,6 +1261,7 @@ mapAliases ({
   openbazaar = throw "openbazzar has been removed from nixpkgs as upstream has abandoned the project"; # Added 2022-01-06
   openbazaar-client = throw "openbazzar-client has been removed from nixpkgs as upstream has abandoned the project"; # Added 2022-01-06
   opencascade_oce = throw "'opencascade_oce' has been renamed to/replaced by 'opencascade'"; # Converted to throw 2022-02-22
+  opencascade = throw "'opencascade' has been removed as it is unmaintained; consider opencascade-occt instead'"; # Added 2023-09-18
   opencl-icd = throw "'opencl-icd' has been renamed to/replaced by 'ocl-icd'"; # Converted to throw 2022-02-22
   openconnect_head = openconnect_unstable; # Added 2022-03-29
   openconnect_gnutls = openconnect; # Added 2022-03-29
@@ -1646,6 +1647,7 @@ mapAliases ({
   slurm-llnl = slurm; # renamed July 2017
   slurm-llnl-full = slurm-full; # renamed July 2017
   smbclient = throw "'smbclient' has been renamed to/replaced by 'samba'"; # Converted to throw 2022-02-22
+  smesh = throw "'smesh' has been removed as it's unmaintained and depends on opencascade-oce, which is also unmaintained"; # Added 2023-09-18
   smugline = throw "smugline has been removed from nixpkgs, as it's unmaintained and depends on deprecated libraries"; # Added 2020-11-04
   snack = throw "snack has been removed: broken for 5+ years"; # Added 2022-04-21
   soldat-unstable = opensoldat; # Added 2022-07-02