Accepting request 810056 from home:badshah400:branches:science

* Update to version 5.0.1
* Drop add_gcc9_support.patch: no longer required with upstream support for up to GCC 10 baked in.
* Pass options to %cmake to set proper install paths when installing; prevents the need to manually move installed libs around. Drop sed BuildRequires that is no longer required as a consequence.
* Enable python3 wrapping (needed for tomviz, for instance); split out separate python3-itk package. Introduces BuildRequires: python3-devel.
* Add BuildRequires: memory-constraints and use %limit_build to require at least 2 GiB memory per thread; OOM failures otherwise.
* Update _constraints file: at least 24 GB (!!!) disk space and 2 GB memory now required.
* Use ninja for build (BuildRequires: ninja); compile using %cmake_build instead of make directly.
* Additional system library dependencies: CastXML-devel, gtest, double-conversion, and gdcm-devel.
* Convert BuildRequires to pkgconfig() or cmake() based ones wherever possible.
* Update URL and Source URL in keeping with upstream's move to github.
* Drop conditionals for old openSUSE versions.

OBS-URL: https://build.opensuse.org/request/show/810056
OBS-URL: https://build.opensuse.org/package/show/Application:Geo/insighttoolkit?expand=0&rev=21

InsightToolkit-4.13.2.tar.xz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:dabe05234d24635c96fd9b1a5f5e3afc34e11f49a31e5107db19bf61da758fa5
-size 12424136

InsightToolkit-5.0.1.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:613b125cbf58481e8d1e36bdeacf7e21aba4b129b4e524b112f70c4d4e6d15a6
+size 20627889

_constraints

@@ -1,7 +1,10 @@
 <constraints>
   <hardware>
      <disk>
-      <size unit="G">6</size>
+      <size unit="G">24</size>
     </disk>
+    <physicalmemory>
+      <size unit="G">2</size>
+    </physicalmemory>
   </hardware>
 </constraints>

add_gcc9_support.patch

@@ -1,21 +0,0 @@
-diff -ur InsightToolkit-4.13.2/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h InsightToolkit-4.13.2_fix/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h
---- InsightToolkit-4.13.2/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h	2019-07-02 15:24:20.401356209 +0200
-+++ InsightToolkit-4.13.2_fix/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h	2019-07-02 15:25:33.639041143 +0200
-@@ -97,6 +97,17 @@
- #  else
- #   define VCL_GCC_80
- #  endif
-+# elif (__GNUC__==9)
-+#  define VCL_GCC_9
-+#  if (__GNUC_MINOR__ > 2 )
-+#   define VCL_GCC_93
-+#  elif (__GNUC_MINOR__ > 1 )
-+#   define VCL_GCC_92
-+#  elif (__GNUC_MINOR__ > 0 )
-+#   define VCL_GCC_91
-+#  else
-+#   define VCL_GCC_90
-+#  endif
- # else
- #  error "Dunno about this gcc"
- # endif

dcmtk-cmake.patch

@@ -1,6 +1,7 @@
-diff -ruN InsightToolkit-4.13.2.orig/Modules/ThirdParty/DCMTK/CMake/FindDCMTK.cmake InsightToolkit-4.13.2/Modules/ThirdParty/DCMTK/CMake/FindDCMTK.cmake
+Index: InsightToolkit-5.0.1/Modules/ThirdParty/DCMTK/CMake/FindDCMTK.cmake
---- InsightToolkit-4.13.2.orig/Modules/ThirdParty/DCMTK/CMake/FindDCMTK.cmake	1970-01-01 02:00:00.000000000 +0200
+===================================================================
-+++ InsightToolkit-4.13.2/Modules/ThirdParty/DCMTK/CMake/FindDCMTK.cmake	2015-11-12 18:21:07.000000000 +0200
+--- /dev/null
++++ InsightToolkit-5.0.1/Modules/ThirdParty/DCMTK/CMake/FindDCMTK.cmake
 @@ -0,0 +1,350 @@
 +# - find DCMTK libraries and applications
 +# The module defines the following variables:
@@ -352,10 +353,11 @@ diff -ruN InsightToolkit-4.13.2.orig/Modules/ThirdParty/DCMTK/CMake/FindDCMTK.cm
 +endif()
 +
 +message(STATUS "Trying to find DCMTK relying on FindDCMTK.cmake - ok")
-diff -ruN InsightToolkit-4.13.2.orig/Modules/ThirdParty/DCMTK/CMakeLists.txt InsightToolkit-4.13.2/Modules/ThirdParty/DCMTK/CMakeLists.txt
+Index: InsightToolkit-5.0.1/Modules/ThirdParty/DCMTK/CMakeLists.txt
---- InsightToolkit-4.13.2.orig/Modules/ThirdParty/DCMTK/CMakeLists.txt	2016-05-26 18:32:22.000000000 +0300
+===================================================================
-+++ InsightToolkit-4.13.2/Modules/ThirdParty/DCMTK/CMakeLists.txt	2016-10-02 12:37:14.117972925 +0300
+--- InsightToolkit-5.0.1.orig/Modules/ThirdParty/DCMTK/CMakeLists.txt
-@@ -154,14 +154,14 @@
++++ InsightToolkit-5.0.1/Modules/ThirdParty/DCMTK/CMakeLists.txt
+@@ -102,14 +102,14 @@ if(ITK_USE_SYSTEM_DCMTK)
    # When this module is loaded by an app, load DCMTK too.
    set(ITKDCMTK_EXPORT_CODE_INSTALL "
  set(DCMTK_DIR \"${DCMTK_DIR}\")
@@ -372,10 +374,11 @@ diff -ruN InsightToolkit-4.13.2.orig/Modules/ThirdParty/DCMTK/CMakeLists.txt Ins
  endif()
  ")
  
-diff -ruN InsightToolkit-4.13.2.orig/Modules/ThirdParty/DCMTK/itk-module-init.cmake InsightToolkit-4.13.2/Modules/ThirdParty/DCMTK/itk-module-init.cmake
+Index: InsightToolkit-5.0.1/Modules/ThirdParty/DCMTK/itk-module-init.cmake
---- InsightToolkit-4.13.2.orig/Modules/ThirdParty/DCMTK/itk-module-init.cmake	2016-05-26 18:32:22.000000000 +0300
+===================================================================
-+++ InsightToolkit-4.13.2/Modules/ThirdParty/DCMTK/itk-module-init.cmake	2016-10-02 12:37:41.557974143 +0300
+--- InsightToolkit-5.0.1.orig/Modules/ThirdParty/DCMTK/itk-module-init.cmake
-@@ -12,7 +12,7 @@
++++ InsightToolkit-5.0.1/Modules/ThirdParty/DCMTK/itk-module-init.cmake
+@@ -24,7 +24,7 @@ endif()
  if(ITK_USE_SYSTEM_DCMTK)
    # Use local FindDCMTK.cmake.
    list(INSERT CMAKE_MODULE_PATH 0 "${CMAKE_CURRENT_LIST_DIR}/CMake")

insighttoolkit.changes

@@ -1,3 +1,34 @@
+-------------------------------------------------------------------
+Mon May 18 01:15:30 UTC 2020 - Atri Bhattacharya <badshah400@gmail.com>
+
+- Update to version 5.0.1: See
+  https://discourse.itk.org/t/itk-5-0-1-has-been-released/2094.
+- Changes from version 5.0.0: See
+  https://discourse.itk.org/t/itk-5-0-0-has-been-released/1931.
+- Drop add_gcc9_support.patch: no longer required with upstream
+  support for up to GCC 10 baked in.
+- Pass options to %cmake to set proper install paths when
+  installing; prevents the need to manually move installed libs
+  around. Drop sed BuildRequires that is no longer required as a
+  consequence.
+- Enable python3 wrapping (needed for tomviz, for instance); split
+  out separate python3-itk package. Introduces BuildRequires:
+  python3-devel.
+- Add BuildRequires: memory-constraints and use %limit_build
+  to require at least 2 GiB memory per thread; OOM failures
+  otherwise.
+- Update _constraints file: at least 24 GB (!!!) disk space and 2
+  GB memory now required.
+- Use ninja for build (BuildRequires: ninja); compile using
+  %cmake_build instead of make directly.
+- Additional system library dependencies: CastXML-devel, gtest,
+  double-conversion, and gdcm-devel.
+- Convert BuildRequires to pkgconfig() or cmake() based ones
+  wherever possible.
+- Update URL and Source URL in keeping with upstream's move to
+  github.
+- Drop conditionals for old openSUSE versions.
+
 -------------------------------------------------------------------
 Sat Jul  6 18:06:51 UTC 2019 - Jan Engelhardt <jengelh@inai.de>
 

insighttoolkit.spec

@@ -1,7 +1,7 @@
 #
 # spec file for package insighttoolkit
 #
-# Copyright (c) 2016 SUSE LINUX GmbH, Nuernberg, Germany.
+# Copyright (c) 2020 SUSE LLC
 # Copyright (c) 2016 Angelos Tzotsos <tzotsos@opensuse.org>.
 #
 # All modifications and additions to the file contributed by third parties
@@ -13,56 +13,60 @@
 # license that conforms to the Open Source Definition (Version 1.9)
 # published by the Open Source Initiative.
 
-# Please submit bugfixes or comments via http://bugs.opensuse.org/
+# Please submit bugfixes or comments via https://bugs.opensuse.org/
 #
 
 
+%global __builder ninja
+
 %define tarname InsightToolkit
-%define baseversion 4.13
+%define baseversion 5.0
+%define libname lib%{name}5
+
 Name:           insighttoolkit
-Version:        %{baseversion}.2
+Version:        5.0.1
 Release:        0
 Summary:        Insight Segmentation and Registration Toolkit
 License:        Apache-2.0
 Group:          Development/Libraries/C and C++
-Url:            http://www.itk.org
+URL:            https://www.itk.org
-#Source0:        http://sourceforge.net/projects/itk/files/itk/%{baseversion}/%{tarname}-%{version}.tar.xz
+Source:         https://github.com/InsightSoftwareConsortium/ITK/releases/download/v%{version}/%{tarname}-%{version}.tar.gz
-Source:         https://netix.dl.sourceforge.net/project/itk/itk/%{baseversion}/%{tarname}-%{version}.tar.xz
 Patch0:         dcmtk-cmake.patch
 # PATCH-FIX-UPSTREAM proper linking against math library
 Patch1:         nrrdio-linking.patch
-# PATCH-FIX-UPSTREAM add support for GCC 9
-Patch2:         add_gcc9_support.patch
 # PATCH-FIX-UPSTREAM proper linking against math library
 Patch3:         itklbfgs-linking.patch
-BuildRequires:  cmake >= 2.8.0
+BuildRequires:  CastXML-devel
+BuildRequires:  cmake
 BuildRequires:  dcmtk
 BuildRequires:  dcmtk-devel
 BuildRequires:  fdupes
-BuildRequires:  fftw3-devel
 BuildRequires:  fftw3-threads-devel
-BuildRequires:  gcc
 BuildRequires:  gcc-c++
-# BuildRequires:  gdcm-devel
+BuildRequires:  gdcm-devel
+BuildRequires:  gtest
 BuildRequires:  hdf5-devel
-BuildRequires:  libexpat-devel
+BuildRequires:  libnsl-devel
-BuildRequires:  libjpeg-devel
+BuildRequires:  memory-constraints
-BuildRequires:  libpng-devel
+BuildRequires:  ninja
-BuildRequires:  libtiff-devel
+BuildRequires:  pkgconfig
-BuildRequires:  libxml2-devel
+BuildRequires:  python3-devel
-BuildRequires:  python-devel
-BuildRequires:  sed
 BuildRequires:  swig
-%if 0%{suse_version} > 1320
 # Indirect DCMTK dep. Should DCMTK be fixed?
 # tcpd-devel is needed for libwrap.so on Tumbleweed (> Leap 42.3)
 BuildRequires:  tcpd-devel
-BuildRequires:  libnsl-devel
-%endif
 BuildRequires:  vtk-devel
+BuildRequires:  vtk-qt
 BuildRequires:  xz
-BuildRequires:  zlib-devel
+BuildRequires:  cmake(double-conversion)
-BuildRoot:      %{_tmppath}/%{name}-%{version}-build
+BuildRequires:  pkgconfig(eigen3)
+BuildRequires:  pkgconfig(expat)
+BuildRequires:  pkgconfig(fftw3)
+BuildRequires:  pkgconfig(libjpeg)
+BuildRequires:  pkgconfig(libpng)
+BuildRequires:  pkgconfig(libtiff-4)
+BuildRequires:  pkgconfig(libxml-2.0)
+BuildRequires:  pkgconfig(zlib)
 
 %description
 ITK is a suite of software tools for image analysis.
@@ -70,11 +74,11 @@ ITK is a suite of software tools for image analysis.
 %package devel
 Summary:        Development files for ITK
 Group:          Development/Libraries/C and C++
+Requires:       %{libname} = %{version}
 Requires:       dcmtk-devel
 Requires:       fftw3-devel
 Requires:       fftw3-threads-devel
 Requires:       hdf5-devel
-Requires:       lib%{name}4 = %{version}
 Requires:       libexpat-devel
 Requires:       libjpeg-devel
 Requires:       libpng-devel
@@ -87,93 +91,77 @@ Provides:       lib%{name}-devel
 Development files for the ITK library.
 ITK is a suite of software tools for image analysis.
 
-%package -n lib%{name}4
+%package -n %{libname}
 Summary:        Insight Segmentation and Registration Toolkit
 Group:          System/Libraries
 
-%description -n lib%{name}4
+%description -n %{libname}
 Shared ITK library.
 ITK is a suite of software tools for image analysis.
 
+%package -n python3-itk
+Summary:        Python bindings for itk
+Group:          Development/Libraries/C and C++
+
+%description -n python3-itk
+ITK is a suite of software tools for image analysis. This package provides the python3 bindings for ITK.
+
 %prep
 %setup -q -n %{tarname}-%{version}
 %patch0 -p1
 %patch1 -p1
-%patch2 -p1
 %patch3 -p1
 
 %build
+%limit_build -m 2000
+# HAS TROUBLE LOCATING gdcm INCLUDEDIRS, ADD IT TO CXXFLAGS
+export CXXFLAGS+=" -I%{_includedir}/gdcm/"
+
 %cmake \
+  -DITK_INSTALL_LIBRARY_DIR:PATH=%{_lib}/ \
+  -DITK_INSTALL_INCLUDE_DIR:PATH=include/%{name}/ \
+  -DITK_INSTALL_PACKAGE_DIR:PATH=%{_lib}/cmake/%{name}/ \
+  -DITK_INSTALL_RUNTIME_DIR:PATH=%{_bindir} \
+  -DITK_INSTALL_DOC_DIR=share/doc/packages/%{name}/ \
   -DBUILD_EXAMPLES:BOOL=ON \
   -DBUILD_SHARED_LIBS:BOOL=ON \
   -DBUILD_TESTING:BOOL=OFF \
   -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=ON \
-  -DUSE_FFTWF=ON \
   -DITK_USE_FFTWD:BOOL=ON \
   -DITK_USE_FFTWF:BOOL=ON \
-  -DITK_USE_SYSTEM_FFTW:BOOL=ON \
+  -DITK_USE_SYSTEM_LIBRARIES:BOOL=ON \
+  -DITK_USE_SYSTEM_GDCM:BOOL=ON \
+  -DITK_USE_SYSTEM_CASTXML:BOOL=ON \
   -DITK_USE_STRICT_CONCEPT_CHECKING:BOOL=ON \
-  -DITK_USE_SYSTEM_DOUBLECONVERSION:BOOL=OFF \
-  -DITK_USE_SYSTEM_DCMTK:BOOL=ON \
-  -DITK_USE_SYSTEM_GDCM:BOOL=OFF \
-  -DITK_USE_SYSTEM_HDF5:BOOL=ON \
-  -DITK_USE_SYSTEM_JPEG:BOOL=ON \
-  -DITK_USE_SYSTEM_PNG:BOOL=ON \
-  -DITK_USE_SYSTEM_TIFF:BOOL=ON \
   -DITK_USE_SYSTEM_VXL:BOOL=OFF \
-  -DITK_USE_SYSTEM_ZLIB:BOOL=ON \
-  -DITK_USE_SYSTEM_EXPAT:BOOL=ON \
-  -DModule_ITKDCMTK:BOOL=ON \
-  -DModule_ITKIOPhilipsREC:BOOL=OFF \
-  -DModule_ITKLevelSetsv4Visualization:BOOL=OFF \
-  -DModule_ITKReview:BOOL=OFF \
-  -DModule_ITKVideoBridgeOpenCV:BOOL=OFF \
-  -DModule_ITKVideoBridgeVXL:BOOL=OFF \
-  -DModule_ITKVtkGlue:BOOL=OFF \
-  -DModule_ITKDeprecated:BOOL=OFF \
-  -DITKV3_COMPATIBILITY:BOOL=ON \
   -DVCL_INCLUDE_CXX_0X:BOOL=ON \
   -DITK_WRAPPING:BOOL=OFF \
-  -DITK_WRAP_PYTHON:BOOL=OFF \
+  -DITK_FORBID_DOWNLOADS=ON \
-  -DCMAKE_BUILD_TYPE:STRING="Release"
+  -DITK_WRAP_PYTHON:BOOL=ON
-
-make VERBOSE=1 %{?_smp_mflags}
 
+%cmake_build
 
 %install
 %cmake_install
 
-%if "%{_lib}" == "lib64"
-mkdir -p %{buildroot}%{_libdir}
-mv %{buildroot}%{_libexecdir}/* %{buildroot}%{_libdir}/
-sed -i 's|/lib/|/lib64/|g' %{buildroot}%{_libdir}/cmake/ITK-%{baseversion}/ITKConfig.cmake
-sed -i 's|/lib/|/lib64/|g' %{buildroot}%{_libdir}/cmake/ITK-%{baseversion}/ITKTargets.cmake
-sed -i 's|/lib/|/lib64/|g' %{buildroot}%{_libdir}/cmake/ITK-%{baseversion}/ITKTargets-release.cmake
-%endif
-rm -rf %{buildroot}%{_libexecdir}/debug
-# move files to a proper place
-mv %{buildroot}%{_libdir}/*itk*.cmake %{buildroot}%{_libdir}/cmake/
-# remove openjp2 file installation
-rm -rf %{buildroot}/%{_includedir}/gdcmopenjpeg %{buildroot}%{_libdir}/gdcmopenjpeg-* %{buildroot}%{_libdir}/pkgconfig/libopenjp2.pc
-rmdir %{buildroot}%{_libdir}/pkgconfig
-
 %fdupes %{buildroot}/%{_prefix}
 
-%post -n lib%{name}4 -p /sbin/ldconfig
+%post -n %{libname} -p /sbin/ldconfig
+%postun -n %{libname} -p /sbin/ldconfig
 
-%postun -n lib%{name}4 -p /sbin/ldconfig
+%files -n %{libname}
-
-%files -n lib%{name}4
-%defattr(644,root,root,755)
 %license LICENSE
 %{_libdir}/*.so.1
 
 %files devel
-%defattr(-,root,root,-)
+%{_includedir}/%{name}/
-%{_includedir}/*
 %{_libdir}/lib*.so
 %{_libdir}/cmake/
 %{_bindir}/itkTestDriver
-%{_datadir}/*
+%doc %{_docdir}/%{name}/
+
+%files -n python3-itk
+%{python3_sitearch}/*.py
+%{python3_sitearch}/itk/
 
 %changelog