[gentoo-commits] proj/sci:master commit in: sci-biology/ants/, sci-biology/ants/files/

["Andrew Ammerlaan" <andrewammerlaan@gentoo.org>]

commit:     3713fffdc80a085c8de112f19a60000f0bd68810
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 15 11:16:22 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Sep 15 11:16:22 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3713fffd

sci-biology/ants: fix compile with itk-5.2

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 .../{ants-2.4.1.ebuild => ants-2.4.1-r1.ebuild}    |  17 +--
 .../ants/files/ants-2.3.1_p20191013-logic.patch    |  37 -------
 .../ants/files/ants-2.3.1_p20191013-paths.patch    |  40 -------
 sci-biology/ants/files/ants-2.3.4-libdir.patch     | 117 ---------------------
 sci-biology/ants/files/ants-2.3.4-version.patch    |  17 ---
 .../ants/files/ants-2.4.1-fix-compile.patch        |  13 +++
 6 files changed, 23 insertions(+), 218 deletions(-)

diff --git a/sci-biology/ants/ants-2.4.1.ebuild b/sci-biology/ants/ants-2.4.1-r1.ebuild
similarity index 75%
rename from sci-biology/ants/ants-2.4.1.ebuild
rename to sci-biology/ants/ants-2.4.1-r1.ebuild
index feba81d2c..70d5d8873 100644
--- a/sci-biology/ants/ants-2.4.1.ebuild
+++ b/sci-biology/ants/ants-2.4.1-r1.ebuild
@@ -10,9 +10,7 @@ MY_PN="ANTs"
 
 DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
 HOMEPAGE="https://stnava.github.io/ANTs/"
-SRC_URI="
-	https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz ->  ${P}.tar.gz
-"
+SRC_URI="https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz ->  ${P}.tar.gz"
 S="${WORKDIR}/${MY_PN}-${PV}"
 
 SLOT="0"
@@ -22,22 +20,27 @@ IUSE="test vtk"
 RESTRICT="test"
 
 DEPEND="
-	=sci-libs/itk-5.2*
+	!vtk? ( =sci-libs/itk-5.2*[fftw,-vtkglue] )
 	vtk? (
-		=sci-libs/itk-5.2*[vtkglue]
+		=sci-libs/itk-5.2*[fftw,vtkglue]
 		=sci-libs/vtk-9.1*
 	)
 "
 RDEPEND="${DEPEND}"
 
+PATCHES=(
+	"${FILESDIR}/${P}-fix-compile.patch"
+)
+
 src_configure() {
 	local mycmakeargs=(
+		-DBUILD_EXAMPLES=OFF
 		-DUSE_SYSTEM_ITK=ON
+		-DITK_USE_SYSTEM_FFTW=ON
 		-DITK_DIR="${EPREFIX}/usr/include/ITK-5.2/"
 		-DBUILD_TESTING="$(usex test ON OFF)"
 		-DUSE_VTK=$(usex vtk ON OFF)
 		-DUSE_SYSTEM_VTK=$(usex vtk ON OFF)
-		-DANTS_SNAPSHOT_VERSION:STRING=${PV}
 	)
 	use vtk && mycmakeargs+=(
 		-DVTK_DIR="${EPREFIX}/usr/include/vtk-9.1/"
@@ -46,7 +49,7 @@ src_configure() {
 }
 
 src_install() {
-	BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build"
+	BUILD_DIR="${WORKDIR}/${MY_PN}-${PV}_build/ANTS-build"
 	cmake_src_install
 	cd "${S}/Scripts" || die "scripts dir not found"
 	dobin *.sh

diff --git a/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch b/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch
deleted file mode 100644
index 932da9954..000000000
--- a/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-From b2c828ff8e5ce537d7096af04b086e965fede9e8 Mon Sep 17 00:00:00 2001
-From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
-Date: Mon, 7 Oct 2019 22:01:51 -0400
-Subject: [PATCH] Fix install logic
-
----
- ANTS.cmake       | 3 ++-
- SuperBuild.cmake | 2 ++
- 2 files changed, 4 insertions(+), 1 deletion(-)
-
-diff --git a/ANTS.cmake b/ANTS.cmake
-index a1baf845..95ffdc74 100644
---- a/ANTS.cmake
-+++ b/ANTS.cmake
-@@ -172,7 +172,8 @@ install(PROGRAMS Scripts/ANTSpexec.sh
-                 COMPONENT SCRIPTS
-         )
- 
--if(BUILD_SHARED_LIBS AND NOT (USE_SYSTEM_ITK AND USE_SYSTEM_VTK))
-+#Only install ITK/VTK libraries if shared build and superbuild is used
-+if(BUILD_SHARED_LIBS AND ((NOT USE_SYSTEM_ITK) OR ((NOT USE_SYSTEM_VTK) AND USE_VTK)))
-   install(DIRECTORY ${CMAKE_BINARY_DIR}/../staging/lib/
-           DESTINATION lib)
- endif()
-diff --git a/SuperBuild.cmake b/SuperBuild.cmake
-index f4630e64..32b930c2 100644
---- a/SuperBuild.cmake
-+++ b/SuperBuild.cmake
-@@ -207,6 +207,8 @@ list(APPEND ${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_VARS
-   CMAKE_C_COMPILER_LAUNCHER:STRING
-   CMAKE_CXX_COMPILER_LAUNCHER:STRING
-   CMAKE_CUDA_COMPILER_LAUNCHER:STRING
-+  USE_SYSTEM_ITK:BOOL
-+  USE_SYSTEM_VTK:BOOL
-   )
- 
- _expand_external_project_vars()

diff --git a/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch b/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch
deleted file mode 100644
index aaea92808..000000000
--- a/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt
---- a/Examples/CMakeLists.txt
-+++ b/Examples/CMakeLists.txt
-@@ -16,8 +16,9 @@
-+include(GNUInstallDirs)
- install(TARGETS antsUtilities
--    RUNTIME DESTINATION bin
-+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-     COMPONENT RUNTIME_antsUtilities
--    LIBRARY DESTINATION lib
-+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-     COMPONENT RUNTIME_antsUtilities
--    ARCHIVE DESTINATION lib
-+    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-     COMPONENT DEVELOPMENT_antsUtilities
-   )
-@@ -38,8 +38,8 @@
-   install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
--    RUNTIME DESTINATION bin
-+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-     COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
--    LIBRARY DESTINATION lib
-+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-     COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
--    ARCHIVE DESTINATION lib
-+    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-     COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
-   )
-@@ -61,8 +61,8 @@
-   install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
--    RUNTIME DESTINATION bin
-+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-     COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
--    LIBRARY DESTINATION lib
-+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-     COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
--    ARCHIVE DESTINATION lib
-+    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-     COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
-   )

diff --git a/sci-biology/ants/files/ants-2.3.4-libdir.patch b/sci-biology/ants/files/ants-2.3.4-libdir.patch
deleted file mode 100644
index b593c2778..000000000
--- a/sci-biology/ants/files/ants-2.3.4-libdir.patch
+++ /dev/null
@@ -1,117 +0,0 @@
-From 329a7be631b33294d9cf3d58e8cdeb62e0aa993c Mon Sep 17 00:00:00 2001
-From: Philip A Cook <cookpa@pennmedicine.upenn.edu>
-Date: Fri, 26 Jun 2020 18:23:08 +0000
-Subject: [PATCH] ENH: Use GNUInstallDirs CMake module
-
-Trying to enable installation to the correct lib dir for each platform
----
- Common.cmake            |  7 +++++--
- Examples/CMakeLists.txt | 32 ++++++++++++++++----------------
- 2 files changed, 21 insertions(+), 18 deletions(-)
-
-diff --git a/Common.cmake b/Common.cmake
-index 5e52d7f1..1e604113 100644
---- a/Common.cmake
-+++ b/Common.cmake
-@@ -103,8 +103,6 @@ if(PLATFORM_CHECK)
-   endif()
- endif()
- 
--
--
- #-------------------------------------------------------------------------
- # Augment compiler flags
- #-------------------------------------------------------------------------
-@@ -124,3 +122,8 @@ if(NOT CMAKE_POSITION_INDEPENDENT_CODE)
-   set(CMAKE_POSITION_INDEPENDENT_CODE ON)
- endif()
- endif()
-+
-+#-------------------------------------------------------------------------
-+# Define install dirs for different platforms
-+#-------------------------------------------------------------------------
-+include(GNUInstallDirs)
-diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt
-index 61781f56..cb352748 100644
---- a/Examples/CMakeLists.txt
-+++ b/Examples/CMakeLists.txt
-@@ -1,4 +1,4 @@
--SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-+SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
- ## Note that the antsUtilities can always be built static.  It will then be linked
- ## Directly into the other libraries.
- add_library(antsUtilities antsUtilities.cxx
-@@ -14,11 +14,11 @@ add_library(antsUtilities antsUtilities.cxx
-             )
- target_link_libraries(antsUtilities ${ITK_LIBRARIES} )
- install(TARGETS antsUtilities
--    RUNTIME DESTINATION bin
-+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-     COMPONENT RUNTIME_antsUtilities
--    LIBRARY DESTINATION lib
-+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-     COMPONENT RUNTIME_antsUtilities
--    ARCHIVE DESTINATION lib
-+    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-     COMPONENT DEVELOPMENT_antsUtilities
-   )
- 
-@@ -34,22 +34,22 @@ macro(STATIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
- 
-   if (ANTS_INSTALL_LIBS_ONLY)
-     install(TARGETS l_${ANTS_FUNCTION_NAME}
-- #    RUNTIME DESTINATION bin
-+ #    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-  #    COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
--      LIBRARY DESTINATION lib
-+      LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-       COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
--      ARCHIVE DESTINATION lib
-+      ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-       COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
-     )
-   else()
-     add_executable( ${ANTS_FUNCTION_NAME} cli_${ANTS_FUNCTION_NAME}.cxx )
-     target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} )
-     install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
--      RUNTIME DESTINATION bin
-+      RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-       COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
--      LIBRARY DESTINATION lib
-+      LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-       COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
--      ARCHIVE DESTINATION lib
-+      ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-       COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
-     )
-   endif()
-@@ -68,11 +68,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
- 
-   if (ANTS_INSTALL_LIBS_ONLY)
-     install(TARGETS l_${ANTS_FUNCTION_NAME}
--  #   RUNTIME DESTINATION bin
-+  #   RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-   #   COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
--      LIBRARY DESTINATION lib
-+      LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-       COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
--      ARCHIVE DESTINATION lib
-+      ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-       COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
-   )
-   else()
-@@ -80,11 +80,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
-     target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} )
- 
-     install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
--      RUNTIME DESTINATION bin
-+      RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-       COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
--      LIBRARY DESTINATION lib
-+      LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-       COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
--      ARCHIVE DESTINATION lib
-+      ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-       COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
-     )
-   endif()

diff --git a/sci-biology/ants/files/ants-2.3.4-version.patch b/sci-biology/ants/files/ants-2.3.4-version.patch
deleted file mode 100644
index 487151d69..000000000
--- a/sci-biology/ants/files/ants-2.3.4-version.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- a/ANTS.cmake	2020-06-08 12:11:14.000000000 -0400
-+++ b/ANTS.cmake	2020-08-03 16:44:00.826633506 -0400
-@@ -37,7 +37,6 @@
-   set(${PROJECT_NAME}_VERSION_MAJOR 0)
-   set(${PROJECT_NAME}_VERSION_MINOR 0)
-   set(${PROJECT_NAME}_VERSION_PATCH 0)
--  set(${PROJECT_NAME}_VERSION_TWEAK 0)
-   set(${PROJECT_NAME}_VERSION "snapshot-${ANTS_SNAPSHOT_VERSION}")
- endif()
-
-@@ -46,7 +45,6 @@
-   set(${PROJECT_NAME}_VERSION_MAJOR 0)
-   set(${PROJECT_NAME}_VERSION_MINOR 0)
-   set(${PROJECT_NAME}_VERSION_PATCH 0)
--  set(${PROJECT_NAME}_VERSION_TWEAK 0)
-   set(${PROJECT_NAME}_VERSION "0.0.0.0")
- endif()

diff --git a/sci-biology/ants/files/ants-2.4.1-fix-compile.patch b/sci-biology/ants/files/ants-2.4.1-fix-compile.patch
new file mode 100644
index 000000000..bd7eecbcf
--- /dev/null
+++ b/sci-biology/ants/files/ants-2.4.1-fix-compile.patch
@@ -0,0 +1,13 @@
+diff --git a/Examples/PrintHeader.cxx b/Examples/PrintHeader.cxx
+index d1e7586..048d934 100644
+--- a/Examples/PrintHeader.cxx
++++ b/Examples/PrintHeader.cxx
+@@ -281,7 +281,7 @@ PrintHeader(int argc, char * argv[])
+       // Get the metadata as a generic object
+       string                                                   key = itMeta->first, v_string;
+       itk::SpatialOrientation::ValidCoordinateOrientationFlags v_oflags =
+-        itk::SpatialOrientationEnums::ValidCoordinateOrientations::ITK_COORDINATE_ORIENTATION_INVALID;
++        itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_INVALID;
+ 
+       if (itk::ExposeMetaData<string>(mdd, key, v_string))
+       {