sci-biology/ants: version bump 2.3.4

Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Horea Christian <chr@chymera.eu>

4 files changed, 213 insertions, 0 deletions

diff --git a/sci-biology/ants/Manifest b/sci-biology/ants/Manifest
index 9f9c4b333..e1d53b38a 100644
--- a/sci-biology/ants/Manifest
+++ b/sci-biology/ants/Manifest
@@ -1,2 +1,4 @@
 DIST ants-2.3.1.tar.gz 2437950 BLAKE2B 60ffb1b017d066efd9cfc689af7877fb394c9828033c9d9e4542df723eb75e52ada490cbf8ecab0d7f149cc1b22a500791fdbe7872f7ae593a70fa1853c54d00 SHA512 c22af10b7aed1dc5c6b06d6b7d3b2c33ced382926ab5972dd55e4766ff0269330bf01e6975712d991e96c5d9d23f78c8081a3ff475ea92d539c695105b5cfe9a
+DIST ants-2.3.4.tar.gz 2455843 BLAKE2B c00a2d3edebc0a121fa3b6618982c64fd986db9ea6aed1a1b2c7ced2f77ab154837a47e5bcb01f432b937160de2248b30a2bb7b526952852946e686858334e12 SHA512 084161505671a19530bec40c8209a67510d7de6e9d5afd151b806755ca703dadbea17c0a8d5c6472c7a81185821e17213ebf1488bc0325bfe858af783e8e6575
 DIST ants_testdata-2.3.1_p20191013.tar.xz 25056144 BLAKE2B 7e7535fbe6d7c2e2e0635782b4678fd2cab072ae629cafb361d21291d5b68de086c31f555e1a2008e112601d7c61713461c27e3ac0a1732e7c14c88f73e89781 SHA512 5a636f11952355be3c85d4a36faa84409bace15a7fcd675b20bc8eee83f1969773f6fe5cde31cb7c46bd1baeca21dc8324b1007e6126717f1653bdeb906c8e50
+DIST ants_testdata-2.3.4.tar.xz 25056552 BLAKE2B 6478ffe0c98fd3700a6de201f1271339276b45b461b02d4753acdcd1335c83196aa2ed89a89b5b4b0b3df33026f77b231ba1418c9eb7a2380356d4e224f9b310 SHA512 a266fbf2de0003ee689a9369c424c97c92cdf7e4d08ba713623948276d96c9f0f02ab14480c329f462db0059217138680bfe39654f9ec4ac99bf947f51da853d
diff --git a/sci-biology/ants/ants-2.3.4.ebuild b/sci-biology/ants/ants-2.3.4.ebuild
new file mode 100644
index 000000000..e00865149
--- /dev/null
+++ b/sci-biology/ants/ants-2.3.4.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+
+inherit cmake multilib
+
+MY_PN="ANTs"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="http://stnava.github.io/ANTs/"
+SRC_URI="
+	https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz ->  ${P}.tar.gz
+	test? (
+		http://chymera.eu/distfiles/ants_testdata-${PV}.tar.xz
+	)
+"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+IUSE="test vtk"
+
+DEPEND="
+	vtk? (
+		~sci-libs/itk-5.1.0[vtkglue]
+		sci-libs/vtk
+	)
+	!vtk? (	~sci-libs/itk-5.1.0 )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${P}-version.patch"
+	"${FILESDIR}/${P}-libdir.patch"
+)
+
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+src_unpack() {
+	default
+	if use test; then
+		mkdir -p "${S}/.ExternalData/MD5" || die "Could not create test data directory."
+		tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/MD5/" > /dev/null || die "Could not unpack test data."
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_SYSTEM_ITK=ON
+		-DITK_DIR="${EROOT}/usr/include/ITK-5.1/"
+		-DBUILD_TESTING="$(usex test ON OFF)"
+		-DUSE_VTK=$(usex vtk ON OFF)
+		-DUSE_SYSTEM_VTK=$(usex vtk ON OFF)
+		-DANTS_SNAPSHOT_VERSION:STRING=${PV}
+	)
+	use vtk && mycmakeargs+=(
+		-DVTK_DIR="${EROOT}/usr/include/vtk-8.1/"
+	)
+	use test && mycmakeargs+=(
+		-DExternalData_OBJECT_STORES="${S}/.ExternalData/MD5"
+	)
+	cmake_src_configure
+}
+
+src_install() {
+	BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build"
+	cmake_src_install
+	cd "${S}/Scripts" || die "scripts dir not found"
+	dobin *.sh
+	dodir /usr/$(get_libdir)/ants
+	insinto "/usr/$(get_libdir)/ants"
+	doins *
+	doenvd "${FILESDIR}"/99ants
+}
diff --git a/sci-biology/ants/files/ants-2.3.4-libdir.patch b/sci-biology/ants/files/ants-2.3.4-libdir.patch
new file mode 100644
index 000000000..b593c2778
--- /dev/null
+++ b/sci-biology/ants/files/ants-2.3.4-libdir.patch
@@ -0,0 +1,117 @@
+From 329a7be631b33294d9cf3d58e8cdeb62e0aa993c Mon Sep 17 00:00:00 2001
+From: Philip A Cook <cookpa@pennmedicine.upenn.edu>
+Date: Fri, 26 Jun 2020 18:23:08 +0000
+Subject: [PATCH] ENH: Use GNUInstallDirs CMake module
+
+Trying to enable installation to the correct lib dir for each platform
+---
+ Common.cmake            |  7 +++++--
+ Examples/CMakeLists.txt | 32 ++++++++++++++++----------------
+ 2 files changed, 21 insertions(+), 18 deletions(-)
+
+diff --git a/Common.cmake b/Common.cmake
+index 5e52d7f1..1e604113 100644
+--- a/Common.cmake
++++ b/Common.cmake
+@@ -103,8 +103,6 @@ if(PLATFORM_CHECK)
+   endif()
+ endif()
+ 
+-
+-
+ #-------------------------------------------------------------------------
+ # Augment compiler flags
+ #-------------------------------------------------------------------------
+@@ -124,3 +122,8 @@ if(NOT CMAKE_POSITION_INDEPENDENT_CODE)
+   set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+ endif()
+ endif()
++
++#-------------------------------------------------------------------------
++# Define install dirs for different platforms
++#-------------------------------------------------------------------------
++include(GNUInstallDirs)
+diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt
+index 61781f56..cb352748 100644
+--- a/Examples/CMakeLists.txt
++++ b/Examples/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-SET(CMAKE_INSTALL_RPATH "${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
new file mode 100644
index 000000000..487151d69
--- /dev/null
+++ b/sci-biology/ants/files/ants-2.3.4-version.patch
@@ -0,0 +1,17 @@
+--- 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()