sci-biology/ants: version bump 2.3.4 ahead of Gentoo Science

Package-Manager: Portage-3.0.0, Repoman-2.3.23
Signed-off-by: Horea Christian <chr@chymera.eu>

sci-biology/ants/ChangeLog

@@ -1,3 +1,11 @@
+*ants-2.3.4 (04 Aug 2020)
+
+  04 Aug 2020;  <chymera@gentoo.org> +ants-2.3.4.ebuild,
+  +files/ants-2.3.4-libdir.patch, +files/ants-2.3.4-version.patch,
+  -ants-2.3.1_p20191013.ebuild, -files/ants-2.3.1_p20191013-logic.patch,
+  -files/ants-2.3.1_p20191013-paths.patch:
+  sci-biology/ants: version bump 2.3.4 ahead of Gentoo Science
+
   16 May 2020;  <chymera@gentoo.org> ants-2.3.1_p20191013.ebuild:
   sci-biology/ants: building from tarball, failing
 

sci-biology/ants/Manifest

@@ -1,2 +1,2 @@
-DIST 2.3.1_p20191013.tar.gz 2445357 SHA256 819e60c215e61abff2990eac20520b85083fba78598a49a5a6ff915d7206a0c4 SHA512 3de360f58de63662be7db7704a1e4b74ccba03c656ee68dde7e82f4231cbeb6e9d6c7f20a01dab57d0e54740f1f33acd40d07fbe67673993230c08d8aecd9359 WHIRLPOOL 0338d27a73f0b01a079f80129727d413833771fce306d7e839c5a2d23a6c9da71c8ee751e67928d07791cb927b746039d8c5ae6396d7baa06e6ee3217347198b
+DIST ants-2.3.4.tar.gz 2455843 SHA256 590b678f6fcbfa2f7bca4ae6059f49d5cf64ad07b2ed5088fb9226cb0f28ffec SHA512 084161505671a19530bec40c8209a67510d7de6e9d5afd151b806755ca703dadbea17c0a8d5c6472c7a81185821e17213ebf1488bc0325bfe858af783e8e6575 WHIRLPOOL bbdd587645580d5e47d5d276fdeba4d76330ab9ad10e7fecc6ebebb1c83f681db1d678bbfbb9bb36775606a2cfdc89dd38a759da0cb8e4a5d8e4a3967e8634c9
-DIST ants_testdata-2.3.1_p20191013.tar.xz 25056428 SHA256 df2396d453a37674945612b2248d4ca818fce6a0b2d97beb88ab3bc59d040657 SHA512 0f86b967cd5e6c7481804c5b1dfb8d638a0560fbb08f86f04d9a3dc508a64e3181d056c2c9cdc26cbcf8eae9e45ecb29fa58580a1377ed8733b87b1b04b15ab2 WHIRLPOOL 08a5adb931b4606a0b03e32effc218d4940395472f7c2b62098472fe999cc0f0a452454619eba2bb2da775a0d5e5eb7baa966bdccf087da1d57d781061006422
+DIST ants_testdata-2.3.4.tar.xz 25056552 SHA256 75fa0ada62533aa1636fa4db9b677564723622e4b25348a0e8b3a366b6d00e82 SHA512 a266fbf2de0003ee689a9369c424c97c92cdf7e4d08ba713623948276d96c9f0f02ab14480c329f462db0059217138680bfe39654f9ec4ac99bf947f51da853d WHIRLPOOL 3d269afa1d7d9b7426000c48c3773c09bc92d3f4c790dfd71ccb6f6fc98db7e8c16534f4e852f7b5eb793819ec40b7054ff7371eb07b9219fe3787b15c118783

sci-biology/ants/ants-2.3.4.ebuild

@@ -5,15 +5,14 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="emake"
 
-inherit cmake-utils multilib
+inherit cmake multilib
 
-MY_COMMIT="f78b2d4a382d3090230641b5ade5da28962dad04"
 MY_PN="ANTs"
 
 DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
 HOMEPAGE="http://stnava.github.io/ANTs/"
 SRC_URI="
-	https://github.com/ANTsX/ANTs/archive/${MY_COMMIT}.tar.gz -> ${PV}.tar.gz
+	https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz ->  ${P}.tar.gz
 	test? (
 		http://chymera.eu/distfiles/ants_testdata-${PV}.tar.xz
 	)
@@ -26,19 +25,19 @@ IUSE="test vtk"
 
 DEPEND="
 	vtk? (
-		~sci-libs/itk-5.0.1[vtkglue]
+		~sci-libs/itk-5.1.0[vtkglue]
 		sci-libs/vtk
 	)
-	!vtk? (	~sci-libs/itk-5.0.1 )
+	!vtk? (	~sci-libs/itk-5.1.0 )
 "
 RDEPEND="${DEPEND}"
 
 PATCHES=(
-	"${FILESDIR}/${P}-logic.patch"
+	"${FILESDIR}/${P}-version.patch"
-	"${FILESDIR}/${P}-paths.patch"
+	"${FILESDIR}/${P}-libdir.patch"
 )
 
-S="${WORKDIR}/${MY_PN}-${MY_COMMIT}"
+S="${WORKDIR}/${MY_PN}-${PV}"
 
 src_unpack() {
 	default
@@ -51,10 +50,11 @@ src_unpack() {
 src_configure() {
 	local mycmakeargs=(
 		-DUSE_SYSTEM_ITK=ON
-		-DITK_DIR="${EROOT}/usr/include/ITK-5.0/"
+		-DITK_DIR="${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="${EROOT}/usr/include/vtk-8.1/"
@@ -62,17 +62,16 @@ src_configure() {
 	use test && mycmakeargs+=(
 		-DExternalData_OBJECT_STORES="${S}/.ExternalData/MD5"
 	)
-	cmake-utils_src_configure
+	cmake_src_configure
 }
 
 src_install() {
 	BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build"
-	cmake-utils_src_install
+	cmake_src_install
-	cd "${WORKDIR}/${P}/Scripts" || die "scripts dir not found"
+	cd "${S}/Scripts" || die "scripts dir not found"
 	dobin *.sh
 	dodir /usr/$(get_libdir)/ants
 	insinto "/usr/$(get_libdir)/ants"
 	doins *
-	#install -t "${D}"/"${EROOT%/}"/usr/$(get_libdir)/ants * || die
 	doenvd "${FILESDIR}"/99ants
 }

sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch

@@ -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()

sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch

@@ -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}
-   )

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()

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()