Gentoo Archives: gentoo-commits

From: Horea Christian <horea.christ@×××××.com>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/ants/, sci-biology/ants/files/
Date: Fri, 25 Sep 2020 19:40:46
Message-Id: 1601062828.40022cd56f21a7152d812b6435734aafa032c7f8.chymera@gentoo
1 commit: 40022cd56f21a7152d812b6435734aafa032c7f8
2 Author: Horea Christian <chr <AT> chymera <DOT> eu>
3 AuthorDate: Fri Sep 25 19:40:28 2020 +0000
4 Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
5 CommitDate: Fri Sep 25 19:40:28 2020 +0000
6 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=40022cd5
7
8 sci-biology/ants: version bump 2.3.4
9
10 Package-Manager: Portage-3.0.7, Repoman-3.0.1
11 Signed-off-by: Horea Christian <chr <AT> chymera.eu>
12
13 sci-biology/ants/ants-2.3.4.ebuild | 77 ++++++++++++++++
14 sci-biology/ants/files/ants-2.3.4-libdir.patch | 117 ++++++++++++++++++++++++
15 sci-biology/ants/files/ants-2.3.4-version.patch | 17 ++++
16 3 files changed, 211 insertions(+)
17
18 diff --git a/sci-biology/ants/ants-2.3.4.ebuild b/sci-biology/ants/ants-2.3.4.ebuild
19 new file mode 100644
20 index 000000000..e00865149
21 --- /dev/null
22 +++ b/sci-biology/ants/ants-2.3.4.ebuild
23 @@ -0,0 +1,77 @@
24 +# Copyright 1999-2020 Gentoo Authors
25 +# Distributed under the terms of the GNU General Public License v2
26 +
27 +EAPI=7
28 +
29 +CMAKE_MAKEFILE_GENERATOR="emake"
30 +
31 +inherit cmake multilib
32 +
33 +MY_PN="ANTs"
34 +
35 +DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
36 +HOMEPAGE="http://stnava.github.io/ANTs/"
37 +SRC_URI="
38 + https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz
39 + test? (
40 + http://chymera.eu/distfiles/ants_testdata-${PV}.tar.xz
41 + )
42 +"
43 +
44 +SLOT="0"
45 +LICENSE="BSD"
46 +KEYWORDS="~amd64 ~x86"
47 +IUSE="test vtk"
48 +
49 +DEPEND="
50 + vtk? (
51 + ~sci-libs/itk-5.1.0[vtkglue]
52 + sci-libs/vtk
53 + )
54 + !vtk? ( ~sci-libs/itk-5.1.0 )
55 +"
56 +RDEPEND="${DEPEND}"
57 +
58 +PATCHES=(
59 + "${FILESDIR}/${P}-version.patch"
60 + "${FILESDIR}/${P}-libdir.patch"
61 +)
62 +
63 +S="${WORKDIR}/${MY_PN}-${PV}"
64 +
65 +src_unpack() {
66 + default
67 + if use test; then
68 + mkdir -p "${S}/.ExternalData/MD5" || die "Could not create test data directory."
69 + tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/MD5/" > /dev/null || die "Could not unpack test data."
70 + fi
71 +}
72 +
73 +src_configure() {
74 + local mycmakeargs=(
75 + -DUSE_SYSTEM_ITK=ON
76 + -DITK_DIR="${EROOT}/usr/include/ITK-5.1/"
77 + -DBUILD_TESTING="$(usex test ON OFF)"
78 + -DUSE_VTK=$(usex vtk ON OFF)
79 + -DUSE_SYSTEM_VTK=$(usex vtk ON OFF)
80 + -DANTS_SNAPSHOT_VERSION:STRING=${PV}
81 + )
82 + use vtk && mycmakeargs+=(
83 + -DVTK_DIR="${EROOT}/usr/include/vtk-8.1/"
84 + )
85 + use test && mycmakeargs+=(
86 + -DExternalData_OBJECT_STORES="${S}/.ExternalData/MD5"
87 + )
88 + cmake_src_configure
89 +}
90 +
91 +src_install() {
92 + BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build"
93 + cmake_src_install
94 + cd "${S}/Scripts" || die "scripts dir not found"
95 + dobin *.sh
96 + dodir /usr/$(get_libdir)/ants
97 + insinto "/usr/$(get_libdir)/ants"
98 + doins *
99 + doenvd "${FILESDIR}"/99ants
100 +}
101
102 diff --git a/sci-biology/ants/files/ants-2.3.4-libdir.patch b/sci-biology/ants/files/ants-2.3.4-libdir.patch
103 new file mode 100644
104 index 000000000..b593c2778
105 --- /dev/null
106 +++ b/sci-biology/ants/files/ants-2.3.4-libdir.patch
107 @@ -0,0 +1,117 @@
108 +From 329a7be631b33294d9cf3d58e8cdeb62e0aa993c Mon Sep 17 00:00:00 2001
109 +From: Philip A Cook <cookpa@××××××××××××××××××.edu>
110 +Date: Fri, 26 Jun 2020 18:23:08 +0000
111 +Subject: [PATCH] ENH: Use GNUInstallDirs CMake module
112 +
113 +Trying to enable installation to the correct lib dir for each platform
114 +---
115 + Common.cmake | 7 +++++--
116 + Examples/CMakeLists.txt | 32 ++++++++++++++++----------------
117 + 2 files changed, 21 insertions(+), 18 deletions(-)
118 +
119 +diff --git a/Common.cmake b/Common.cmake
120 +index 5e52d7f1..1e604113 100644
121 +--- a/Common.cmake
122 ++++ b/Common.cmake
123 +@@ -103,8 +103,6 @@ if(PLATFORM_CHECK)
124 + endif()
125 + endif()
126 +
127 +-
128 +-
129 + #-------------------------------------------------------------------------
130 + # Augment compiler flags
131 + #-------------------------------------------------------------------------
132 +@@ -124,3 +122,8 @@ if(NOT CMAKE_POSITION_INDEPENDENT_CODE)
133 + set(CMAKE_POSITION_INDEPENDENT_CODE ON)
134 + endif()
135 + endif()
136 ++
137 ++#-------------------------------------------------------------------------
138 ++# Define install dirs for different platforms
139 ++#-------------------------------------------------------------------------
140 ++include(GNUInstallDirs)
141 +diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt
142 +index 61781f56..cb352748 100644
143 +--- a/Examples/CMakeLists.txt
144 ++++ b/Examples/CMakeLists.txt
145 +@@ -1,4 +1,4 @@
146 +-SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
147 ++SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
148 + ## Note that the antsUtilities can always be built static. It will then be linked
149 + ## Directly into the other libraries.
150 + add_library(antsUtilities antsUtilities.cxx
151 +@@ -14,11 +14,11 @@ add_library(antsUtilities antsUtilities.cxx
152 + )
153 + target_link_libraries(antsUtilities ${ITK_LIBRARIES} )
154 + install(TARGETS antsUtilities
155 +- RUNTIME DESTINATION bin
156 ++ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
157 + COMPONENT RUNTIME_antsUtilities
158 +- LIBRARY DESTINATION lib
159 ++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
160 + COMPONENT RUNTIME_antsUtilities
161 +- ARCHIVE DESTINATION lib
162 ++ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
163 + COMPONENT DEVELOPMENT_antsUtilities
164 + )
165 +
166 +@@ -34,22 +34,22 @@ macro(STATIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
167 +
168 + if (ANTS_INSTALL_LIBS_ONLY)
169 + install(TARGETS l_${ANTS_FUNCTION_NAME}
170 +- # RUNTIME DESTINATION bin
171 ++ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
172 + # COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
173 +- LIBRARY DESTINATION lib
174 ++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
175 + COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
176 +- ARCHIVE DESTINATION lib
177 ++ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
178 + COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
179 + )
180 + else()
181 + add_executable( ${ANTS_FUNCTION_NAME} cli_${ANTS_FUNCTION_NAME}.cxx )
182 + target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} )
183 + install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
184 +- RUNTIME DESTINATION bin
185 ++ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
186 + COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
187 +- LIBRARY DESTINATION lib
188 ++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
189 + COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
190 +- ARCHIVE DESTINATION lib
191 ++ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
192 + COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
193 + )
194 + endif()
195 +@@ -68,11 +68,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
196 +
197 + if (ANTS_INSTALL_LIBS_ONLY)
198 + install(TARGETS l_${ANTS_FUNCTION_NAME}
199 +- # RUNTIME DESTINATION bin
200 ++ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
201 + # COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
202 +- LIBRARY DESTINATION lib
203 ++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
204 + COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
205 +- ARCHIVE DESTINATION lib
206 ++ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
207 + COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
208 + )
209 + else()
210 +@@ -80,11 +80,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
211 + target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} )
212 +
213 + install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
214 +- RUNTIME DESTINATION bin
215 ++ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
216 + COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
217 +- LIBRARY DESTINATION lib
218 ++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
219 + COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
220 +- ARCHIVE DESTINATION lib
221 ++ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
222 + COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
223 + )
224 + endif()
225
226 diff --git a/sci-biology/ants/files/ants-2.3.4-version.patch b/sci-biology/ants/files/ants-2.3.4-version.patch
227 new file mode 100644
228 index 000000000..487151d69
229 --- /dev/null
230 +++ b/sci-biology/ants/files/ants-2.3.4-version.patch
231 @@ -0,0 +1,17 @@
232 +--- a/ANTS.cmake 2020-06-08 12:11:14.000000000 -0400
233 ++++ b/ANTS.cmake 2020-08-03 16:44:00.826633506 -0400
234 +@@ -37,7 +37,6 @@
235 + set(${PROJECT_NAME}_VERSION_MAJOR 0)
236 + set(${PROJECT_NAME}_VERSION_MINOR 0)
237 + set(${PROJECT_NAME}_VERSION_PATCH 0)
238 +- set(${PROJECT_NAME}_VERSION_TWEAK 0)
239 + set(${PROJECT_NAME}_VERSION "snapshot-${ANTS_SNAPSHOT_VERSION}")
240 + endif()
241 +
242 +@@ -46,7 +45,6 @@
243 + set(${PROJECT_NAME}_VERSION_MAJOR 0)
244 + set(${PROJECT_NAME}_VERSION_MINOR 0)
245 + set(${PROJECT_NAME}_VERSION_PATCH 0)
246 +- set(${PROJECT_NAME}_VERSION_TWEAK 0)
247 + set(${PROJECT_NAME}_VERSION "0.0.0.0")
248 + endif()