From b0a124bbb27af19a02cf8909eb9de3837a9a66b7 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Fri, 25 Sep 2020 15:46:29 -0400 Subject: [PATCH] sci-biology/ants: pushed to Gentoo Science https://gitweb.gentoo.org/proj/sci.git/commit/?id=40022cd56f21a7152d812b6435734aafa032c7f8 Signed-off-by: Horea Christian --- sci-biology/ants/ChangeLog | 50 -------- sci-biology/ants/Manifest | 2 - sci-biology/ants/ants-2.3.4.ebuild | 77 ------------ sci-biology/ants/files/99ants | 1 - .../ants/files/ants-2.3.4-libdir.patch | 117 ------------------ .../ants/files/ants-2.3.4-version.patch | 17 --- sci-biology/ants/metadata.xml | 24 ---- 7 files changed, 288 deletions(-) delete mode 100644 sci-biology/ants/ChangeLog delete mode 100644 sci-biology/ants/Manifest delete mode 100644 sci-biology/ants/ants-2.3.4.ebuild delete mode 100644 sci-biology/ants/files/99ants delete mode 100644 sci-biology/ants/files/ants-2.3.4-libdir.patch delete mode 100644 sci-biology/ants/files/ants-2.3.4-version.patch delete mode 100644 sci-biology/ants/metadata.xml diff --git a/sci-biology/ants/ChangeLog b/sci-biology/ants/ChangeLog deleted file mode 100644 index f8e3a05..0000000 --- a/sci-biology/ants/ChangeLog +++ /dev/null @@ -1,50 +0,0 @@ -*ants-2.3.4 (04 Aug 2020) - - 04 Aug 2020; +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; ants-2.3.1_p20191013.ebuild: - sci-biology/ants: building from tarball, failing - -*ants-2.3.1_p20191013 (14 Dec 2019) - - 14 Dec 2019; +ants-2.3.1_p20191013.ebuild, - -ants-9999.ebuild, metadata.xml: - sci-biology/ants: prefix fix ahead of Gentoo Science - - 25 Nov 2019; -ants-2.3.1_p20191013.ebuild: - sci-biology/ants: migrated version bump to Gentoo Scinece https://gitweb.gent - oo.org/proj/sci.git/commit/?id=402183f38c721910fe038ed4ce04e0a98a37c584 - - 17 Oct 2019; ants-9999.ebuild: - sci-biology/ants: patch merged by ANTs upstream - - 13 Oct 2019; +files/ants-2.3.1_p20191013-logic.patch, - +files/ants-2.3.1_p20191013-paths.patch, ants-2.3.1_p20191013.ebuild, - ants-9999.ebuild: - sci-biology/ants: updated ebuild style - - 23 Sep 2019; ants-2.3.1_p20190704.ebuild: - sci-biology/ants: improved testing support - -*ants-2.3.1_p20190704 (21 Sep 2019) - - 21 Sep 2019; +ants-2.3.1_p20190704.ebuild, - -ants-2.3.1-r1.ebuild, -ants-2.3.1.ebuild, ants-9999.ebuild: - sci-biology/ants: version bump 2.3.1_p20190704 - -*ants-2.3.1 (18 May 2019) - - 18 May 2019; +ants-2.3.1.ebuild: - sci-biology/ants: unsandboxed fix fro bundling Do not include in Gentoo - Science, work on unbundled revbump - -*ants-2.3.1-r1 (25 Mar 2019) -*ants-9999 (25 Mar 2019) - - 25 Mar 2019; +ants-2.3.1-r1.ebuild, +ants-9999.ebuild, - +files/99ants, +metadata.xml: - sci-biology/ants: fixes ahead of Gentoo Science diff --git a/sci-biology/ants/Manifest b/sci-biology/ants/Manifest deleted file mode 100644 index 95766db..0000000 --- a/sci-biology/ants/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST ants-2.3.4.tar.gz 2455843 SHA256 590b678f6fcbfa2f7bca4ae6059f49d5cf64ad07b2ed5088fb9226cb0f28ffec SHA512 084161505671a19530bec40c8209a67510d7de6e9d5afd151b806755ca703dadbea17c0a8d5c6472c7a81185821e17213ebf1488bc0325bfe858af783e8e6575 WHIRLPOOL bbdd587645580d5e47d5d276fdeba4d76330ab9ad10e7fecc6ebebb1c83f681db1d678bbfbb9bb36775606a2cfdc89dd38a759da0cb8e4a5d8e4a3967e8634c9 -DIST ants_testdata-2.3.4.tar.xz 25056552 SHA256 75fa0ada62533aa1636fa4db9b677564723622e4b25348a0e8b3a366b6d00e82 SHA512 a266fbf2de0003ee689a9369c424c97c92cdf7e4d08ba713623948276d96c9f0f02ab14480c329f462db0059217138680bfe39654f9ec4ac99bf947f51da853d WHIRLPOOL 3d269afa1d7d9b7426000c48c3773c09bc92d3f4c790dfd71ccb6f6fc98db7e8c16534f4e852f7b5eb793819ec40b7054ff7371eb07b9219fe3787b15c118783 diff --git a/sci-biology/ants/ants-2.3.4.ebuild b/sci-biology/ants/ants-2.3.4.ebuild deleted file mode 100644 index e008651..0000000 --- a/sci-biology/ants/ants-2.3.4.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# 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 "${FILESDIR}"/99ants -} diff --git a/sci-biology/ants/files/99ants b/sci-biology/ants/files/99ants deleted file mode 100644 index c0d7bef..0000000 --- a/sci-biology/ants/files/99ants +++ /dev/null @@ -1 +0,0 @@ -ANTSPATH=/usr/bin/ diff --git a/sci-biology/ants/files/ants-2.3.4-libdir.patch b/sci-biology/ants/files/ants-2.3.4-libdir.patch deleted file mode 100644 index b593c27..0000000 --- a/sci-biology/ants/files/ants-2.3.4-libdir.patch +++ /dev/null @@ -1,117 +0,0 @@ -From 329a7be631b33294d9cf3d58e8cdeb62e0aa993c Mon Sep 17 00:00:00 2001 -From: Philip A Cook -Date: Fri, 26 Jun 2020 18:23:08 +0000 -Subject: [PATCH] ENH: Use GNUInstallDirs CMake module - -Trying to enable installation to the correct lib dir for each platform ---- - Common.cmake | 7 +++++-- - Examples/CMakeLists.txt | 32 ++++++++++++++++---------------- - 2 files changed, 21 insertions(+), 18 deletions(-) - -diff --git a/Common.cmake b/Common.cmake -index 5e52d7f1..1e604113 100644 ---- a/Common.cmake -+++ b/Common.cmake -@@ -103,8 +103,6 @@ if(PLATFORM_CHECK) - endif() - endif() - -- -- - #------------------------------------------------------------------------- - # Augment compiler flags - #------------------------------------------------------------------------- -@@ -124,3 +122,8 @@ if(NOT CMAKE_POSITION_INDEPENDENT_CODE) - set(CMAKE_POSITION_INDEPENDENT_CODE ON) - endif() - endif() -+ -+#------------------------------------------------------------------------- -+# Define install dirs for different platforms -+#------------------------------------------------------------------------- -+include(GNUInstallDirs) -diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt -index 61781f56..cb352748 100644 ---- a/Examples/CMakeLists.txt -+++ b/Examples/CMakeLists.txt -@@ -1,4 +1,4 @@ --SET(CMAKE_INSTALL_RPATH "${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 487151d..0000000 --- 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/metadata.xml b/sci-biology/ants/metadata.xml deleted file mode 100644 index 87d2feb..0000000 --- a/sci-biology/ants/metadata.xml +++ /dev/null @@ -1,24 +0,0 @@ - - - - - chr@chymera.eu - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - - ANTs extracts information from complex datasets that include imaging - (Word Cloud). Paired with ANTsR (answer), ANTs is useful for managing, - interpreting and visualizing multidimensional data. ANTs is popularly - considered a state-of-the-art medical image registration and segmentation - toolkit. ANTsR is an emerging tool supporting standardized multimodality - image analysis. ANTs depends on the Insight ToolKit (ITK), a widely used - medical image processing library to which ANTs developers contribute. - - - Optional support for a number of surface enabled tools (via sci-libs/vtk). - -