commit: cf9d2e5e7d5ea97ff690ee5f5ab79595a765a8b5 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Thu May 1 13:50:07 2014 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Thu May 1 13:50:07 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cf9d2e5e
sci-chemistry/apbs: Add live ebuild Package-Manager: portage-2.2.10 --- sci-chemistry/apbs/ChangeLog | 10 +++ sci-chemistry/apbs/apbs-9999.ebuild | 91 ++++++++++++++++++++++ sci-chemistry/apbs/files/apbs-9999-manip.patch | 15 ++++ sci-chemistry/apbs/files/apbs-9999-prll.patch | 101 +++++++++++++++++++++++++ sci-chemistry/apbs/metadata.xml | 21 +++++ 5 files changed, 238 insertions(+) diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog new file mode 100644 index 0000000..7ce467c --- /dev/null +++ b/sci-chemistry/apbs/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-chemistry/apbs +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*apbs-9999 (01 May 2014) + + 01 May 2014; Justin Lecher <j...@gentoo.org> +apbs-9999.ebuild, + +files/apbs-9999-manip.patch, +files/apbs-9999-prll.patch, +metadata.xml: + Add live ebuild + diff --git a/sci-chemistry/apbs/apbs-9999.ebuild b/sci-chemistry/apbs/apbs-9999.ebuild new file mode 100644 index 0000000..dcbc0f9 --- /dev/null +++ b/sci-chemistry/apbs/apbs-9999.ebuild @@ -0,0 +1,91 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.3-r3.ebuild,v 1.5 2013/05/02 15:16:35 jlec Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils flag-o-matic git-r3 multilib python-single-r1 toolchain-funcs + +DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems" +HOMEPAGE="http://www.poissonboltzmann.org/apbs/"; +SRC_URI="" +EGIT_REPO_URI="git://git.code.sf.net/p/apbs/code" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="" +IUSE="debug examples +fetk mpi +openmp +tools" + +RDEPEND="${PYTHON_DEPS} + dev-libs/maloc[mpi=] + virtual/blas + sys-libs/readline + fetk? ( + sci-libs/fetk + sci-libs/amd + sci-libs/umfpack + sci-libs/superlu ) + mpi? ( virtual/mpi )" +DEPEND="${DEPEND} + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}"/${P}-manip.patch + "${FILESDIR}"/${P}-prll.patch +) + +DOCS=( + doc/{APBS-1.4-README.txt,ChangeLog,README} +) + +src_prepare() { + local _examples + + use examples || examples=$(ls examples/*) + + rm -rf \ + contrib/maloc* include/Eigen/* \ + doc/{license,release_procedure.txt,programmer,CMakeLists.txt} \ + ${examples} \ + || die + + append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) + + sed \ + -e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \ + -e 's:-lg2c::g' \ + -i CMakeLists.txt || die + + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir) + -DLIBRARY_INSTALL_PATH=$(get_libdir) + -DFETK_PATH="${EPREFIX}"/usr/ + -DBUILD_SHARED_LIBS=ON + -DENABLE_PYTHON=ON + $(cmake-utils_use_build tools) + $(cmake-utils_use_enable debug) +# Not acitve in the code yet +# $(cmake-utils_use_enable fast) + $(cmake-utils_use_enable fetk) + $(cmake-utils_use_enable mpi) + $(cmake-utils_use_enable openmp) + ) + cmake-utils_src_configure +} + +src_test() { + cd tests || die + "${PYTHON}" apbs_tester.py -l log || die + grep -q 'FAILED' log && die "Tests failed" +} + +src_install() { + cmake-utils_src_install + python_optimize "${ED}" +} diff --git a/sci-chemistry/apbs/files/apbs-9999-manip.patch b/sci-chemistry/apbs/files/apbs-9999-manip.patch new file mode 100644 index 0000000..fd5c1a2 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-9999-manip.patch @@ -0,0 +1,15 @@ + tools/CMakeLists.txt | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt +index 1982a3c..30ab17a 100644 +--- a/tools/CMakeLists.txt ++++ b/tools/CMakeLists.txt +@@ -1,7 +1,6 @@ + set(EXECUTABLE_OUTPUT_PATH ${TOOLS_PATH}/bin) + + add_subdirectory(mesh) +-add_subdirectory(manip) + + if(ENABLE_PYTHON) + add_subdirectory(manip) diff --git a/sci-chemistry/apbs/files/apbs-9999-prll.patch b/sci-chemistry/apbs/files/apbs-9999-prll.patch new file mode 100644 index 0000000..99e1845 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-9999-prll.patch @@ -0,0 +1,101 @@ + CMakeLists.txt | 16 ++++++++-------- + src/CMakeLists.txt | 1 - + src/fem/CMakeLists.txt | 2 +- + src/pmgc/CMakeLists.txt | 2 +- + 4 files changed, 10 insertions(+), 11 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index e3f720c..6b7db4c 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -61,7 +61,7 @@ set(LIBRARY_OUTPUT_PATH ${APBS_ROOT}/lib) + set(TOOLS_PATH ${APBS_ROOT}/tools) + set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs) + +-set(LIBRARY_INSTALL_PATH lib) ++set(LIBRARY_INSTALL_PATH ${CMAKE_INSTALL_LIBDIR}) + set(HEADER_INSTALL_PATH include/apbs) + set(EXECUTABLE_INSTALL_PATH bin) + set(SHARE_INSTALL_PATH share/apbs) +@@ -93,8 +93,6 @@ set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}") + list(APPEND CMAKE_INCLUDE_PATH /usr/include) + list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) + +-set(APBS_LIBS "-L${APBS_ROOT}/lib -lapbs_geoflow") +- + ################################################################################ + # Enable ansi pedantic compiling # + ################################################################################ +@@ -202,9 +200,11 @@ if(ENABLE_BEM) + else() + set(TABI_LIBRARY_BASENAME ${CMAKE_STATIC_LIBRARY_PREFIX}${TABI}${CMAKE_STATIC_LIBRARY_SUFFIX}) + endif() +- ++ ++ file(GLOB MODS ${LIBRARY_OUTPUT_PATH}/*.mod) ++ + install( +- FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${LIBRARY_OUTPUT_PATH}/*.mod ++ FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${MODS} + DESTINATION ${LIBRARY_INSTALL_PATH} + ) + set(TABI_LIBRARY ${APBS_ROOT}/${LIBRARY_INSTALL_PATH}/${TABI_LIBRARY_BASENAME}) +@@ -219,7 +219,7 @@ if(ENABLE_BEM) + endif() + get_filename_component(LIBGFORTRANPATH ${LIBGFORTRANPATH} PATH) + find_path(LIBGFORTRAN_PATH ${LIBGFORTRAN_NAME} PATH ${LIBGFORTRANPATH}) +- list(APPEND APBS_LIBS "-L${APBS_ROOT}/${LIBRARY_INSTALL_PATH} -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" ) ++ list(APPEND APBS_LIBS "-L${APBS_ROOT}/lib -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" ) + endif() + + find_file( # this should be find path... +@@ -237,7 +237,7 @@ endif() + + + find_library(MALOC_LIBRARY "maloc" +- PATHS ${FETK_PATH}/lib ${CONTRIB_PATH} ++ PATHS ${FETK_PATH}/${CMAKE_INSTALL_LIBDIR} ${CONTRIB_PATH} + DOC "The fetk/maloc library" + ) + if(MALOC_LIBRARY) +@@ -295,7 +295,7 @@ if(ENABLE_FETK) + set(FETK_ENALBED 1) + + list(APPEND APBS_LIBS "-lstdc++") +- list(APPEND APBS_LIBS "-L${FETK_PATH}/lib") ++ list(APPEND APBS_LIBS "-L${FETK_PATH}/${CMAKE_INSTALL_LIBDIR}") + list(APPEND APBS_LIBS -lamd -lpunc -lmc -lgamer -lsuperlu -lumfpack + -lblas -lvf2c -ltetgen -ltriangle -lg2c -lreadline ) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index 44d20fa..5d5150b 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -23,7 +23,6 @@ macro(add_items TYPE) + endmacro() + + +- + macro(add_sublibrary LIBRARY) + set(LIBRARY_NAME "apbs_${LIBRARY}") + set(LIBRARY_DEPENDENCIES ${APBS_LIBS} ${ARGN}) +diff --git a/src/fem/CMakeLists.txt b/src/fem/CMakeLists.txt +index 5a950c2..dc37f48 100644 +--- a/src/fem/CMakeLists.txt ++++ b/src/fem/CMakeLists.txt +@@ -12,4 +12,4 @@ add_items( + vpee.h + ) + +-add_sublibrary(fem) ++add_sublibrary(fem apbs_geoflow) +diff --git a/src/pmgc/CMakeLists.txt b/src/pmgc/CMakeLists.txt +index 85b0c1e..97c95f0 100644 +--- a/src/pmgc/CMakeLists.txt ++++ b/src/pmgc/CMakeLists.txt +@@ -42,4 +42,4 @@ add_items( + mgfasd.h + ) + +-add_sublibrary(pmgc) ++add_sublibrary(pmgc apbs_geoflow) diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml new file mode 100644 index 0000000..b8e5095 --- /dev/null +++ b/sci-chemistry/apbs/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>j...@gentoo.org</email> + <name>Justin Lecher</name> + <description>Ebuild Crasher</description> + </maintainer> + <use> + <flag name="fetk">Include support for FeTK</flag> + <flag name="tools">Install optional tools</flag> + </use> + <longdescription> +APBS is a software package for modeling biomolecular solvation through solution +of the Poisson-Boltzmann equation (PBE), one of the most popular continuum +models for describing electrostatic interactions between molecular solutes in +salty, aqueous media. Continuum electrostatics plays an important role in +several areas of biomolecular simulation +</longdescription> +</pkgmetadata>
