[gentoo-commits] proj/sci:master commit in: sci-chemistry/apbs/, sci-chemistry/apbs/files/

[Justin Lecher]

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 <jlec@g.o> +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>jlec@g.o</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>