proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

6 files changed, 419 insertions, 0 deletions

diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
new file mode 100644
index 000000000000..fef1437b89f5
--- /dev/null
+++ b/sci-chemistry/apbs/Manifest
@@ -0,0 +1 @@
+DIST apbs-1.4.1.zip 37999283 SHA256 1156c44fb65bb7c884801f3111ca1cdb1dfba6f5308226587db112aac4969027 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a WHIRLPOOL 6729571f13c953ec0bcf90da73ef0c39cf769f1498a767d3280de3ffbeea18eda718373efca0468436c4b18357fe450865f661daba79eeb66778c572c43ff39a
diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
new file mode 100644
index 000000000000..cabbd1e45e92
--- /dev/null
+++ b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
@@ -0,0 +1,128 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+DISTUTILS_SINGLE_IMPL=true
+
+inherit cmake-utils distutils-r1 flag-o-matic multilib toolchain-funcs
+
+GITHUB_REV="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
+
+DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems"
+HOMEPAGE="http://www.poissonboltzmann.org/apbs/"
+#SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
+SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${GITHUB_REV}.zip -> ${P}.zip"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+IUSE="debug doc examples fast +fetk iapbs mpi openmp python tools"
+
+REQUIRED_USE="
+	iapbs? ( fetk )
+	mpi? ( !python )
+	python? ( tools fetk iapbs ${PYTHON_REQUIRED_USE} )"
+
+RDEPEND="
+	dev-cpp/eigen:3
+	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 )
+	python? ( ${PYTHON_DEPS} )
+"
+DEPEND="${DEPEND}
+	virtual/pkgconfig
+	doc? ( app-doc/doxygen )
+"
+
+S="${WORKDIR}"/${PN}-pdb2pqr-${GITHUB_REV}/${PN}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-multilib.patch
+	"${FILESDIR}"/${P}-manip.patch
+	"${FILESDIR}"/${P}-python.patch
+)
+
+src_prepare() {
+	cmake-utils_src_prepare
+	append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
+
+	sed \
+		-e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \
+		-e "/TOOLS_PATH/d" \
+		-i CMakeLists.txt || die
+	use doc && MAKEOPTS+=" -j1"
+	if use python; then
+		unset PATCHES || die
+		cd tools/python && distutils-r1_src_prepare
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_SKIP_RPATH=ON
+		-DTOOLS_PATH="${ED}"/usr
+		-DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir)
+		-DLIBRARY_INSTALL_PATH=$(get_libdir)
+		-DFETK_PATH="${EPREFIX}"/usr/
+		-DBUILD_SHARED_LIBS=ON
+		-DENABLE_QUIT=OFF
+		$(cmake-utils_use_build doc DOC)
+		$(cmake-utils_use_build tools TOOLS)
+		-DENABLE_BEM=OFF
+# ENABLE_BEM: Boundary element method using TABIPB
+		$(cmake-utils_use_enable debug DEBUG)
+		$(cmake-utils_use_enable debug VERBOSE_DEBUG)
+		$(cmake-utils_use_enable fast FAST)
+		$(cmake-utils_use_enable fetk FETK)
+		$(cmake-utils_use_enable mpi MPI)
+		$(cmake-utils_use_enable python PYTHON)
+# ENABLE_TINKER: Enable TINKER support
+		$(cmake-utils_use_enable iapbs iAPBS)
+# MAX_MEMORY: Set the maximum memory (in MB) to be used for a job
+	)
+	cmake-utils_src_configure
+	if use python; then
+		cd tools/python && distutils-r1_src_configure
+	fi
+}
+
+src_compile(){
+	cmake-utils_src_compile
+	if use python; then
+		append-ldflags -L"${S}"/lib
+		cd tools/python && distutils-r1_src_compile
+	fi
+}
+
+src_test() {
+	python_export_best
+	cd tests || die
+	LD_LIBRARY_PATH="${S}"/lib "${PYTHON}" apbs_tester.py -l log || die
+	grep -q 'FAILED' log && die "Tests failed"
+}
+
+src_install() {
+	dodir /usr/bin
+	cmake-utils_src_install
+	local i
+	for i in "${ED}"/usr/bin/*; do
+		if [[ ! "${i}" =~ .*apbs$ ]]; then
+			mv "${i}" "${i}-apbs" || die
+		fi
+	done
+	if use python; then
+		cd tools/python && distutils-r1_src_install
+		rm -rf "${ED}"/usr/share/apbs/tools/python || die
+	fi
+}
diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
new file mode 100644
index 000000000000..378223397594
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
@@ -0,0 +1,50 @@
+ apbs/CMakeLists.txt             | 2 +-
+ apbs/tools/CMakeLists.txt       | 4 ----
+ apbs/tools/mesh/CMakeLists.txt  | 4 ++--
+ 4 files changed, 5 insertions(+), 9 deletions(-)
+
+diff --git a/apbs/CMakeLists.txt b/apbs/CMakeLists.txt
+index 8917fc4..5152008 100644
+--- a/apbs/CMakeLists.txt
++++ b/apbs/CMakeLists.txt
+@@ -293,7 +293,7 @@ option(ENABLE_FETK "Enable the finite element solver" OFF)
+ 
+ if(ENABLE_FETK)
+     message(STATUS "Checking for fetk components")
+-    set(FETK_ENALBED 1)
++    set(FETK_ENABLED 1)
+ 
+     list(APPEND APBS_LIBS "-lstdc++")
+     list(APPEND APBS_LIBS "-L${FETK_PATH}/lib")
+diff --git a/apbs/tools/manip/CMakeLists.txt b/apbs/tools/manip/CMakeLists.txt
+index 937dac7..5768cc5 100644
+--- a/apbs/tools/manip/CMakeLists.txt
++++ b/apbs/tools/manip/CMakeLists.txt
+@@ -4,9 +4,9 @@ set(LIBS "")
+ list(APPEND LIBS "apbs_generic")
+ list(APPEND LIBS "apbs_mg")
+ list(APPEND LIBS "apbs_pmgc")
+-if(FETK_ENALBED)
++if(FETK_ENABLED)
+     list(APPEND LIBS "apbs_fem")
+-endif(FETK_ENALBED)
++endif(FETK_ENABLED)
+ 
+ message(STATUS "libraries: ${LIBS}")
+ 
+diff --git a/apbs/tools/mesh/CMakeLists.txt b/apbs/tools/mesh/CMakeLists.txt
+index 1406377..6e6dfb9 100644
+--- a/apbs/tools/mesh/CMakeLists.txt
++++ b/apbs/tools/mesh/CMakeLists.txt
+@@ -4,9 +4,9 @@ set(LIBS "")
+ list(APPEND LIBS "apbs_generic")
+ list(APPEND LIBS "apbs_mg")
+ list(APPEND LIBS "apbs_pmgc")
+-if(FETK_ENALBED)
++if(FETK_ENABLED)
+     list(APPEND LIBS "apbs_fem")
+-endif(FETK_ENALBED)
++endif(FETK_ENABLED)
+ 
+ message(STATUS "libraries: ${LIBS}")
+ 
diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch
new file mode 100644
index 000000000000..a4e2d1761cf4
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch
@@ -0,0 +1,92 @@
+ CMakeLists.txt          | 18 +++++++++---------
+ src/CMakeLists.txt      |  1 -
+ src/fem/CMakeLists.txt  |  2 +-
+ src/pmgc/CMakeLists.txt |  2 +-
+ 4 files changed, 11 insertions(+), 12 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 75ddbdd..c46f5e7 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                                               #
+ ################################################################################
+@@ -193,9 +191,11 @@ 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})
+@@ -210,7 +210,7 @@ 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() # ENABLE_BEM
+ 
+ find_file( # this should be find path...
+@@ -228,7 +228,7 @@ endif()
+ 
+ 
+ find_library(MALOC_LIBRARY  "maloc"
+-    PATHS ${FETK_PATH}/lib ${CONTRIB_PATH}
++    PATHS ${FETK_PATH}/${CMAKE_INSTALL_LIBDIR} ${CONTRIB_PATH}
+     DOC   "The fetk/maloc library"
+ )
+ if(MALOC_LIBRARY)
+@@ -296,9 +296,9 @@ if(ENABLE_FETK)
+     set(FETK_ENALBED 1)
+ 
+     list(APPEND APBS_LIBS "-lstdc++")
+-    list(APPEND APBS_LIBS "-L${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 )
++-lblas -lvf2c -ltetgen -ltriangle -lreadline )
+     
+     SET(HAVE_MC_H YES)
+ endif()
+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/files/apbs-1.4.1-python.patch b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
new file mode 100644
index 000000000000..db9f86ba120a
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
@@ -0,0 +1,122 @@
+ apbs/contrib/iapbs/src/apbs_driver.c |  6 +++---
+ apbs/src/CMakeLists.txt              |  1 +
+ apbs/tools/CMakeLists.txt            |  2 +-
+ apbs/tools/python/CMakeLists.txt     |  1 +
+ apbs/tools/python/apbslib.c          |  4 ++--
+ apbs/tools/python/apbslib.i          |  4 ++--
+ apbs/tools/python/setup.py           | 16 ++++++++++++++++
+ 7 files changed, 26 insertions(+), 8 deletions(-)
+
+diff --git a/apbs/contrib/iapbs/src/apbs_driver.c b/apbs/contrib/iapbs/src/apbs_driver.c
+index c9e443b..e1ad67f 100644
+--- a/apbs/contrib/iapbs/src/apbs_driver.c
++++ b/apbs/contrib/iapbs/src/apbs_driver.c
+@@ -595,7 +595,7 @@ int apbsdrv_(
+ 		printPBEPARM(pbeparm);
+ 
+ 		/* Refine mesh */
+-		if (!preRefineFE(i, nosh, feparm, fetk)) {
++		if (!preRefineFE(i, feparm, fetk)) {
+ 		    Vnm_tprint( 2, "Error pre-refining mesh!\n");
+ 		    VJMPERR1(0);
+ 		}
+@@ -609,7 +609,7 @@ int apbsdrv_(
+ 		Vnm_tprint(1, "  Beginning solve-estimate-refine cycle:\n");
+ 		for (isolve=0; isolve<feparm->maxsolve; isolve++) {
+ 		    Vnm_tprint(1, "    Solve #%d...\n", isolve);
+-		    if (!solveFE(i, nosh, pbeparm, feparm, fetk)) {
++		    if (!solveFE(i, pbeparm, feparm, fetk)) {
+ 			Vnm_tprint(2, "ERROR SOLVING EQUATION!\n");
+ 			VJMPERR1(0);
+ 		    }
+@@ -622,7 +622,7 @@ int apbsdrv_(
+ 		    /* We're not going to refine if we've hit the max number
+ 		     * of solves */
+ 		    if (isolve < (feparm->maxsolve)-1) {
+-			if (!postRefineFE(i, nosh, feparm, fetk)) break;
++			if (!postRefineFE(i, feparm, fetk)) break;
+ 		    }
+ 		    bytesTotal = Vmem_bytesTotal();
+ 		    highWater = Vmem_highWaterTotal();
+diff --git a/apbs/src/CMakeLists.txt b/apbs/src/CMakeLists.txt
+index 44d20fa..2577343 100644
+--- a/apbs/src/CMakeLists.txt
++++ b/apbs/src/CMakeLists.txt
+@@ -68,6 +68,7 @@ configure_file(
+ 
+ if(ENABLE_iAPBS)
+     ADD_LIBRARY(apbs_routines routines.c routines.h)
++    target_link_libraries(apbs_routines apbs_mg apbs_fem)
+     INSTALL(TARGETS apbs_routines DESTINATION ${LIBRARY_INSTALL_PATH})
+     INSTALL(FILES apbscfg.h DESTINATION ${HEADER_INSTALL_PATH})
+ endif()
+diff --git a/apbs/tools/CMakeLists.txt b/apbs/tools/CMakeLists.txt
+index 1982a3c..4acbe68 100644
+--- a/apbs/tools/CMakeLists.txt
++++ b/apbs/tools/CMakeLists.txt
+@@ -4,5 +4,5 @@ add_subdirectory(mesh)
+ add_subdirectory(manip)
+ 
+ if(ENABLE_PYTHON)
+-    add_subdirectory(manip)
++    add_subdirectory(python)
+ endif(ENABLE_PYTHON)
+diff --git a/apbs/tools/python/CMakeLists.txt b/apbs/tools/python/CMakeLists.txt
+new file mode 100644
+index 0000000..8b13789
+--- /dev/null
++++ b/apbs/tools/python/CMakeLists.txt
+@@ -0,0 +1 @@
++
+diff --git a/apbs/tools/python/apbslib.c b/apbs/tools/python/apbslib.c
+index fef5cc8..feaaa2c 100644
+--- a/apbs/tools/python/apbslib.c
++++ b/apbs/tools/python/apbslib.c
+@@ -2504,8 +2504,8 @@ static swig_module_info swig_module = {swig_types, 24, 0, 0, 0, 0};
+ #include "maloc/maloc.h"
+ #include "apbscfg.h" 
+ #include "routines.h"
+-#include "apbs/valist.h"
+-#include "apbs/vatom.h"
++#include "generic/valist.h"
++#include "generic/vatom.h"
+ 
+ 
+ #include <limits.h>
+diff --git a/apbs/tools/python/apbslib.i b/apbs/tools/python/apbslib.i
+index 17fe521..44d05ea 100644
+--- a/apbs/tools/python/apbslib.i
++++ b/apbs/tools/python/apbslib.i
+@@ -15,8 +15,8 @@ Header files:
+ #include "maloc/maloc.h"
+ #include "apbscfg.h" 
+ #include "routines.h"
+-#include "apbs/valist.h"
+-#include "apbs/vatom.h"
++#include "generic/valist.h"
++#include "generic/vatom.h"
+ %} 
+ 
+ /* 
+diff --git a/apbs/tools/python/setup.py b/apbs/tools/python/setup.py
+new file mode 100644
+index 0000000..4a20198
+--- /dev/null
++++ b/apbs/tools/python/setup.py
+@@ -0,0 +1,16 @@
++from distutils.core import setup, Extension
++setup(name='apbs',
++    version='1.4.1',
++    package_dir={'apbs': '', 'vgrid': 'vgrid'},
++    packages=['apbs', 'vgrid'],
++    py_modules=['apbslib', 'main', 'noinput'],
++    ext_modules=[
++        Extension(
++            '_apbslib',
++            ['apbslib.i'],
++            swig_opts=['-module', 'apbslib', '-I../include'],
++            include_dirs=["../../src"],
++            libraries=["apbs_generic", "apbs_routines"]
++            )
++        ],
++    )
diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml
new file mode 100644
index 000000000000..f1b8467dd96e
--- /dev/null
+++ b/sci-chemistry/apbs/metadata.xml
@@ -0,0 +1,26 @@
+<?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@gentoo.org</email>
+    <name>Justin Lecher</name>
+    <description>Ebuild Crasher</description>
+  </maintainer>
+  <use>
+    <flag name="fetk">Include support for FeTK</flag>
+    <flag name="fast">APBS fast mode (experimental)</flag>
+    <flag name="iapbs">C/C++/Fortran interface</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>
+  <upstream>
+    <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id>
+  </upstream>
+</pkgmetadata>