gentoo resync : 25.08.2020

6 files changed, 0 insertions, 424 deletions

diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
deleted file mode 100644
index f00e4eaa7c6d..000000000000
--- a/sci-chemistry/apbs/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-AUX apbs-1.4.1-manip.patch 1462 BLAKE2B f4559008a1fc4dc367bc770ed29b7fa9ae9489ab57cfc8dd6e5cff358e27e2ac71b1e786bf9a4e3d96dfb4eea3596305beb5078746324769b582abf8a702a1c5 SHA512 70679623621fb56eeffc79166aa6fd35b5fa2fec828f6800a27b795a4e94c9eee673a7ba5f872c3266c9e78af8935d684fb5c4679b57da6a969189ce45e31468
-AUX apbs-1.4.1-multilib.patch 3301 BLAKE2B 4268a21ec878d780c7a1efe433bf2c82ef2e72f49a6071b6df695bf672ee999be9c29fed06e949b80cc230333d8deca1094c946662ec657d31e3b6f86e873969 SHA512 cdd72fd23a57ee8413f72bf674ae246543b1c9f326727ff07c3b8848d59f98ab7d2daf28677460cb4726f919832079c1d280bcdc86a8bef5c0875583c789b7c0
-AUX apbs-1.4.1-python.patch 3979 BLAKE2B b21633655df329f5d445c4e53140367b0a8a6cfbfafccba8943206ed9bae46839bae532e3efd19d75e89bc70a1fa59d05f3ed977b1a59f949649d3e89b887a96 SHA512 a38ca3bbf692f42268d192aff61949ece95d9b043ac10b4eec33e383773beec1c60425a12e84843a602e828528f6cf0ed6b8c90e99aeea679c5abc8c093c68ae
-DIST apbs-1.4.1.zip 37999283 BLAKE2B 2301deb7ab4eb2f20098cf63df180bb53189e42a89cd5559357cdcf08e84d27a44eafe8557bb460574802d24d29741ad4606dc3bd7f32911d0d0f2c7453d6470 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a
-EBUILD apbs-1.4.1-r2.ebuild 3033 BLAKE2B c5373211c86c086bd7fd1898ba2437496c4a9fb8971a7847625b5a5a438ae21b10a2c733d323c692b5a6f1a8c94c78b4630a326c7af84bb90b3200f8970a197c SHA512 7fba09a563be088193ab58b57c5f45288497f222058ab2189decc755f6a761ec15ceacf5fe5a8619224c75603e80db86d427c77f37ec4edb163f6d75d63747ef
-MISC metadata.xml 1048 BLAKE2B 53a61bd7e05e53b294f0cbd1a21b86f391429ad5f23a545e7cbb27625b152589247a08db06c5d7f6658425de032be970fae0230ad1ac14ac4f6de42663d6c97c SHA512 7d68049cb9b044676430fe879890cc4cd869b99f85696f579d9cbf3b156081301792fd7f03205a9b9d429d71c9a35b4815f4236573f68d3ef6b4718e6e1f0bb3
diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
deleted file mode 100644
index 4ea1cfcd1fad..000000000000
--- a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
+++ /dev/null
@@ -1,129 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-DISTUTILS_SINGLE_IMPL=true
-COMMIT="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
-inherit cmake-utils distutils-r1 flag-o-matic toolchain-funcs
-
-DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems"
-HOMEPAGE="https://www.poissonboltzmann.org/apbs/"
-#SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
-SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${COMMIT}.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=]
-	sys-libs/readline
-	virtual/blas
-	fetk? (
-		sci-libs/amd
-		sci-libs/fetk
-		sci-libs/superlu
-		sci-libs/umfpack
-	)
-	mpi? ( virtual/mpi )
-	python? ( ${PYTHON_DEPS} )
-"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	doc? ( app-doc/doxygen )
-"
-
-S="${WORKDIR}"/${PN}-pdb2pqr-${COMMIT}/${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 || die
-		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="${EPREFIX}"/usr/
-		-DBUILD_SHARED_LIBS=ON
-		-DENABLE_QUIT=OFF
-		-DBUILD_DOC=$(usex doc)
-		-DBUILD_TOOLS=$(usex tools)
-		-DENABLE_BEM=OFF
-# ENABLE_BEM: Boundary element method using TABIPB
-		-DENABLE_DEBUG=$(usex debug)
-		-DENABLE_VERBOSE_DEBUG=$(usex debug)
-		-DENABLE_FAST=$(usex fast)
-		-DENABLE_FETK=$(usex fetk)
-		-DENABLE_MPI=$(usex mpi)
-		-DENABLE_PYTHON=$(usex python)
-# ENABLE_TINKER: Enable TINKER support
-		-DENABLE_iAPBS=$(usex 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 || die
-		distutils-r1_src_configure
-	fi
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	if use python; then
-		append-ldflags -L"${S}"/lib
-		cd tools/python || die
-		distutils-r1_src_compile
-	fi
-}
-
-src_test() {
-	python_setup
-	cd tests || die
-	LD_LIBRARY_PATH="${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 || die
-		distutils-r1_src_install
-		rm -rf "${ED}"/usr/share/apbs/tools/python || die
-	fi
-}
diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
deleted file mode 100644
index 090a27d8a5a6..000000000000
--- a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
+++ /dev/null
@@ -1,50 +0,0 @@
- apbs/CMakeLists.txt             | 2 +-
- apbs/tools/CMakeLists.txt       | 4 ----
- apbs/tools/mesh/CMakeLists.txt  | 4 ++--
- 4 files changed, 5 insertions(+), 9 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 8917fc4..5152008 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -293,7 +293,7 @@ option(ENABLE_FETK "Enable the finite element solver" OFF)
- 
- if(ENABLE_FETK)
-     message(STATUS "Checking for fetk components")
--    set(FETK_ENALBED 1)
-+    set(FETK_ENABLED 1)
- 
-     list(APPEND APBS_LIBS "-lstdc++")
-     list(APPEND APBS_LIBS "-L${FETK_PATH}/lib")
-diff --git a/tools/manip/CMakeLists.txt b/tools/manip/CMakeLists.txt
-index 937dac7..5768cc5 100644
---- a/tools/manip/CMakeLists.txt
-+++ b/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/tools/mesh/CMakeLists.txt b/tools/mesh/CMakeLists.txt
-index 1406377..6e6dfb9 100644
---- a/tools/mesh/CMakeLists.txt
-+++ b/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
deleted file mode 100644
index a4e2d1761cf4..000000000000
--- a/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch
+++ /dev/null
@@ -1,92 +0,0 @@
- 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
deleted file mode 100644
index 5ad6613615f2..000000000000
--- a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
+++ /dev/null
@@ -1,122 +0,0 @@
- 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/contrib/iapbs/src/apbs_driver.c b/contrib/iapbs/src/apbs_driver.c
-index c9e443b..e1ad67f 100644
---- a/contrib/iapbs/src/apbs_driver.c
-+++ b/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/src/CMakeLists.txt b/src/CMakeLists.txt
-index 44d20fa..2577343 100644
---- a/src/CMakeLists.txt
-+++ b/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/tools/CMakeLists.txt b/tools/CMakeLists.txt
-index 1982a3c..4acbe68 100644
---- a/tools/CMakeLists.txt
-+++ b/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/tools/python/CMakeLists.txt b/tools/python/CMakeLists.txt
-new file mode 100644
-index 0000000..8b13789
---- /dev/null
-+++ b/tools/python/CMakeLists.txt
-@@ -0,0 +1 @@
-+
-diff --git a/tools/python/apbslib.c b/tools/python/apbslib.c
-index fef5cc8..feaaa2c 100644
---- a/tools/python/apbslib.c
-+++ b/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/tools/python/apbslib.i b/tools/python/apbslib.i
-index 17fe521..44d05ea 100644
---- a/tools/python/apbslib.i
-+++ b/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/tools/python/setup.py b/tools/python/setup.py
-new file mode 100644
-index 0000000..4a20198
---- /dev/null
-+++ b/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
deleted file mode 100644
index a33a5468d19c..000000000000
--- a/sci-chemistry/apbs/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </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>
-    <remote-id type="sourceforge">apbs</remote-id>
-  </upstream>
-</pkgmetadata>