gentoo resync : 25.08.2020

5 files changed, 0 insertions, 386 deletions

diff --git a/sci-libs/chemkit/Manifest b/sci-libs/chemkit/Manifest
deleted file mode 100644
index 8639b6d20b90..000000000000
--- a/sci-libs/chemkit/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX chemkit-0.1-multilib.patch 4694 BLAKE2B f52836ec887b9673c8eabac6ca4fb008aa23def355419f02704605438de44457f2a017a56a7fdd3ce387df08e5b57a0352052d2b88ff0e051a6cf47a192ffd1e SHA512 dedde9e5db14f088e5a70ebfcd9f46b6fbb2d60b1800a61ece1f7afef24caac502f129573823807caec050ba1515ad402a3615953b903a239c5287a5b96aa8b8
-AUX chemkit-0.1-unbundle.patch 6103 BLAKE2B 9ee0f121fec938a528abb837ab386fec62a8576b5c7d123538ce95604953f4f30d0b285b27a153ef98629f053954324f7c384329fe3ca6873f2d18700e914ff8 SHA512 9edd39008763b56eb7697562536c4c4d476880a414ae1a305d1af64cee04e4ccb82585cfd15d2f7608b5200e39863a9a97c2a152110b28e501fbd055737ce015
-DIST chemkit-0.1.tar.gz 5842235 BLAKE2B 9cf28dc6d2c067403172c4f54a057bf38ea9aeaebc96b9be819f4861d1559c1db440dd33baf15f739b2b0e6dc6ba3e73010e0b5aa1b46309435e7bbffb889259 SHA512 0273f8735333000b04007ccd7adc58f0c4809a570fa5a72e4161652d72e8953bf89cad0893c20ecbb3484d6c13a8828c92f12366dddeedaf591815c35f6ef011
-EBUILD chemkit-0.1-r2.ebuild 1904 BLAKE2B 8e047c10ed8fb80fb35bbd6176e508ba13c52e97e458783c42e0d978b001c7367e9427dd1198e86143fc6211d310fe3bb18b5bc091df0ed918f2449e1649f4f4 SHA512 1078f0af1f8b32d324e25e8bd790559f0ce8cd86170ebb52c15318b058ca490e9b85416e9ce1d11abdc607af76ca02093a4f9f356cd7ac80ba75e7be3d257ed2
-MISC metadata.xml 352 BLAKE2B fbab9c9aa637ace5d90660942c8a34550c45bdf692b98ef583a77e5ed8d666877c09076314f6ec4081f91d12803fd1d8f50b7a715991e8e0ed0541e8473563b3 SHA512 b197aa62c04a5f668822db2e277407e7e871505f7adf5cfceaab36b5bc808f0b7582f17f9a00c7d4013eb4728b7a6ef61a52325deb182d6cd4a344e5d1e98cb1
diff --git a/sci-libs/chemkit/chemkit-0.1-r2.ebuild b/sci-libs/chemkit/chemkit-0.1-r2.ebuild
deleted file mode 100644
index c687d55922e1..000000000000
--- a/sci-libs/chemkit/chemkit-0.1-r2.ebuild
+++ /dev/null
@@ -1,89 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-single-r1 virtualx
-
-DESCRIPTION="Library for chemistry applications"
-HOMEPAGE="https://github.com/kylelutz/chemkit"
-SRC_URI="mirror://sourceforge/project/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD PSF-2.2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples python test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	dev-cpp/eigen:3
-	dev-libs/boost:=
-	dev-libs/rapidxml
-	media-libs/glu
-	sci-libs/inchi
-	sci-libs/lemon
-	virtual/opengl
-	examples? (
-		x11-libs/libX11
-		x11-libs/libXext
-	)
-	python? ( ${PYTHON_DEPS} )
-"
-DEPEND="${RDEPEND}"
-
-RESTRICT="test" # requires disabled Qt4
-
-S="${WORKDIR}"/${PN}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-multilib.patch
-	"${FILESDIR}"/${P}-unbundle.patch
-)
-
-src_prepare() {
-	# jsoncpp API change
-	# xdrf != xdrfile
-	rm -rvf src/3rdparty/{inchi,khronos,lemon,rapidxml} || die
-	cmake-utils_src_prepare
-
-	# bug 640206
-	sed -e "/add_subdirectory(xtc/s/^/#DONT /" \
-		-i src/plugins/CMakeLists.txt || die "Failed to disable xtc"
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCHEMKIT_BUILD_EXAMPLES=$(usex examples)
-		-DCHEMKIT_BUILD_DEMOS=$(usex examples)
-		-DCHEMKIT_BUILD_BINDINGS_PYTHON=$(usex python)
-		-DCHEMKIT_BUILD_APPS=OFF
-		-DCHEMKIT_BUILD_PLUGIN_BABEL=OFF
-		-DCHEMKIT_BUILD_QT_DESIGNER_PLUGINS=OFF
-		-DCHEMKIT_WITH_GRAPHICS=OFF
-		-DCHEMKIT_WITH_GUI=OFF
-		-DCHEMKIT_WITH_WEB=OFF
-		-DCHEMKIT_BUILD_TESTS=$(usex test)
-		-DUSE_SYSTEM_INCHI=ON
-		-DUSE_SYSTEM_JSONCPP=OFF
-		-DUSE_SYSTEM_RAPIDXML=ON
-		-DUSE_SYSTEM_XDRF=OFF
-	)
-	cmake-utils_src_configure
-}
-
-src_test() {
-	VIRTUALX_COMMAND="cmake-utils_src_test"
-	virtualmake
-}
-
-src_install() {
-	use examples && \
-		dobin \
-			"${BUILD_DIR}"/demos/*-viewer/*-viewer \
-			"${BUILD_DIR}"/examples/uff-energy/uff-energy
-
-	cmake-utils_src_install
-}
diff --git a/sci-libs/chemkit/files/chemkit-0.1-multilib.patch b/sci-libs/chemkit/files/chemkit-0.1-multilib.patch
deleted file mode 100644
index b6a61d58ed8c..000000000000
--- a/sci-libs/chemkit/files/chemkit-0.1-multilib.patch
+++ /dev/null
@@ -1,90 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index e531be4..e0d6b2d 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -44,7 +44,7 @@ configure_file(
-     "${CMAKE_MODULE_PATH}/ChemkitConfig.cmake.in"
-     "${CMAKE_BINARY_DIR}/ChemkitConfig.cmake"
-     IMMEDIATE @ONLY)
--install(FILES ${CMAKE_BINARY_DIR}/ChemkitConfig.cmake DESTINATION lib/chemkit)
-+install(FILES ${CMAKE_BINARY_DIR}/ChemkitConfig.cmake DESTINATION lib${LIB_SUFFIX}/chemkit)
- 
- # Create a ChemkitBuildTreeSettings.cmake file for the use from the build tree
- configure_file(
-diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
-index 88c6b5f..1100c3b 100644
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -8,12 +8,12 @@ macro(add_chemkit_library library_name)
-   add_library(${library_name} SHARED ${ARGN})
- 
-   # add install target
--  install(TARGETS ${library_name} DESTINATION lib)
-+  install(TARGETS ${library_name} DESTINATION lib${LIB_SUFFIX})
- 
-   # copy library into build directory
-   get_target_property(library_location ${library_name} LOCATION)
-   get_filename_component(library_filename ${library_location} NAME)
--  add_custom_command(TARGET ${library_name} POST_BUILD COMMAND ${CMAKE_COMMAND} ARGS -E copy ${library_location} ${CMAKE_BINARY_DIR}/lib/${library_filename})
-+  add_custom_command(TARGET ${library_name} POST_BUILD COMMAND ${CMAKE_COMMAND} ARGS -E copy ${library_location} ${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/${library_filename})
- 
- endmacro(add_chemkit_library)
- 
-diff --git a/src/plugins/CMakeLists.txt b/src/plugins/CMakeLists.txt
-index dc8970f..77029b7 100644
---- a/src/plugins/CMakeLists.txt
-+++ b/src/plugins/CMakeLists.txt
-@@ -3,7 +3,7 @@ macro(add_chemkit_plugin plugin_name)
-   add_library(${plugin_name} SHARED ${ARGN})
- 
-   # add install target
--  install(TARGETS ${plugin_name} DESTINATION lib/chemkit/plugins/)
-+  install(TARGETS ${plugin_name} DESTINATION lib${LIB_SUFFIX}/chemkit/plugins/)
- 
-   # remove 'lib' prefix
-   set_target_properties(${plugin_name} PROPERTIES PREFIX "")
-@@ -11,15 +11,15 @@ macro(add_chemkit_plugin plugin_name)
-   # copy plugin into build directory
-   get_target_property(plugin_location ${plugin_name} LOCATION)
-   get_filename_component(plugin_filename ${plugin_location} NAME)
--  add_custom_command(TARGET ${plugin_name} POST_BUILD COMMAND ${CMAKE_COMMAND} ARGS -E copy ${plugin_location} ${CMAKE_BINARY_DIR}/lib/chemkit/plugins/${plugin_filename})
-+  add_custom_command(TARGET ${plugin_name} POST_BUILD COMMAND ${CMAKE_COMMAND} ARGS -E copy ${plugin_location} ${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/chemkit/plugins/${plugin_filename})
- 
-   # plugin data
-   if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/data)
-     # copy plugin data into build directory
--    file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/data/ DESTINATION ${CMAKE_BINARY_DIR}/lib/chemkit/plugins/data/${plugin_name}/)
-+    file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/data/ DESTINATION ${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/chemkit/plugins/data/${plugin_name}/)
-     
-     # install plugin data directory
--    install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/data/ DESTINATION lib/chemkit/plugins/data/${plugin_name})
-+    install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/data/ DESTINATION lib${LIB_SUFFIX}/chemkit/plugins/data/${plugin_name})
-   endif()
- endmacro(add_chemkit_plugin)
- 
-diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
-index b191b82..a4ea0b0 100644
---- a/tests/CMakeLists.txt
-+++ b/tests/CMakeLists.txt
-@@ -4,7 +4,7 @@ endif()
- 
- macro(add_chemkit_test test_name test_executable)
-   add_test(NAME ${test_name} COMMAND ${test_executable})
--  set_tests_properties(${test_name} PROPERTIES ENVIRONMENT "CHEMKIT_PLUGIN_PATH=${CMAKE_BINARY_DIR}/lib/chemkit/plugins/")
-+  set_tests_properties(${test_name} PROPERTIES ENVIRONMENT "CHEMKIT_PLUGIN_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/chemkit/plugins/")
- endmacro(add_chemkit_test)
- 
- add_subdirectory(auto)
-diff --git a/tests/auto/bindings/python/CMakeLists.txt b/tests/auto/bindings/python/CMakeLists.txt
-index 9859867..70da693 100644
---- a/tests/auto/bindings/python/CMakeLists.txt
-+++ b/tests/auto/bindings/python/CMakeLists.txt
-@@ -5,7 +5,7 @@ endif()
- macro(add_chemkit_python_test test_name test_script)
-   add_test(${test_name} ${PYTHON_EXECUTABLE} ${test_script})
-   set_tests_properties(${test_name} PROPERTIES
--                       ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/bindings/python/;CHEMKIT_PLUGIN_PATH=${CMAKE_BINARY_DIR}/lib/chemkit/plugins")
-+                       ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/bindings/python/;CHEMKIT_PLUGIN_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/chemkit/plugins")
- endmacro(add_chemkit_python_test)
- 
- add_chemkit_python_test(python.Atom ${CMAKE_CURRENT_SOURCE_DIR}/atomtest.py)
diff --git a/sci-libs/chemkit/files/chemkit-0.1-unbundle.patch b/sci-libs/chemkit/files/chemkit-0.1-unbundle.patch
deleted file mode 100644
index e8c9d18dca6e..000000000000
--- a/sci-libs/chemkit/files/chemkit-0.1-unbundle.patch
+++ /dev/null
@@ -1,191 +0,0 @@
- CMakeLists.txt                              | 21 +++++++++++++++++++++
- src/plugins/chemjson/CMakeLists.txt         |  6 +++++-
- src/plugins/chemjson/chemjsonfileformat.cpp |  4 ++++
- src/plugins/cml/cmlfileformat.h             |  4 ++++
- src/plugins/inchi/CMakeLists.txt            |  4 +++-
- src/plugins/inchi/inchikeylineformat.cpp    |  4 ++++
- src/plugins/inchi/inchilineformat.cpp       |  4 ++++
- src/plugins/pdb/pdbmlfileformat.cpp         |  4 ++++
- src/plugins/xtc/CMakeLists.txt              |  9 +++++++--
- src/plugins/xtc/xtcfileformat.cpp           |  4 ++++
- 10 files changed, 60 insertions(+), 4 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index e531be4..622ea9d 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -55,6 +55,27 @@ configure_file(
- # export the Chemkit package
- export(PACKAGE Chemkit)
- 
-+option(USE_SYSTEM_INCHI "Use inchi installed in system" OFF)
-+option(USE_SYSTEM_JSONCPP "Use json cpp installed in system" OFF)
-+option(USE_SYSTEM_RAPIXML "Use rapidxml installed in system" OFF)
-+option(USE_SYSTEM_XDRF "Use xdrflib installed in system" OFF)
-+
-+if(USE_SYSTEM_INCHI)
-+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_INCHI")
-+endif()
-+
-+if(USE_SYSTEM_JSONCPP)
-+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_JSONCPP")
-+endif()
-+
-+if(USE_SYSTEM_RAPIDXML)
-+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_RAPIDXML")
-+endif()
-+
-+if(USE_SYSTEM_XDRF)
-+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_XDRF")
-+endif()
-+
- # build options
- option(CHEMKIT_WITH_GRAPHICS "Build the chemkit-graphics library." ON)
- option(CHEMKIT_WITH_IO "Build the chemkit-io library." ON)
-diff --git a/src/plugins/chemjson/CMakeLists.txt b/src/plugins/chemjson/CMakeLists.txt
-index 0e115b5..a5e6f48 100644
---- a/src/plugins/chemjson/CMakeLists.txt
-+++ b/src/plugins/chemjson/CMakeLists.txt
-@@ -10,7 +10,11 @@ set(SOURCES
-   chemjsonplugin.cpp
- )
- 
--aux_source_directory(../../3rdparty/jsoncpp/ JSONCPP_SOURCES)
-+if(NOT USE_SYSTEM_JSONCPP)
-+	aux_source_directory(../../3rdparty/jsoncpp/ JSONCPP_SOURCES)
-+else()
-+	target_link_libraries(chemjson jsoncpp)
-+endif()
- 
- add_chemkit_plugin(chemjson ${SOURCES} ${JSONCPP_SOURCES})
- target_link_libraries(chemjson ${CHEMKIT_LIBRARIES})
-diff --git a/src/plugins/chemjson/chemjsonfileformat.cpp b/src/plugins/chemjson/chemjsonfileformat.cpp
-index a0d271e..3cd5827 100644
---- a/src/plugins/chemjson/chemjsonfileformat.cpp
-+++ b/src/plugins/chemjson/chemjsonfileformat.cpp
-@@ -43,7 +43,11 @@
- #include <chemkit/molecule.h>
- #include <chemkit/moleculefile.h>
- 
-+#ifdef SYSTEM_JSONCPP
-+#include <jsoncpp/json/json.h>
-+#else
- #include "../../3rdparty/jsoncpp/json/json.h"
-+#endif
- 
- namespace {
- 
-diff --git a/src/plugins/cml/cmlfileformat.h b/src/plugins/cml/cmlfileformat.h
-index e813223..61a547d 100644
---- a/src/plugins/cml/cmlfileformat.h
-+++ b/src/plugins/cml/cmlfileformat.h
-@@ -38,7 +38,11 @@
- 
- #include <chemkit/moleculefileformat.h>
- 
-+#ifdef SYSTEM_RAPIDXML
-+#include <rapidxml/rapidxml.hpp>
-+#else
- #include "../../3rdparty/rapidxml/rapidxml.hpp"
-+#endif
- 
- class CmlFileFormat : public chemkit::MoleculeFileFormat
- {
-diff --git a/src/plugins/inchi/CMakeLists.txt b/src/plugins/inchi/CMakeLists.txt
-index 2b25d9b..5f45f8a 100644
---- a/src/plugins/inchi/CMakeLists.txt
-+++ b/src/plugins/inchi/CMakeLists.txt
-@@ -7,7 +7,9 @@ set(SOURCES
-   inchiplugin.cpp
- )
- 
--aux_source_directory(../../3rdparty/inchi/ IUPAC_INCHI_SOURCES)
-+if(NOT USE_SYSTEM_INCHI)
-+	aux_source_directory(../../3rdparty/inchi/ IUPAC_INCHI_SOURCES)
-+endif()
- 
- add_chemkit_plugin(inchi ${SOURCES} ${IUPAC_INCHI_SOURCES})
- target_link_libraries(inchi ${CHEMKIT_LIBRARIES})
-diff --git a/src/plugins/inchi/inchikeylineformat.cpp b/src/plugins/inchi/inchikeylineformat.cpp
-index 2682f95..cec0a17 100644
---- a/src/plugins/inchi/inchikeylineformat.cpp
-+++ b/src/plugins/inchi/inchikeylineformat.cpp
-@@ -38,7 +38,11 @@
- #include <boost/format.hpp>
- 
- #include "inchilineformat.h"
-+#ifdef SYSTEM_INCHI
-+#include <inchi_api.h>
-+#else
- #include "../../3rdparty/inchi/inchi_api.h"
-+#endif
- 
- InchiKeyLineFormat::InchiKeyLineFormat()
-     : chemkit::LineFormat("inchikey")
-diff --git a/src/plugins/inchi/inchilineformat.cpp b/src/plugins/inchi/inchilineformat.cpp
-index 5b9bc42..ea5977c 100644
---- a/src/plugins/inchi/inchilineformat.cpp
-+++ b/src/plugins/inchi/inchilineformat.cpp
-@@ -42,7 +42,11 @@
- 
- #include <boost/algorithm/string.hpp>
- 
-+#ifdef SYSTEM_INCHI
-+#include <inchi_api.h>
-+#else
- #include "../../3rdparty/inchi/inchi_api.h"
-+#endif
- 
- #include <chemkit/atom.h>
- #include <chemkit/bond.h>
-diff --git a/src/plugins/pdb/pdbmlfileformat.cpp b/src/plugins/pdb/pdbmlfileformat.cpp
-index 081a4ec..2ca4269 100644
---- a/src/plugins/pdb/pdbmlfileformat.cpp
-+++ b/src/plugins/pdb/pdbmlfileformat.cpp
-@@ -35,7 +35,11 @@
- 
- #include "pdbmlfileformat.h"
- 
-+#ifdef SYSTEM_RAPIDXML
-+#include <rapidxml/rapidxml.hpp>
-+#else
- #include "../../3rdparty/rapidxml/rapidxml.hpp"
-+#endif
- 
- #include <chemkit/atom.h>
- #include <chemkit/polymer.h>
-diff --git a/src/plugins/xtc/CMakeLists.txt b/src/plugins/xtc/CMakeLists.txt
-index 98d8ba7..8c09e64 100644
---- a/src/plugins/xtc/CMakeLists.txt
-+++ b/src/plugins/xtc/CMakeLists.txt
-@@ -13,7 +13,12 @@ set(SOURCES
-   xtcplugin.cpp
- )
- 
--aux_source_directory(../../3rdparty/xdrf/ XDRF_SOURCES)
-+
-+if(USE_SYSTEM_XDRF)
-+	find_library(XDRF_LIBRARY NAMES xdrfile libxdrfile)
-+else()
-+	aux_source_directory(../../3rdparty/xdrf/ XDRF_SOURCES)
-+endif()
- 
- add_chemkit_plugin(xtc ${SOURCES} ${XDRF_SOURCES})
--target_link_libraries(xtc ${CHEMKIT_LIBRARIES} ${Boost_LIBRARIES})
-+target_link_libraries(xtc ${CHEMKIT_LIBRARIES} ${Boost_LIBRARIES} ${XDRF_LIBRARY} )
-diff --git a/src/plugins/xtc/xtcfileformat.cpp b/src/plugins/xtc/xtcfileformat.cpp
-index 0f00cb6..f8659ca 100644
---- a/src/plugins/xtc/xtcfileformat.cpp
-+++ b/src/plugins/xtc/xtcfileformat.cpp
-@@ -47,7 +47,11 @@
- #include <chemkit/trajectoryframe.h>
- #include <chemkit/cartesiancoordinates.h>
- 
-+#ifdef SYSTEM_XDRF
-+#include <xdrfile/xdrfile.h>
-+#else
- #include "../../3rdparty/xdrf/xdrf.h"
-+#endif
- 
- XtcFileFormat::XtcFileFormat()
-     : chemkit::TrajectoryFileFormat("xtc")
diff --git a/sci-libs/chemkit/metadata.xml b/sci-libs/chemkit/metadata.xml
deleted file mode 100644
index ec37d80cac64..000000000000
--- a/sci-libs/chemkit/metadata.xml
+++ /dev/null
@@ -1,11 +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>
-  <upstream>
-    <remote-id type="sourceforge">chemkit</remote-id>
-  </upstream>
-</pkgmetadata>