sci-libs/shogun: Version bump to 5.0.0

Gentoo-bug: 550134, 570014, 587324, 593310,
            602534, 604670, 606770, 607122

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3782

4 files changed, 261 insertions, 27 deletions

diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
index 0469645c0845..b92de5fc7716 100644
--- a/sci-libs/shogun/Manifest
+++ b/sci-libs/shogun/Manifest
@@ -1,2 +1,3 @@
 DIST shogun-4.1.0.tar.bz2 2908955 SHA256 0eb313a95606edee046768a4577d63f32f7ccce340bed7bf0ff0d69225567185 SHA512 01950d5186a94735df5331752e1b97a5464015973ddba38a70bc977f9872b3aad02b162ae87919631cce56d1f10b0bea1fa7b463bf959816e5a15a726214f52a WHIRLPOOL 300bd0d887fe8ee4a1ac2aca7f3fbaebd4344dcffe2b20f9b5bb05e83d6973e8a98e54a216d99329c03eea2c02666c557a3c50ff7e11556298d119b8c262f762
+DIST shogun-5.0.0.tar.bz2 2448509 SHA256 e82c6a58db9db6624192b018750b0e41f793481791fdc9a6d328bf278d0ae70d SHA512 fa8d9dee4596acce12022540a6927cbdb62e08f8468c8be3790de07ebf3a53055032bcc532b28334ca83284c38f2b0153602634f12bafe4019acb9121b9ff236 WHIRLPOOL 532058c44680909f3717785035c13fb3cf48efec22924101975d80990cb2a9e151814c673ad1a03fa33e363abbaf21fc9edc99d7d25686cc67e907547217bf69
 DIST shogun-data-0.9.tar.bz2 287533841 SHA256 691dd37ccc9bdd4f56d6b7a8e061e80567c241219d70210f8148bc4b7b815559 SHA512 ab501640e2db650603899c857866b451fac5c7bbbc7b4ef98559581928869cea49aa326dfca1bb398eee7ebc8843dcc8ee3105c9f462718f1af672aac6b9340a WHIRLPOOL 19aa7a6d84be9ac7d8aaf7fb12747e17e0ba5a7ec8770b83cc1833b07cd1c6c397684a96eb8ebe709d544967ffaf23bcfbeea52dc8ddedf487fcf54a6d2b3ef7
diff --git a/sci-libs/shogun/files/shogun-5.0.0-fix-buildsystem.patch b/sci-libs/shogun/files/shogun-5.0.0-fix-buildsystem.patch
new file mode 100644
index 000000000000..1eb7cd075ece
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-5.0.0-fix-buildsystem.patch
@@ -0,0 +1,72 @@
+* Remove setting of user flags
+* Remove erroneous bundling of Eigen
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -33,15 +33,6 @@
+ SET(EIGEN_VERSION_MINIMUM 3.1.2)
+ SET(VIENNACL_VERSION_MINIMUM 1.5.0)
+ 
+-# Store system's or distribution's C[XX]FLAGS.
+-SET(SYSTEM_C_FLAGS "${CMAKE_C_FLAGS}")
+-SET(SYSTEM_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+-STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BUILD_TYPE_UC)
+-IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+-	SET(CMAKE_C_FLAGS "")
+-	SET(CMAKE_CXX_FLAGS "")
+-ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+-
+ # CCACHE
+ OPTION(ENABLE_CCACHE "Enable ccache for compilation" ON)
+ FIND_PACKAGE(CCache)
+@@ -174,24 +165,6 @@
+ 	SET(COMPILER_WARNINGS "-Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated")
+ ENDIF()
+ 
+-IF(CMAKE_COMPILER_IS_GNUCXX)
+-	SET(RELEASE_COMPILER_FLAGS "-fexpensive-optimizations -frerun-cse-after-loop -fcse-follow-jumps -finline-functions -fschedule-insns2 -fthread-jumps -fforce-addr -fstrength-reduce -funroll-loops")
+-	IF (${MACHINE} MATCHES "x86_64" OR ${MACHINE} MATCHES "i686")
+-		SET(RELEASE_COMPILER_FLAGS "${RELEASE_COMPILER_FLAGS} -mfpmath=sse")
+-	ENDIF()
+-ELSEIF(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
+-	SET(RELEASE_COMPILER_FLAGS "-funroll-loops")
+-ENDIF()
+-SET(SWIG_CXX_COMPILER_FLAGS "-O0 -g")
+-SET(CMAKE_C_FLAGS "${COMPILER_WARNINGS} ${CMAKE_C_FLAGS}")
+-SET(CMAKE_CXX_FLAGS "${COMPILER_WARNINGS} ${CMAKE_CXX_FLAGS}")
+-SET(CMAKE_C_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}")
+-SET(CMAKE_CXX_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}")
+-SET(CMAKE_C_FLAGS_DISTRIBUTION "-O2")
+-SET(CMAKE_CXX_FLAGS_DISTRIBUTION "-O2")
+-SET(CMAKE_C_FLAGS_DEBUG "-g")
+-SET(CMAKE_CXX_FLAGS_DEBUG "-g")
+-
+ OPTION(ENABLE_COVERAGE "Enable code coverage" OFF)
+ IF(ENABLE_COVERAGE)
+ 	IF(NOT CMAKE_COMPILER_IS_GNUCXX)
+@@ -617,13 +590,6 @@
+ 	include(external/Eigen3)
+ 	LIST(APPEND SYSTEM_INCLUDES ${EIGEN_INCLUDE_DIR})
+ ELSE()
+-    # eigen3 bug related to aliasing operators and self-storing.
+-    # TODO put in proper reference and version from when this is fixed
+-    IF(${EIGEN_VERSION} VERSION_GREATER 3.2.90)
+-        MESSAGE(WARNING "The system Eigen3 version ${EIGEN_VERSION} is buggy, manually bundling.")
+-        include(external/Eigen3)
+-    ENDIF()
+-
+ 	LIST(APPEND SYSTEM_INCLUDES ${EIGEN_INCLUDE_DIR})
+ ENDIF()
+ 
+@@ -957,11 +923,6 @@
+ # Respect system's or distribution's C[XX]FLAGS.
+ OPTION(SWIG_WITH_SYSTEM_CFLAGS "Enable system's C[XX]FLAGS for compilation of swig-binaries" ON)
+ 
+-IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+-	SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${SYSTEM_C_FLAGS}")
+-	SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SYSTEM_CXX_FLAGS}")
+-ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+-
+ IF(SWIG_WITH_SYSTEM_CFLAGS)
+ 	SET(SWIG_CXX_COMPILER_FLAGS "${SWIG_CXX_COMPILER_FLAGS} ${SYSTEM_CXX_FLAGS}")
+ ENDIF(SWIG_WITH_SYSTEM_CFLAGS)
diff --git a/sci-libs/shogun/metadata.xml b/sci-libs/shogun/metadata.xml
index fd2f5a44a6ef..88454ce87eb6 100644
--- a/sci-libs/shogun/metadata.xml
+++ b/sci-libs/shogun/metadata.xml
@@ -1,31 +1,32 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <maintainer type="project">
-    <email>sci@gentoo.org</email>
-    <name>Gentoo Science Project</name>
-  </maintainer>
-  <longdescription lang="en">
-  SHOGUN - is a new machine learning toolbox with focus on large
-  scale kernel methods and especially on Support Vector Machines
-  (SVM) with focus to bioinformatics. It provides a generic SVM
-  object interfacing to several different SVM implementations. Each
-  of the SVMs can be combined with a variety of the many kernels
-  implemented. It can deal with weighted linear combination of a
-  number of sub-kernels, each of which not necessarily working on the
-  same domain, where  an optimal sub-kernel weighting can be learned
-  using Multiple Kernel Learning.  Apart from SVM 2-class
-  classification and regression problems, a number of linear methods
-  like Linear Discriminant Analysis (LDA), Linear Programming Machine
-  (LPM), (Kernel) Perceptrons and also algorithms to train hidden
-  markov models are implemented. The input feature-objects can be
-  dense, sparse or strings and of type int/short/double/char and can
-  be converted into different feature types. Chains of preprocessors
-  (e.g. substracting the mean) can be attached to each feature object
-  allowing for on-the-fly pre-processing.
-</longdescription>
-  <use>
-    <flag name="R">Enable support for <pkg>dev-lang/R</pkg></flag>
-    <flag name="octave">Enable support for <pkg>sci-mathematics/octave</pkg></flag>
-  </use>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+	SHOGUN - is a new machine learning toolbox with focus on large
+	scale kernel methods and especially on Support Vector Machines
+	(SVM) with focus to bioinformatics. It provides a generic SVM
+	object interfacing to several different SVM implementations. Each
+	of the SVMs can be combined with a variety of the many kernels
+	implemented. It can deal with weighted linear combination of a
+	number of sub-kernels, each of which not necessarily working on the
+	same domain, where	an optimal sub-kernel weighting can be learned
+	using Multiple Kernel Learning.	Apart from SVM 2-class
+	classification and regression problems, a number of linear methods
+	like Linear Discriminant Analysis (LDA), Linear Programming Machine
+	(LPM), (Kernel) Perceptrons and also algorithms to train hidden
+	markov models are implemented. The input feature-objects can be
+	dense, sparse or strings and of type int/short/double/char and can
+	be converted into different feature types. Chains of preprocessors
+	(e.g. substracting the mean) can be attached to each feature object
+	allowing for on-the-fly pre-processing.
+	</longdescription>
+	<use>
+		<flag name="R">Enable support for <pkg>dev-lang/R</pkg></flag>
+		<flag name="octave">Enable support for <pkg>sci-mathematics/octave</pkg></flag>
+		<flag name="opencl">Enable support for building against OpenCL</flag>
+	</use>
 </pkgmetadata>
diff --git a/sci-libs/shogun/shogun-5.0.0.ebuild b/sci-libs/shogun/shogun-5.0.0.ebuild
new file mode 100644
index 000000000000..b3984dba4bae
--- /dev/null
+++ b/sci-libs/shogun/shogun-5.0.0.ebuild
@@ -0,0 +1,160 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5} )
+
+inherit cmake-utils flag-o-matic python-single-r1 toolchain-funcs versionator
+
+MYPV=$(get_version_component_range 1-2)
+MYPD=${PN}-data-0.9
+
+DESCRIPTION="Large Scale Machine Learning Toolbox"
+HOMEPAGE="http://shogun-toolbox.org/"
+SRC_URI="
+	ftp://shogun-toolbox.org/shogun/releases/${MYPV}/sources/${P}.tar.bz2
+	test? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )
+	examples? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )"
+
+LICENSE="GPL-3 free-noncomm"
+SLOT="0/16"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cpu_flags_x86_sse doc examples lua octave opencl python R ruby static-libs test"
+
+REQUIRED_USE="
+	python? ( ${PYTHON_REQUIRED_USE} )
+	test? ( python )"
+
+RDEPEND="
+	app-arch/bzip2
+	app-arch/gzip
+	app-arch/lzma
+	app-arch/snappy
+	dev-libs/lzo
+	dev-cpp/eigen:3
+	dev-libs/json-c:=
+	dev-libs/libxml2
+	dev-libs/protobuf:=
+	net-misc/curl
+	sci-libs/arpack
+	sci-libs/arprec
+	sci-libs/colpack
+	sci-libs/hdf5:=
+	sci-libs/nlopt
+	sci-mathematics/glpk:=
+	sci-mathematics/lpsolve:=
+	sys-libs/readline:0=
+	sys-libs/zlib
+	virtual/blas
+	virtual/cblas
+	virtual/lapack
+	lua? ( dev-lang/lua:0 )
+	octave? ( >=sci-mathematics/octave-4.2.0:=[hdf5] )
+	opencl? ( virtual/opencl )
+	python? ( dev-python/numpy[${PYTHON_USEDEP}] )
+	R? ( dev-lang/R )
+	ruby? ( dev-ruby/narray )"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig
+	doc? (
+		>=app-doc/doxygen-1.8.13-r1[dot]
+		dev-python/sphinx
+	)
+	lua? ( >=dev-lang/swig-3.0.12 )
+	octave? ( >=dev-lang/swig-3.0.12 )
+	python? (
+		>=dev-lang/swig-3.0.12
+		test? (
+			sci-libs/scipy
+		)
+	)
+	R? ( >=dev-lang/swig-3.0.12 )
+	ruby? ( >=dev-lang/swig-3.0.12 )
+	test? (
+		dev-python/jinja[${PYTHON_USEDEP}]
+		dev-cpp/gmock
+	)"
+
+# javamodular needs jblas (painful to package properly)
+# permodular work in progress (as 3.2.0)
+# could actually support multiple pythons, multiple rubys
+# feel free to do work for it
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-5.0.0-fix-buildsystem.patch
+	"${FILESDIR}"/${PN}-4.1.0-remove-C-linkage.patch
+)
+
+pkg_setup() {
+	use python && python-single-r1_pkg_setup
+}
+
+src_configure() {
+	export ATLAS_LIBRARY="$($(tc-getPKG_CONFIG) --libs cblas lapack)"
+	export CBLAS_LIBRARY="$($(tc-getPKG_CONFIG) --libs cblas)"
+	export ATLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas cblas lapack)"
+	export LAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
+
+	append-cppflags "$($(tc-getPKG_CONFIG) --cflags cblas)"
+
+	local mycmakeargs=(
+		-DCMAKE_SKIP_RPATH=ON
+		-DCMAKE_SKIP_INSTALL_RPATH=ON
+		-DLIB_INSTALL_DIR=$(get_libdir)
+		-DENABLE_TESTING=$(usex test)
+		-DBUILD_EXAMPLES=$(usex examples)
+		-DDISABLE_SSE=$(usex !cpu_flags_x86_sse)
+		-DCMAKE_DISABLE_FIND_PACKAGE_Pandoc=ON
+		$(cmake-utils_use_find_package doc Sphinx)
+		$(cmake-utils_use_find_package doc Doxygen)
+
+		# Features:
+		-DENABLE_COVERAGE=OFF
+		-DENABLE_COLPACK=ON
+		-DENABLE_PROTOBUF=ON
+		-DENABLE_PYTHON_DEBUG=OFF
+		-DENABLE_VIENNACL=$(usex opencl)
+		-DUSE_ARPREC=ON
+		-DUSE_HDF5=ON
+
+		# Bindings:
+		-DJavaModular=OFF
+		-DPerlModular=OFF
+		-DCSharpModular=OFF
+		-DLuaModular=$(usex lua)
+		-DOctaveModular=$(usex octave)
+		-DPythonModular=$(usex python)
+		-DRModular=$(usex R)
+		-DRubyModular=$(usex ruby)
+
+		# Disable bundled libs
+		-DBUNDLE_COLPACK=OFF
+		-DBUNDLE_JSON=OFF
+		-DBUNDLE_NLOPT=OFF
+	)
+	cmake-utils_src_configure
+
+	# gentoo bug #302621
+	has_version 'sci-libs/hdf5[mpi]' && export CXX=mpicxx CC=mpicc
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	use doc && cmake-utils_src_compile -C doc
+}
+
+src_install() {
+	cmake-utils_src_install
+
+	if use doc; then
+		local i
+		for i in lua octave python R ruby; do
+			if use $i; then
+				docinto html/${i,}_modular
+				dodoc -r "${BUILD_DIR}"/src/interfaces/${i,}_modular/modshogun/doxygen_xml/.
+			fi
+		done
+	fi
+}