add shogun 6.1.3 (#2977)

* add shogun 6.1.3

* [shogun] Add additional dependencies, force static linking

ports/shogun/CONTROL

@@ -0,0 +1,4 @@
+Source: shogun
+Version: 6.1.3
+Build-Depends: bzip2, eigen3, liblzma, libxml2, openblas, nlopt, rxcpp, snappy, zlib, protobuf, curl, lzo, dirent
+Description: Unified and efficient Machine Learning

ports/shogun/MSDirent.cmake

@@ -0,0 +1 @@
+find_path(MSDIRENT_INCLUDE_DIR NAMES dirent.h)

ports/shogun/cmake.patch

@@ -0,0 +1,73 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 6c48bed..6f97c8b 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -60,8 +60,8 @@ 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 "")
++#	SET(CMAKE_C_FLAGS "")
++#	SET(CMAKE_CXX_FLAGS "")
+ ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+ 
+ # CCACHE
+@@ -184,12 +184,12 @@ SET(SWIG_CXX_COMPILER_FLAGS "-O0 -g")
+ SET(CMAKE_C_FLAGS "${COMPILER_WARNINGS} ${CMAKE_C_FLAGS}")
+ SET(CMAKE_CXX_FLAGS "${COMPILER_WARNINGS} ${CMAKE_CXX_FLAGS}")
+ IF(MSVC)
+-	SET(CMAKE_C_FLAGS_RELEASE "/O2 ${RELEASE_COMPILER_FLAGS}")
+-	SET(CMAKE_CXX_FLAGS_RELEASE "/O2 ${RELEASE_COMPILER_FLAGS}")
+-	SET(CMAKE_C_FLAGS_DISTRIBUTION "/Ot")
+-	SET(CMAKE_CXX_FLAGS_DISTRIBUTION "/Ot")
+-	SET(CMAKE_C_FLAGS_DEBUG "/DEBUG /Od /Zi")
+-	SET(CMAKE_CXX_FLAGS_DEBUG "/DEBUG /Od /Zi")
++	# SET(CMAKE_C_FLAGS_RELEASE "/O2 ${RELEASE_COMPILER_FLAGS}")
++	# SET(CMAKE_CXX_FLAGS_RELEASE "/O2 ${RELEASE_COMPILER_FLAGS}")
++	# SET(CMAKE_C_FLAGS_DISTRIBUTION "/Ot")
++	# SET(CMAKE_CXX_FLAGS_DISTRIBUTION "/Ot")
++	# SET(CMAKE_C_FLAGS_DEBUG "/DEBUG /Od /Zi")
++	# SET(CMAKE_CXX_FLAGS_DEBUG "/DEBUG /Od /Zi")
+ 	add_compile_options("/bigobj")
+ ELSE()
+ 	SET(CMAKE_C_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}")
+diff --git a/cmake/version.cmake b/cmake/version.cmake
+index fbca111..f6847f7 100644
+--- a/cmake/version.cmake
++++ b/cmake/version.cmake
+@@ -5,7 +5,7 @@ SET(MAINVERSION ${VERSION})
+ 
+ SET(EXTRA "")
+ 
+-IF(EXISTS "${ROOT_DIR}/.git/")
++IF(EXISTS "${ROOT_DIR}/.git/" AND FALSE)
+ 	FIND_PACKAGE(Git QUIET)
+ 	IF (NOT GIT_FOUND)
+ 		MESSAGE(FATAL_ERROR "The source is checked out from a git repository, but cannot find git executable!")
+diff --git a/src/shogun/CMakeLists.txt b/src/shogun/CMakeLists.txt
+index 9e79786..fd76961 100644
+--- a/src/shogun/CMakeLists.txt
++++ b/src/shogun/CMakeLists.txt
+@@ -145,7 +145,7 @@ endif()
+ # add target for static library if enabled
+ if (LIBSHOGUN_BUILD_STATIC)
+   add_library(shogun-static STATIC $<TARGET_OBJECTS:libshogun> ${CMAKE_CURRENT_BINARY_DIR}/lib/config.h)
+-  set_property(TARGET shogun-static PROPERTY OUTPUT_NAME shogun)
++  set_property(TARGET shogun-static PROPERTY OUTPUT_NAME libshogun)
+   target_include_directories(shogun-static PUBLIC
+     $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src>
+     $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/src>
+@@ -492,10 +492,12 @@ ELSE()
+ ENDIF()
+ 
+ # set the desidered targets to be installed
++if(NOT INSTALL_TARGETS)
+ set(INSTALL_TARGETS shogun)
+ if (LIBSHOGUN_BUILD_STATIC)
+   LIST(APPEND INSTALL_TARGETS shogun-static)
+ endif()
++endif()
+ 
+ INSTALL(
+   TARGETS ${INSTALL_TARGETS}

ports/shogun/portfile.cmake

@@ -0,0 +1,67 @@
+if(VCPKG_LIBRARY_LINKAGE STREQUAL "dynamic")
+    message("shogun only supports static library linkage")
+    set(VCPKG_LIBRARY_LINKAGE "static")
+endif()
+
+include(vcpkg_common_functions)
+
+vcpkg_from_github(
+    OUT_SOURCE_PATH SOURCE_PATH
+    REPO shogun-toolbox/shogun
+    REF shogun_6.1.3
+    SHA512 11aeed456b13720099ca820ab9742c90ce4af2dc049602a425f8c44d2fa155327c7f1d3af2ec840666f600a91e75902d914ffe784d76ed35810da4f3a5815673
+    HEAD_REF master
+)
+
+vcpkg_apply_patches(
+    SOURCE_PATH ${SOURCE_PATH}
+    PATCHES ${CMAKE_CURRENT_LIST_DIR}/cmake.patch
+)
+
+file(REMOVE_RECURSE ${SOURCE_PATH}/cmake/external)
+file(MAKE_DIRECTORY ${SOURCE_PATH}/cmake/external)
+file(COPY ${CMAKE_CURRENT_LIST_DIR}/MSDirent.cmake DESTINATION ${SOURCE_PATH}/cmake/external)
+
+vcpkg_configure_cmake(
+    SOURCE_PATH ${SOURCE_PATH}
+    PREFER_NINJA
+    OPTIONS
+        -DBUILD_META_EXAMPLES=OFF
+        -DBUILD_EXAMPLES=OFF
+        -DUSE_SVMLIGHT=OFF
+        -DENABLE_TESTING=OFF
+        -DLICENSE_GPL_SHOGUN=OFF
+        # Conflicting definitions in OpenBLAS and Eigen
+        -DENABLE_EIGEN_LAPACK=OFF
+
+        -DCMAKE_DISABLE_FIND_PACKAGE_JSON=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_ViennaCL=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_TFLogger=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_GLPK=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_CPLEX=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_ARPACK=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_Mosek=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_LpSolve=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_ColPack=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_ARPREC=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_Ctags=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_CCache=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_Doxygen=TRUE
+
+        -DINSTALL_TARGETS=shogun-static
+)
+
+vcpkg_install_cmake()
+
+vcpkg_fixup_cmake_targets(CONFIG_PATH lib/cmake/shogun)
+
+file(REMOVE_RECURSE
+    # This directory is empty given the settings above
+    ${CURRENT_PACKAGES_DIR}/include/shogun/mathematics/linalg/backend
+    ${CURRENT_PACKAGES_DIR}/debug/include
+    ${CURRENT_PACKAGES_DIR}/debug/share
+)
+
+# Handle copyright
+file(COPY ${SOURCE_PATH}/COPYING DESTINATION ${CURRENT_PACKAGES_DIR}/share/shogun)
+file(RENAME ${CURRENT_PACKAGES_DIR}/share/shogun/COPYING ${CURRENT_PACKAGES_DIR}/share/shogun/copyright)

scripts/buildsystems/vcpkg.cmake

@@ -260,6 +260,11 @@ macro(find_package name)
                     "optimized" "${_VCPKG_INSTALLED_DIR}/${VCPKG_TARGET_TRIPLET}/lib/nghttp2.lib")
             endif()
         endif()
+    elseif("${name}" STREQUAL "LibXml2")
+        _find_package(${ARGV})
+        if(LibXml2_FOUND AND (CMAKE_SYSTEM_NAME STREQUAL "Windows" OR CMAKE_SYSTEM_NAME STREQUAL "WindowsStore"))
+            list(APPEND LIBXML2_LIBRARIES libiconv libcharset ws2_32)
+        endif()
     else()
         _find_package(${ARGV})
     endif()