early-access version 2853

2022-07-23 03:01:36 +02:00
parent 1f2b5081b5
commit 1f111bb69c
8955 changed files with 418777 additions and 999 deletions
--- a/externals/vcpkg/ports/shogun/cmake-config.in.patch
+++ b/externals/vcpkg/ports/shogun/cmake-config.in.patch
@@ -0,0 +1,11 @@
+diff --git a/cmake/ShogunConfig.cmake.in b/cmake/ShogunConfig.cmake.in
+index e8e8035..a5097cb 100644
+--- a/cmake/ShogunConfig.cmake.in
+++ b/cmake/ShogunConfig.cmake.in
+@@ -2,5 +2,5 @@
+ 
+ set_and_check(shogun_INCLUDE_DIR "@PACKAGE_INCLUDE_INSTALL_DIR@")
+ 
+-include("@PACKAGE_CONFIG_PACKAGE_DIR@/ShogunTargets.cmake")
+include("@PACKAGE_CONFIG_PACKAGE_DIR@/../../../share/shogun/ShogunTargets.cmake")
+ check_required_components(shogun)
--- a/externals/vcpkg/ports/shogun/cmake.patch
+++ b/externals/vcpkg/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}
--- a/externals/vcpkg/ports/shogun/eigen-3.4.patch
+++ b/externals/vcpkg/ports/shogun/eigen-3.4.patch
@@ -0,0 +1,65 @@
+--- a/src/shogun/machine/gp/MultiLaplaceInferenceMethod.cpp
+++ b/src/shogun/machine/gp/MultiLaplaceInferenceMethod.cpp
+@@ -84,9 +84,9 @@ class CMultiPsiLine : public func_base
+ 		float64_t result=0;
+ 		for(index_t bl=0; bl<C; bl++)
+ 		{
+-			eigen_f.block(bl*n,0,n,1)=K*alpha->block(bl*n,0,n,1)*CMath::exp(log_scale*2.0);
+-			result+=alpha->block(bl*n,0,n,1).dot(eigen_f.block(bl*n,0,n,1))/2.0;
+-			eigen_f.block(bl*n,0,n,1)+=eigen_m;
+			eigen_f.segment(bl*n,n)=K*alpha->segment(bl*n,n)*CMath::exp(log_scale*2.0);
+			result+=alpha->segment(bl*n,n).dot(eigen_f.segment(bl*n,n))/2.0;
+			eigen_f.segment(bl*n,n)+=eigen_m;
+ 		}
+ 
+ 		// get first and second derivatives of log likelihood
+@@ -272,7 +272,7 @@ void CMultiLaplaceInferenceMethod::update_alpha()
+ 	{
+ 		Map<VectorXd> alpha(m_alpha.vector, m_alpha.vlen);
+ 		for(index_t bl=0; bl<C; bl++)
+-			eigen_mu.block(bl*n,0,n,1)=eigen_ktrtr*CMath::exp(m_log_scale*2.0)*alpha.block(bl*n,0,n,1);
+			eigen_mu.segment(bl*n,n)=eigen_ktrtr*CMath::exp(m_log_scale*2.0)*alpha.segment(bl*n,n);
+ 
+ 		//alpha'*(f-m)/2.0
+ 		Psi_New=alpha.dot(eigen_mu)/2.0;
+@@ -316,7 +316,7 @@ void CMultiLaplaceInferenceMethod::update_alpha()
+ 
+ 		for(index_t bl=0; bl<C; bl++)
+ 		{
+-			VectorXd eigen_sD=eigen_dpi.block(bl*n,0,n,1).cwiseSqrt();
+			VectorXd eigen_sD=eigen_dpi.segment(bl*n,n).cwiseSqrt();
+ 			LLT<MatrixXd> chol_tmp((eigen_sD*eigen_sD.transpose()).cwiseProduct(eigen_ktrtr*CMath::exp(m_log_scale*2.0))+
+ 				MatrixXd::Identity(m_ktrtr.num_rows, m_ktrtr.num_cols));
+ 			MatrixXd eigen_L_tmp=chol_tmp.matrixU();
+@@ -341,11 +341,11 @@ void CMultiLaplaceInferenceMethod::update_alpha()
+ 		VectorXd tmp2=m_tmp.array().rowwise().sum();
+ 
+ 		for(index_t bl=0; bl<C; bl++)
+-			eigen_b.block(bl*n,0,n,1)+=eigen_dpi.block(bl*n,0,n,1).cwiseProduct(eigen_mu.block(bl*n,0,n,1)-eigen_mean_bl-tmp2);
+			eigen_b.segment(bl*n,n)+=eigen_dpi.segment(bl*n,n).cwiseProduct(eigen_mu.segment(bl*n,n)-eigen_mean_bl-tmp2);
+ 
+ 		Map<VectorXd> &eigen_c=eigen_W;
+ 		for(index_t bl=0; bl<C; bl++)
+-			eigen_c.block(bl*n,0,n,1)=eigen_E.block(0,bl*n,n,n)*(eigen_ktrtr*CMath::exp(m_log_scale*2.0)*eigen_b.block(bl*n,0,n,1));
+			eigen_c.segment(bl*n,n)=eigen_E.block(0,bl*n,n,n)*(eigen_ktrtr*CMath::exp(m_log_scale*2.0)*eigen_b.segment(bl*n,n));
+ 
+ 		Map<MatrixXd> c_tmp(eigen_c.data(),n,C);
+ 
+@@ -409,7 +409,7 @@ float64_t CMultiLaplaceInferenceMethod::get_derivative_helper(SGMatrix<float64_t
+ 	{
+ 		result+=((eigen_E.block(0,bl*n,n,n)-eigen_U.block(0,bl*n,n,n).transpose()*eigen_U.block(0,bl*n,n,n)).array()
+ 			*eigen_dK.array()).sum();
+-		result-=(eigen_dK*eigen_alpha.block(bl*n,0,n,1)).dot(eigen_alpha.block(bl*n,0,n,1));
+		result-=(eigen_dK*eigen_alpha.segment(bl*n,n)).dot(eigen_alpha.segment(bl*n,n));
+ 	}
+ 
+ 	return result/2.0;
+@@ -489,7 +489,7 @@ SGVector<float64_t> CMultiLaplaceInferenceMethod::get_derivative_wrt_mean(
+ 		result[i]=0;
+ 		//currently only compute the explicit term
+ 		for(index_t bl=0; bl<C; bl++)
+-			result[i]-=eigen_alpha.block(bl*n,0,n,1).dot(eigen_dmu);
+			result[i]-=eigen_alpha.segment(bl*n,n).dot(eigen_dmu);
+ 	}
+ 
+ 	return result;
--- a/externals/vcpkg/ports/shogun/fix-ASSERT-not-found.patch
+++ b/externals/vcpkg/ports/shogun/fix-ASSERT-not-found.patch
@@ -0,0 +1,12 @@
+diff --git a/src/shogun/base/Parallel.cpp b/src/shogun/base/Parallel.cpp
+index 78ba319..53ac6c0 100644
+--- a/src/shogun/base/Parallel.cpp
+++ b/src/shogun/base/Parallel.cpp
+@@ -12,6 +12,7 @@
+ #include <shogun/lib/RefCount.h>
+ #include <shogun/lib/config.h>
+ #include <shogun/lib/memory.h>
+#include <shogun/io/SGIO.h>
+ 
+ #ifdef HAVE_CXX11
+ #include <thread>
--- a/externals/vcpkg/ports/shogun/fix-cblas-path.patch
+++ b/externals/vcpkg/ports/shogun/fix-cblas-path.patch
@@ -0,0 +1,13 @@
+diff --git a/src/shogun/mathematics/lapack.h b/src/shogun/mathematics/lapack.h
+index 6ba466f..f5de479 100644
+--- a/src/shogun/mathematics/lapack.h
+++ b/src/shogun/mathematics/lapack.h
+@@ -38,7 +38,7 @@ extern "C" {
+ #include <vecLib/cblas.h>
+ #endif
+ #else
+-#include <cblas.h>
+#include <openblas/cblas.h>
+ #endif
+ 
+ #ifdef HAVE_ACML
--- a/externals/vcpkg/ports/shogun/fix-dirent.patch
+++ b/externals/vcpkg/ports/shogun/fix-dirent.patch
@@ -0,0 +1,17 @@
+diff --git a/src/shogun/CMakeLists.txt b/src/shogun/CMakeLists.txt
+index fd76961..396251c 100644
+--- a/src/shogun/CMakeLists.txt
+++ b/src/shogun/CMakeLists.txt
+@@ -170,10 +170,10 @@ IF(MSVC)
+   ENDIF()
+ 
+   # bundle dirent
+-  include(external/MSDirent)
+  find_path(MSDIRENT_INCLUDE_DIR NAMES dirent.h)
+   SHOGUN_INCLUDE_DIRS(SCOPE PUBLIC
+     $<BUILD_INTERFACE:${MSDIRENT_INCLUDE_DIR}>
+-    $<INSTALL_INTERFACE:include/shogun/lib/external/MSDirent>
+    $<INSTALL_INTERFACE:include>
+   )
+ 
+   target_link_libraries(shogun PUBLIC winmm)
--- a/externals/vcpkg/ports/shogun/portfile.cmake
+++ b/externals/vcpkg/ports/shogun/portfile.cmake
@@ -0,0 +1,61 @@
+vcpkg_check_linkage(ONLY_STATIC_LIBRARY)
+
+vcpkg_from_github(
+    OUT_SOURCE_PATH SOURCE_PATH
+    REPO shogun-toolbox/shogun
+    REF ab274e7ab6bf24dd598c1daf1e626cb686d6e1cc
+    SHA512 fb90e5bf802c6fd59bf35ab7bbde5e8cfcdc5d46c69c52097140b30c6b29e28b8341dd1ece7f8a1f9d9123f4bc06d44d288584ce7dfddccf3d33fe05106884ae
+    HEAD_REF master
+    PATCHES
+        cmake.patch
+        cmake-config.in.patch
+        eigen-3.4.patch
+        fix-dirent.patch
+        fix-ASSERT-not-found.patch
+        fix-cblas-path.patch
+)
+
+vcpkg_find_acquire_program(PYTHON3)
+get_filename_component(PYTHON3_DIR "${PYTHON3}" DIRECTORY)
+vcpkg_add_to_path(${PYTHON3_DIR})
+
+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
+        -DLIBSHOGUN_BUILD_STATIC=ON
+        -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
+        -DCMAKE_DISABLE_FIND_PACKAGE_CURL=TRUE
+        -DCMAKE_DISABLE_FIND_PACKAGE_OpenMP=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(INSTALL ${SOURCE_PATH}/COPYING DESTINATION ${CURRENT_PACKAGES_DIR}/share/${PORT} RENAME copyright)
--- a/externals/vcpkg/ports/shogun/vcpkg.json
+++ b/externals/vcpkg/ports/shogun/vcpkg.json
@@ -0,0 +1,22 @@
+{
+  "name": "shogun",
+  "version-string": "6.1.4",
+  "port-version": 7,
+  "description": "Unified and efficient Machine Learning",
+  "homepage": "https://github.com/shogun-toolbox/shogun",
+  "dependencies": [
+    "blas",
+    "bzip2",
+    "curl",
+    "dirent",
+    "eigen3",
+    "liblzma",
+    "libxml2",
+    "lzo",
+    "nlopt",
+    "protobuf",
+    "rxcpp",
+    "snappy",
+    "zlib"
+  ]
+}