Merge pull request #108 from STulling/master

Fix Windows MSVC install by updating Eigen Library

pydensecrf/densecrf/include/Eigen/CMakeLists.txt

@@ -16,4 +16,4 @@ install(FILES
   DESTINATION ${INCLUDE_INSTALL_DIR}/Eigen COMPONENT Devel
   )
 
-add_subdirectory(src)
+install(DIRECTORY src DESTINATION ${INCLUDE_INSTALL_DIR}/Eigen COMPONENT Devel FILES_MATCHING PATTERN "*.h")

pydensecrf/densecrf/include/Eigen/Cholesky

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_CHOLESKY_MODULE_H
 #define EIGEN_CHOLESKY_MODULE_H
 
 #include "Core"
+#include "Jacobi"
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
@@ -10,20 +18,26 @@
   *
   *
   * This module provides two variants of the Cholesky decomposition for selfadjoint (hermitian) matrices.
-  * Those decompositions are accessible via the following MatrixBase methods:
-  *  - MatrixBase::llt(),
+  * Those decompositions are also accessible via the following methods:
+  *  - MatrixBase::llt()
   *  - MatrixBase::ldlt()
+  *  - SelfAdjointView::llt()
+  *  - SelfAdjointView::ldlt()
   *
   * \code
   * #include <Eigen/Cholesky>
   * \endcode
   */
 
-#include "src/misc/Solve.h"
 #include "src/Cholesky/LLT.h"
 #include "src/Cholesky/LDLT.h"
 #ifdef EIGEN_USE_LAPACKE
-#include "src/Cholesky/LLT_MKL.h"
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
+#include "src/misc/lapacke.h"
+#endif
+#include "src/Cholesky/LLT_LAPACKE.h"
 #endif
 
 #include "src/Core/util/ReenableStupidWarnings.h"

pydensecrf/densecrf/include/Eigen/CholmodSupport

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_CHOLMODSUPPORT_MODULE_H
 #define EIGEN_CHOLMODSUPPORT_MODULE_H
 
@@ -12,7 +19,7 @@ extern "C" {
 /** \ingroup Support_modules
   * \defgroup CholmodSupport_Module CholmodSupport module
   *
-  * This module provides an interface to the Cholmod library which is part of the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">suitesparse</a> package.
+  * This module provides an interface to the Cholmod library which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
   * It provides the two following main factorization classes:
   * - class CholmodSupernodalLLT: a supernodal LLT Cholesky factorization.
   * - class CholmodDecomposiiton: a general L(D)LT Cholesky factorization with automatic or explicit runtime selection of the underlying factorization method (supernodal or simplicial).
@@ -33,12 +40,8 @@ extern "C" {
   *
   */
 
-#include "src/misc/Solve.h"
-#include "src/misc/SparseSolve.h"
-
 #include "src/CholmodSupport/CholmodSupport.h"
 
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_CHOLMODSUPPORT_MODULE_H

pydensecrf/densecrf/include/Eigen/Core

@@ -14,37 +14,111 @@
 // first thing Eigen does: stop the compiler from committing suicide
 #include "src/Core/util/DisableStupidWarnings.h"
 
+#if defined(__CUDACC__) && !defined(EIGEN_NO_CUDA)
+  #define EIGEN_CUDACC __CUDACC__
+#endif
+
+#if defined(__CUDA_ARCH__) && !defined(EIGEN_NO_CUDA)
+  #define EIGEN_CUDA_ARCH __CUDA_ARCH__
+#endif
+
+#if defined(__CUDACC_VER_MAJOR__) && (__CUDACC_VER_MAJOR__ >= 9)
+#define EIGEN_CUDACC_VER  ((__CUDACC_VER_MAJOR__ * 10000) + (__CUDACC_VER_MINOR__ * 100))
+#elif defined(__CUDACC_VER__)
+#define EIGEN_CUDACC_VER __CUDACC_VER__
+#else
+#define EIGEN_CUDACC_VER 0
+#endif
+
+// Handle NVCC/CUDA/SYCL
+#if defined(__CUDACC__) || defined(__SYCL_DEVICE_ONLY__)
+  // Do not try asserts on CUDA and SYCL!
+  #ifndef EIGEN_NO_DEBUG
+  #define EIGEN_NO_DEBUG
+  #endif
+
+  #ifdef EIGEN_INTERNAL_DEBUGGING
+  #undef EIGEN_INTERNAL_DEBUGGING
+  #endif
+
+  #ifdef EIGEN_EXCEPTIONS
+  #undef EIGEN_EXCEPTIONS
+  #endif
+
+  // All functions callable from CUDA code must be qualified with __device__
+  #ifdef __CUDACC__
+    // Do not try to vectorize on CUDA and SYCL!
+    #ifndef EIGEN_DONT_VECTORIZE
+    #define EIGEN_DONT_VECTORIZE
+    #endif
+
+    #define EIGEN_DEVICE_FUNC __host__ __device__
+    // We need cuda_runtime.h to ensure that that EIGEN_USING_STD_MATH macro
+    // works properly on the device side
+    #include <cuda_runtime.h>
+  #else
+    #define EIGEN_DEVICE_FUNC
+  #endif
+
+#else
+  #define EIGEN_DEVICE_FUNC
+
+#endif
+
+// When compiling CUDA device code with NVCC, pull in math functions from the
+// global namespace.  In host mode, and when device doee with clang, use the
+// std versions.
+#if defined(__CUDA_ARCH__) && defined(__NVCC__)
+  #define EIGEN_USING_STD_MATH(FUNC) using ::FUNC;
+#else
+  #define EIGEN_USING_STD_MATH(FUNC) using std::FUNC;
+#endif
+
+#if (defined(_CPPUNWIND) || defined(__EXCEPTIONS)) && !defined(__CUDA_ARCH__) && !defined(EIGEN_EXCEPTIONS) && !defined(EIGEN_USE_SYCL)
+  #define EIGEN_EXCEPTIONS
+#endif
+
+#ifdef EIGEN_EXCEPTIONS
+  #include <new>
+#endif
+
 // then include this file where all our macros are defined. It's really important to do it first because
 // it's where we do all the alignment settings (platform detection and honoring the user's will if he
 // defined e.g. EIGEN_DONT_ALIGN) so it needs to be done before we do anything with vectorization.
 #include "src/Core/util/Macros.h"
 
+// Disable the ipa-cp-clone optimization flag with MinGW 6.x or newer (enabled by default with -O3)
+// See http://eigen.tuxfamily.org/bz/show_bug.cgi?id=556 for details.
+#if EIGEN_COMP_MINGW && EIGEN_GNUC_AT_LEAST(4,6)
+  #pragma GCC optimize ("-fno-ipa-cp-clone")
+#endif
+
 #include <complex>
 
 // this include file manages BLAS and MKL related macros
 // and inclusion of their respective header files
 #include "src/Core/util/MKL_support.h"
 
-// if alignment is disabled, then disable vectorization. Note: EIGEN_ALIGN is the proper check, it takes into
-// account both the user's will (EIGEN_DONT_ALIGN) and our own platform checks
-#if !EIGEN_ALIGN
+// if alignment is disabled, then disable vectorization. Note: EIGEN_MAX_ALIGN_BYTES is the proper check, it takes into
+// account both the user's will (EIGEN_MAX_ALIGN_BYTES,EIGEN_DONT_ALIGN) and our own platform checks
+#if EIGEN_MAX_ALIGN_BYTES==0
   #ifndef EIGEN_DONT_VECTORIZE
     #define EIGEN_DONT_VECTORIZE
   #endif
 #endif
 
-#ifdef _MSC_VER
+#if EIGEN_COMP_MSVC
   #include <malloc.h> // for _aligned_malloc -- need it regardless of whether vectorization is enabled
-  #if (_MSC_VER >= 1500) // 2008 or later
+  #if (EIGEN_COMP_MSVC >= 1500) // 2008 or later
     // Remember that usage of defined() in a #define is undefined by the standard.
     // a user reported that in 64-bit mode, MSVC doesn't care to define _M_IX86_FP.
-    #if (defined(_M_IX86_FP) && (_M_IX86_FP >= 2)) || defined(_M_X64)
+    #if (defined(_M_IX86_FP) && (_M_IX86_FP >= 2)) || EIGEN_ARCH_x86_64
       #define EIGEN_SSE2_ON_MSVC_2008_OR_LATER
     #endif
   #endif
 #else
   // Remember that usage of defined() in a #define is undefined by the standard
-  #if (defined __SSE2__) && ( (!defined __GNUC__) || (defined __INTEL_COMPILER) || EIGEN_GNUC_AT_LEAST(4,2) )
+  #if (defined __SSE2__) && ( (!EIGEN_COMP_GNUC) || EIGEN_COMP_ICC || EIGEN_GNUC_AT_LEAST(4,2) )
     #define EIGEN_SSE2_ON_NON_MSVC_BUT_NOT_OLD_GCC
   #endif
 #endif
@@ -76,6 +150,31 @@
     #ifdef __SSE4_2__
       #define EIGEN_VECTORIZE_SSE4_2
     #endif
+    #ifdef __AVX__
+      #define EIGEN_VECTORIZE_AVX
+      #define EIGEN_VECTORIZE_SSE3
+      #define EIGEN_VECTORIZE_SSSE3
+      #define EIGEN_VECTORIZE_SSE4_1
+      #define EIGEN_VECTORIZE_SSE4_2
+    #endif
+    #ifdef __AVX2__
+      #define EIGEN_VECTORIZE_AVX2
+    #endif
+    #ifdef __FMA__
+      #define EIGEN_VECTORIZE_FMA
+    #endif
+    #if defined(__AVX512F__) && defined(EIGEN_ENABLE_AVX512)
+      #define EIGEN_VECTORIZE_AVX512
+      #define EIGEN_VECTORIZE_AVX2
+      #define EIGEN_VECTORIZE_AVX
+      #define EIGEN_VECTORIZE_FMA
+      #ifdef __AVX512DQ__
+        #define EIGEN_VECTORIZE_AVX512DQ
+      #endif
+      #ifdef __AVX512ER__
+        #define EIGEN_VECTORIZE_AVX512ER
+      #endif
+    #endif
 
     // include files
 
@@ -87,6 +186,12 @@
     // so, to avoid compile errors when windows.h is included after Eigen/Core, ensure intrinsics are extern "C" here too.
     // notice that since these are C headers, the extern "C" is theoretically needed anyways.
     extern "C" {
+      // In theory we should only include immintrin.h and not the other *mmintrin.h header files directly.
+      // Doing so triggers some issues with ICC. However old gcc versions seems to not have this file, thus:
+      #if EIGEN_COMP_ICC >= 1110
+        #include <immintrin.h>
+      #else
+        #include <mmintrin.h>
         #include <emmintrin.h>
         #include <xmmintrin.h>
         #ifdef  EIGEN_VECTORIZE_SSE3
@@ -101,7 +206,20 @@
         #ifdef EIGEN_VECTORIZE_SSE4_2
         #include <nmmintrin.h>
         #endif
+        #if defined(EIGEN_VECTORIZE_AVX) || defined(EIGEN_VECTORIZE_AVX512)
+        #include <immintrin.h>
+        #endif
+      #endif
     } // end extern "C"
+  #elif defined __VSX__
+    #define EIGEN_VECTORIZE
+    #define EIGEN_VECTORIZE_VSX
+    #include <altivec.h>
+    // We need to #undef all these ugly tokens defined in <altivec.h>
+    // => use __vector instead of vector
+    #undef bool
+    #undef vector
+    #undef pixel
   #elif defined __ALTIVEC__
     #define EIGEN_VECTORIZE
     #define EIGEN_VECTORIZE_ALTIVEC
@@ -111,13 +229,35 @@
     #undef bool
     #undef vector
     #undef pixel
-  #elif defined  __ARM_NEON__
+  #elif (defined  __ARM_NEON) || (defined __ARM_NEON__)
     #define EIGEN_VECTORIZE
     #define EIGEN_VECTORIZE_NEON
     #include <arm_neon.h>
+  #elif (defined __s390x__ && defined __VEC__)
+    #define EIGEN_VECTORIZE
+    #define EIGEN_VECTORIZE_ZVECTOR
+    #include <vecintrin.h>
   #endif
 #endif
 
+#if defined(__F16C__) && !defined(EIGEN_COMP_CLANG)
+  // We can use the optimized fp16 to float and float to fp16 conversion routines
+  #define EIGEN_HAS_FP16_C
+#endif
+
+#if defined __CUDACC__
+  #define EIGEN_VECTORIZE_CUDA
+  #include <vector_types.h>
+  #if EIGEN_CUDACC_VER >= 70500
+    #define EIGEN_HAS_CUDA_FP16
+  #endif
+#endif
+
+#if defined EIGEN_HAS_CUDA_FP16
+  #include <host_defines.h>
+  #include <cuda_fp16.h>
+#endif
+
 #if (defined _OPENMP) && (!defined EIGEN_DONT_PARALLELIZE)
   #define EIGEN_HAS_OPENMP
 #endif
@@ -127,7 +267,7 @@
 #endif
 
 // MSVC for windows mobile does not have the errno.h file
-#if !(defined(_MSC_VER) && defined(_WIN32_WCE)) && !defined(__ARMCC_VERSION)
+#if !(EIGEN_COMP_MSVC && EIGEN_OS_WINCE) && !EIGEN_COMP_ARM
 #define EIGEN_HAS_ERRNO
 #endif
 
@@ -139,7 +279,10 @@
 #include <cmath>
 #include <cassert>
 #include <functional>
-#include <iosfwd>
+#include <sstream>
+#ifndef EIGEN_NO_IO
+  #include <iosfwd>
+#endif
 #include <cstring>
 #include <string>
 #include <limits>
@@ -147,29 +290,30 @@
 // for min/max:
 #include <algorithm>
 
+// for std::is_nothrow_move_assignable
+#ifdef EIGEN_INCLUDE_TYPE_TRAITS
+#include <type_traits>
+#endif
+
 // for outputting debug info
 #ifdef EIGEN_DEBUG_ASSIGN
 #include <iostream>
 #endif
 
 // required for __cpuid, needs to be included after cmath
-#if defined(_MSC_VER) && (defined(_M_IX86)||defined(_M_X64))
+#if EIGEN_COMP_MSVC && EIGEN_ARCH_i386_OR_x86_64 && !EIGEN_OS_WINCE
   #include <intrin.h>
 #endif
 
-#if defined(_CPPUNWIND) || defined(__EXCEPTIONS)
-  #define EIGEN_EXCEPTIONS
-#endif
-
-#ifdef EIGEN_EXCEPTIONS
-  #include <new>
-#endif
-
 /** \brief Namespace containing all symbols from the %Eigen library. */
 namespace Eigen {
 
 inline static const char *SimdInstructionSetsInUse(void) {
-#if defined(EIGEN_VECTORIZE_SSE4_2)
+#if defined(EIGEN_VECTORIZE_AVX512)
+  return "AVX512, FMA, AVX2, AVX, SSE, SSE2, SSE3, SSSE3, SSE4.1, SSE4.2";
+#elif defined(EIGEN_VECTORIZE_AVX)
+  return "AVX SSE, SSE2, SSE3, SSSE3, SSE4.1, SSE4.2";
+#elif defined(EIGEN_VECTORIZE_SSE4_2)
   return "SSE, SSE2, SSE3, SSSE3, SSE4.1, SSE4.2";
 #elif defined(EIGEN_VECTORIZE_SSE4_1)
   return "SSE, SSE2, SSE3, SSSE3, SSE4.1";
@@ -181,8 +325,12 @@ inline static const char *SimdInstructionSetsInUse(void) {
   return "SSE, SSE2";
 #elif defined(EIGEN_VECTORIZE_ALTIVEC)
   return "AltiVec";
+#elif defined(EIGEN_VECTORIZE_VSX)
+  return "VSX";
 #elif defined(EIGEN_VECTORIZE_NEON)
   return "ARM NEON";
+#elif defined(EIGEN_VECTORIZE_ZVECTOR)
+  return "S390X ZVECTOR";
 #else
   return "None";
 #endif
@@ -190,35 +338,12 @@ inline static const char *SimdInstructionSetsInUse(void) {
 
 } // end namespace Eigen
 
-#define STAGE10_FULL_EIGEN2_API             10
-#define STAGE20_RESOLVE_API_CONFLICTS       20
-#define STAGE30_FULL_EIGEN3_API             30
-#define STAGE40_FULL_EIGEN3_STRICTNESS      40
-#define STAGE99_NO_EIGEN2_SUPPORT           99
-
-#if   defined EIGEN2_SUPPORT_STAGE40_FULL_EIGEN3_STRICTNESS
-  #define EIGEN2_SUPPORT
-  #define EIGEN2_SUPPORT_STAGE STAGE40_FULL_EIGEN3_STRICTNESS
-#elif defined EIGEN2_SUPPORT_STAGE30_FULL_EIGEN3_API
-  #define EIGEN2_SUPPORT
-  #define EIGEN2_SUPPORT_STAGE STAGE30_FULL_EIGEN3_API
-#elif defined EIGEN2_SUPPORT_STAGE20_RESOLVE_API_CONFLICTS
-  #define EIGEN2_SUPPORT
-  #define EIGEN2_SUPPORT_STAGE STAGE20_RESOLVE_API_CONFLICTS
-#elif defined EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API
-  #define EIGEN2_SUPPORT
-  #define EIGEN2_SUPPORT_STAGE STAGE10_FULL_EIGEN2_API
-#elif defined EIGEN2_SUPPORT
-  // default to stage 3, that's what it's always meant
-  #define EIGEN2_SUPPORT_STAGE30_FULL_EIGEN3_API
-  #define EIGEN2_SUPPORT_STAGE STAGE30_FULL_EIGEN3_API
-#else
-  #define EIGEN2_SUPPORT_STAGE STAGE99_NO_EIGEN2_SUPPORT
+#if defined EIGEN2_SUPPORT_STAGE40_FULL_EIGEN3_STRICTNESS || defined EIGEN2_SUPPORT_STAGE30_FULL_EIGEN3_API || defined EIGEN2_SUPPORT_STAGE20_RESOLVE_API_CONFLICTS || defined EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API || defined EIGEN2_SUPPORT
+// This will generate an error message:
+#error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information
 #endif
 
-#ifdef EIGEN2_SUPPORT
-#undef minor
-#endif
+namespace Eigen {
 
 // we use size_t frequently and we'll never remember to prepend it with std:: everytime just to
 // ensure QNX/QCC support
@@ -226,6 +351,8 @@ using std::size_t;
 // gcc 4.6.0 wants std:: for ptrdiff_t
 using std::ptrdiff_t;
 
+}
+
 /** \defgroup Core_Module Core module
   * This is the main module of Eigen providing dense matrix and vector support
   * (both fixed and dynamic size) with all the features corresponding to a BLAS library
@@ -236,55 +363,106 @@ using std::ptrdiff_t;
   * \endcode
   */
 
-/** \defgroup Support_modules Support modules [category]
-  * Category of modules which add support for external libraries.
-  */
-
 #include "src/Core/util/Constants.h"
-#include "src/Core/util/ForwardDeclarations.h"
 #include "src/Core/util/Meta.h"
-#include "src/Core/util/XprHelper.h"
+#include "src/Core/util/ForwardDeclarations.h"
 #include "src/Core/util/StaticAssert.h"
+#include "src/Core/util/XprHelper.h"
 #include "src/Core/util/Memory.h"
 
 #include "src/Core/NumTraits.h"
 #include "src/Core/MathFunctions.h"
 #include "src/Core/GenericPacketMath.h"
+#include "src/Core/MathFunctionsImpl.h"
+#include "src/Core/arch/Default/ConjHelper.h"
 
-#if defined EIGEN_VECTORIZE_SSE
+#if defined EIGEN_VECTORIZE_AVX512
+  #include "src/Core/arch/SSE/PacketMath.h"
+  #include "src/Core/arch/SSE/MathFunctions.h"
+  #include "src/Core/arch/AVX/PacketMath.h"
+  #include "src/Core/arch/AVX/MathFunctions.h"
+  #include "src/Core/arch/AVX512/PacketMath.h"
+  #include "src/Core/arch/AVX512/MathFunctions.h"
+#elif defined EIGEN_VECTORIZE_AVX
+  // Use AVX for floats and doubles, SSE for integers
+  #include "src/Core/arch/SSE/PacketMath.h"
+  #include "src/Core/arch/SSE/Complex.h"
+  #include "src/Core/arch/SSE/MathFunctions.h"
+  #include "src/Core/arch/AVX/PacketMath.h"
+  #include "src/Core/arch/AVX/MathFunctions.h"
+  #include "src/Core/arch/AVX/Complex.h"
+  #include "src/Core/arch/AVX/TypeCasting.h"
+  #include "src/Core/arch/SSE/TypeCasting.h"
+#elif defined EIGEN_VECTORIZE_SSE
   #include "src/Core/arch/SSE/PacketMath.h"
   #include "src/Core/arch/SSE/MathFunctions.h"
   #include "src/Core/arch/SSE/Complex.h"
-#elif defined EIGEN_VECTORIZE_ALTIVEC
+  #include "src/Core/arch/SSE/TypeCasting.h"
+#elif defined(EIGEN_VECTORIZE_ALTIVEC) || defined(EIGEN_VECTORIZE_VSX)
   #include "src/Core/arch/AltiVec/PacketMath.h"
+  #include "src/Core/arch/AltiVec/MathFunctions.h"
   #include "src/Core/arch/AltiVec/Complex.h"
 #elif defined EIGEN_VECTORIZE_NEON
   #include "src/Core/arch/NEON/PacketMath.h"
+  #include "src/Core/arch/NEON/MathFunctions.h"
   #include "src/Core/arch/NEON/Complex.h"
+#elif defined EIGEN_VECTORIZE_ZVECTOR
+  #include "src/Core/arch/ZVector/PacketMath.h"
+  #include "src/Core/arch/ZVector/MathFunctions.h"
+  #include "src/Core/arch/ZVector/Complex.h"
+#endif
+
+// Half float support
+#include "src/Core/arch/CUDA/Half.h"
+#include "src/Core/arch/CUDA/PacketMathHalf.h"
+#include "src/Core/arch/CUDA/TypeCasting.h"
+
+#if defined EIGEN_VECTORIZE_CUDA
+  #include "src/Core/arch/CUDA/PacketMath.h"
+  #include "src/Core/arch/CUDA/MathFunctions.h"
 #endif
 
 #include "src/Core/arch/Default/Settings.h"
 
-#include "src/Core/Functors.h"
+#include "src/Core/functors/TernaryFunctors.h"
+#include "src/Core/functors/BinaryFunctors.h"
+#include "src/Core/functors/UnaryFunctors.h"
+#include "src/Core/functors/NullaryFunctors.h"
+#include "src/Core/functors/StlFunctors.h"
+#include "src/Core/functors/AssignmentFunctors.h"
+
+// Specialized functors to enable the processing of complex numbers
+// on CUDA devices
+#include "src/Core/arch/CUDA/Complex.h"
+
+#include "src/Core/IO.h"
 #include "src/Core/DenseCoeffsBase.h"
 #include "src/Core/DenseBase.h"
 #include "src/Core/MatrixBase.h"
 #include "src/Core/EigenBase.h"
 
+#include "src/Core/Product.h"
+#include "src/Core/CoreEvaluators.h"
+#include "src/Core/AssignEvaluator.h"
+
 #ifndef EIGEN_PARSED_BY_DOXYGEN // work around Doxygen bug triggered by Assign.h r814874
                                 // at least confirmed with Doxygen 1.5.5 and 1.5.6
   #include "src/Core/Assign.h"
 #endif
 
+#include "src/Core/ArrayBase.h"
 #include "src/Core/util/BlasUtil.h"
 #include "src/Core/DenseStorage.h"
 #include "src/Core/NestByValue.h"
-#include "src/Core/ForceAlignedAccess.h"
+
+// #include "src/Core/ForceAlignedAccess.h"
+
 #include "src/Core/ReturnByValue.h"
 #include "src/Core/NoAlias.h"
 #include "src/Core/PlainObjectBase.h"
 #include "src/Core/Matrix.h"
 #include "src/Core/Array.h"
+#include "src/Core/CwiseTernaryOp.h"
 #include "src/Core/CwiseBinaryOp.h"
 #include "src/Core/CwiseUnaryOp.h"
 #include "src/Core/CwiseNullaryOp.h"
@@ -292,31 +470,32 @@ using std::ptrdiff_t;
 #include "src/Core/SelfCwiseBinaryOp.h"
 #include "src/Core/Dot.h"
 #include "src/Core/StableNorm.h"
-#include "src/Core/MapBase.h"
 #include "src/Core/Stride.h"
+#include "src/Core/MapBase.h"
 #include "src/Core/Map.h"
+#include "src/Core/Ref.h"
 #include "src/Core/Block.h"
 #include "src/Core/VectorBlock.h"
 #include "src/Core/Transpose.h"
 #include "src/Core/DiagonalMatrix.h"
 #include "src/Core/Diagonal.h"
 #include "src/Core/DiagonalProduct.h"
-#include "src/Core/PermutationMatrix.h"
-#include "src/Core/Transpositions.h"
 #include "src/Core/Redux.h"
 #include "src/Core/Visitor.h"
 #include "src/Core/Fuzzy.h"
-#include "src/Core/IO.h"
 #include "src/Core/Swap.h"
 #include "src/Core/CommaInitializer.h"
-#include "src/Core/Flagged.h"
-#include "src/Core/ProductBase.h"
 #include "src/Core/GeneralProduct.h"
+#include "src/Core/Solve.h"
+#include "src/Core/Inverse.h"
+#include "src/Core/SolverBase.h"
+#include "src/Core/PermutationMatrix.h"
+#include "src/Core/Transpositions.h"
 #include "src/Core/TriangularMatrix.h"
 #include "src/Core/SelfAdjointView.h"
 #include "src/Core/products/GeneralBlockPanelKernel.h"
 #include "src/Core/products/Parallelizer.h"
-#include "src/Core/products/CoeffBasedProduct.h"
+#include "src/Core/ProductEvaluators.h"
 #include "src/Core/products/GeneralMatrixVector.h"
 #include "src/Core/products/GeneralMatrixMatrix.h"
 #include "src/Core/SolveTriangular.h"
@@ -330,6 +509,8 @@ using std::ptrdiff_t;
 #include "src/Core/products/TriangularSolverMatrix.h"
 #include "src/Core/products/TriangularSolverVector.h"
 #include "src/Core/BandMatrix.h"
+#include "src/Core/CoreIterators.h"
+#include "src/Core/ConditionEstimator.h"
 
 #include "src/Core/BooleanRedux.h"
 #include "src/Core/Select.h"
@@ -337,18 +518,17 @@ using std::ptrdiff_t;
 #include "src/Core/Random.h"
 #include "src/Core/Replicate.h"
 #include "src/Core/Reverse.h"
-#include "src/Core/ArrayBase.h"
 #include "src/Core/ArrayWrapper.h"
 
 #ifdef EIGEN_USE_BLAS
-#include "src/Core/products/GeneralMatrixMatrix_MKL.h"
-#include "src/Core/products/GeneralMatrixVector_MKL.h"
-#include "src/Core/products/GeneralMatrixMatrixTriangular_MKL.h"
-#include "src/Core/products/SelfadjointMatrixMatrix_MKL.h"
-#include "src/Core/products/SelfadjointMatrixVector_MKL.h"
-#include "src/Core/products/TriangularMatrixMatrix_MKL.h"
-#include "src/Core/products/TriangularMatrixVector_MKL.h"
-#include "src/Core/products/TriangularSolverMatrix_MKL.h"
+#include "src/Core/products/GeneralMatrixMatrix_BLAS.h"
+#include "src/Core/products/GeneralMatrixVector_BLAS.h"
+#include "src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h"
+#include "src/Core/products/SelfadjointMatrixMatrix_BLAS.h"
+#include "src/Core/products/SelfadjointMatrixVector_BLAS.h"
+#include "src/Core/products/TriangularMatrixMatrix_BLAS.h"
+#include "src/Core/products/TriangularMatrixVector_BLAS.h"
+#include "src/Core/products/TriangularSolverMatrix_BLAS.h"
 #endif // EIGEN_USE_BLAS
 
 #ifdef EIGEN_USE_MKL_VML
@@ -359,8 +539,4 @@ using std::ptrdiff_t;
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 
-#ifdef EIGEN2_SUPPORT
-#include "Eigen2Support"
-#endif
-
 #endif // EIGEN_CORE_H

pydensecrf/densecrf/include/Eigen/Eigen

 #include "Dense"
-//#include "Sparse"
+#include "Sparse"

pydensecrf/densecrf/include/Eigen/Eigenvalues

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_EIGENVALUES_MODULE_H
 #define EIGEN_EIGENVALUES_MODULE_H
 
 #include "Core"
 
-#include "src/Core/util/DisableStupidWarnings.h"
-
 #include "Cholesky"
 #include "Jacobi"
 #include "Householder"
 #include "LU"
 #include "Geometry"
 
+#include "src/Core/util/DisableStupidWarnings.h"
+
 /** \defgroup Eigenvalues_Module Eigenvalues module
   *
   *
@@ -25,6 +32,7 @@
   * \endcode
   */
 
+#include "src/misc/RealSvd2x2.h"
 #include "src/Eigenvalues/Tridiagonalization.h"
 #include "src/Eigenvalues/RealSchur.h"
 #include "src/Eigenvalues/EigenSolver.h"
@@ -33,11 +41,18 @@
 #include "src/Eigenvalues/HessenbergDecomposition.h"
 #include "src/Eigenvalues/ComplexSchur.h"
 #include "src/Eigenvalues/ComplexEigenSolver.h"
+#include "src/Eigenvalues/RealQZ.h"
+#include "src/Eigenvalues/GeneralizedEigenSolver.h"
 #include "src/Eigenvalues/MatrixBaseEigenvalues.h"
 #ifdef EIGEN_USE_LAPACKE
-#include "src/Eigenvalues/RealSchur_MKL.h"
-#include "src/Eigenvalues/ComplexSchur_MKL.h"
-#include "src/Eigenvalues/SelfAdjointEigenSolver_MKL.h"
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
+#include "src/misc/lapacke.h"
+#endif
+#include "src/Eigenvalues/RealSchur_LAPACKE.h"
+#include "src/Eigenvalues/ComplexSchur_LAPACKE.h"
+#include "src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h"
 #endif
 
 #include "src/Core/util/ReenableStupidWarnings.h"

pydensecrf/densecrf/include/Eigen/Geometry

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_GEOMETRY_MODULE_H
 #define EIGEN_GEOMETRY_MODULE_H
 
 #include "Core"
 
-#include "src/Core/util/DisableStupidWarnings.h"
-
 #include "SVD"
 #include "LU"
 #include <limits>
 
-#ifndef M_PI
-#define M_PI 3.14159265358979323846
-#endif
+#include "src/Core/util/DisableStupidWarnings.h"
 
 /** \defgroup Geometry_Module Geometry module
-  *
-  *
   *
   * This module provides support for:
   *  - fixed-size homogeneous transformations
   *  - translation, scaling, 2D and 3D rotations
-  *  - quaternions
-  *  - \ref MatrixBase::cross() "cross product"
-  *  - \ref MatrixBase::unitOrthogonal() "orthognal vector generation"
-  *  - some linear components: parametrized-lines and hyperplanes
+  *  - \link Quaternion quaternions \endlink
+  *  - cross products (\ref MatrixBase::cross, \ref MatrixBase::cross3)
+  *  - orthognal vector generation (\ref MatrixBase::unitOrthogonal)
+  *  - some linear components: \link ParametrizedLine parametrized-lines \endlink and \link Hyperplane hyperplanes \endlink
+  *  - \link AlignedBox axis aligned bounding boxes \endlink
+  *  - \link umeyama least-square transformation fitting \endlink
   *
   * \code
   * #include <Eigen/Geometry>
@@ -33,27 +36,23 @@
 #include "src/Geometry/OrthoMethods.h"
 #include "src/Geometry/EulerAngles.h"
 
-#if EIGEN2_SUPPORT_STAGE > STAGE20_RESOLVE_API_CONFLICTS
-  #include "src/Geometry/Homogeneous.h"
-  #include "src/Geometry/RotationBase.h"
-  #include "src/Geometry/Rotation2D.h"
-  #include "src/Geometry/Quaternion.h"
-  #include "src/Geometry/AngleAxis.h"
-  #include "src/Geometry/Transform.h"
-  #include "src/Geometry/Translation.h"
-  #include "src/Geometry/Scaling.h"
-  #include "src/Geometry/Hyperplane.h"
-  #include "src/Geometry/ParametrizedLine.h"
-  #include "src/Geometry/AlignedBox.h"
-  #include "src/Geometry/Umeyama.h"
-
-  #if defined EIGEN_VECTORIZE_SSE
-    #include "src/Geometry/arch/Geometry_SSE.h"
-  #endif
-#endif
-
-#ifdef EIGEN2_SUPPORT
-#include "src/Eigen2Support/Geometry/All.h"
+#include "src/Geometry/Homogeneous.h"
+#include "src/Geometry/RotationBase.h"
+#include "src/Geometry/Rotation2D.h"
+#include "src/Geometry/Quaternion.h"
+#include "src/Geometry/AngleAxis.h"
+#include "src/Geometry/Transform.h"
+#include "src/Geometry/Translation.h"
+#include "src/Geometry/Scaling.h"
+#include "src/Geometry/Hyperplane.h"
+#include "src/Geometry/ParametrizedLine.h"
+#include "src/Geometry/AlignedBox.h"
+#include "src/Geometry/Umeyama.h"
+
+// Use the SSE optimized version whenever possible. At the moment the
+// SSE version doesn't compile when AVX is enabled
+#if defined EIGEN_VECTORIZE_SSE && !defined EIGEN_VECTORIZE_AVX
+#include "src/Geometry/arch/Geometry_SSE.h"
 #endif
 
 #include "src/Core/util/ReenableStupidWarnings.h"

pydensecrf/densecrf/include/Eigen/Householder

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_HOUSEHOLDER_MODULE_H
 #define EIGEN_HOUSEHOLDER_MODULE_H
 

pydensecrf/densecrf/include/Eigen/IterativeLinearSolvers

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_ITERATIVELINEARSOLVERS_MODULE_H
 #define EIGEN_ITERATIVELINEARSOLVERS_MODULE_H
 
@@ -6,34 +13,35 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-/** \ingroup Sparse_modules
+/** 
   * \defgroup IterativeLinearSolvers_Module IterativeLinearSolvers module
   *
   * This module currently provides iterative methods to solve problems of the form \c A \c x = \c b, where \c A is a squared matrix, usually very large and sparse.
   * Those solvers are accessible via the following classes:
   *  - ConjugateGradient for selfadjoint (hermitian) matrices,
+  *  - LeastSquaresConjugateGradient for rectangular least-square problems,
   *  - BiCGSTAB for general square matrices.
   *
   * These iterative solvers are associated with some preconditioners:
   *  - IdentityPreconditioner - not really useful
-  *  - DiagonalPreconditioner - also called JAcobi preconditioner, work very well on diagonal dominant matrices.
-  *  - IncompleteILUT - incomplete LU factorization with dual thresholding
+  *  - DiagonalPreconditioner - also called Jacobi preconditioner, work very well on diagonal dominant matrices.
+  *  - IncompleteLUT - incomplete LU factorization with dual thresholding
   *
   * Such problems can also be solved using the direct sparse decomposition modules: SparseCholesky, CholmodSupport, UmfPackSupport, SuperLUSupport.
   *
-  * \code
-  * #include <Eigen/IterativeLinearSolvers>
-  * \endcode
+    \code
+    #include <Eigen/IterativeLinearSolvers>
+    \endcode
   */
 
-#include "src/misc/Solve.h"
-#include "src/misc/SparseSolve.h"
-
+#include "src/IterativeLinearSolvers/SolveWithGuess.h"
 #include "src/IterativeLinearSolvers/IterativeSolverBase.h"
 #include "src/IterativeLinearSolvers/BasicPreconditioners.h"
 #include "src/IterativeLinearSolvers/ConjugateGradient.h"
+#include "src/IterativeLinearSolvers/LeastSquareConjugateGradient.h"
 #include "src/IterativeLinearSolvers/BiCGSTAB.h"
 #include "src/IterativeLinearSolvers/IncompleteLUT.h"
+#include "src/IterativeLinearSolvers/IncompleteCholesky.h"
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 

pydensecrf/densecrf/include/Eigen/Jacobi

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_JACOBI_MODULE_H
 #define EIGEN_JACOBI_MODULE_H
 

pydensecrf/densecrf/include/Eigen/LU

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_LU_MODULE_H
 #define EIGEN_LU_MODULE_H
 
@@ -16,25 +23,27 @@
   * \endcode
   */
 
-#include "src/misc/Solve.h"
 #include "src/misc/Kernel.h"
 #include "src/misc/Image.h"
 #include "src/LU/FullPivLU.h"
 #include "src/LU/PartialPivLU.h"
 #ifdef EIGEN_USE_LAPACKE
-#include "src/LU/PartialPivLU_MKL.h"
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
+#include "src/misc/lapacke.h"
+#endif
+#include "src/LU/PartialPivLU_LAPACKE.h"
 #endif
 #include "src/LU/Determinant.h"
-#include "src/LU/Inverse.h"
+#include "src/LU/InverseImpl.h"
 
-#if defined EIGEN_VECTORIZE_SSE
+// Use the SSE optimized version whenever possible. At the moment the
+// SSE version doesn't compile when AVX is enabled
+#if defined EIGEN_VECTORIZE_SSE && !defined EIGEN_VECTORIZE_AVX
   #include "src/LU/arch/Inverse_SSE.h"
 #endif
 
-#ifdef EIGEN2_SUPPORT
-  #include "src/Eigen2Support/LU.h"
-#endif
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_LU_MODULE_H

pydensecrf/densecrf/include/Eigen/MetisSupport

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+#ifndef EIGEN_METISSUPPORT_MODULE_H
+#define EIGEN_METISSUPPORT_MODULE_H
+
+#include "SparseCore"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+extern "C" {
+#include <metis.h>
+}
+
+
+/** \ingroup Support_modules
+  * \defgroup MetisSupport_Module MetisSupport module
+  *
+  * \code
+  * #include <Eigen/MetisSupport>
+  * \endcode
+  * This module defines an interface to the METIS reordering package (http://glaros.dtc.umn.edu/gkhome/views/metis). 
+  * It can be used just as any other built-in method as explained in \link OrderingMethods_Module here. \endlink
+  */
+
+
+#include "src/MetisSupport/MetisSupport.h"
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_METISSUPPORT_MODULE_H

pydensecrf/densecrf/include/Eigen/OrderingMethods

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_ORDERINGMETHODS_MODULE_H
 #define EIGEN_ORDERINGMETHODS_MODULE_H
 
@@ -5,19 +12,62 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-/** \ingroup Sparse_modules
+/** 
   * \defgroup OrderingMethods_Module OrderingMethods module
   *
-  * This module is currently for internal use only.
+  * This module is currently for internal use only
+  * 
+  * It defines various built-in and external ordering methods for sparse matrices. 
+  * They are typically used to reduce the number of elements during 
+  * the sparse matrix decomposition (LLT, LU, QR).
+  * Precisely, in a preprocessing step, a permutation matrix P is computed using 
+  * those ordering methods and applied to the columns of the matrix. 
+  * Using for instance the sparse Cholesky decomposition, it is expected that 
+  * the nonzeros elements in LLT(A*P) will be much smaller than that in LLT(A).
   * 
   * 
+  * Usage : 
   * \code
   * #include <Eigen/OrderingMethods>
   * \endcode
+  * 
+  * A simple usage is as a template parameter in the sparse decomposition classes : 
+  * 
+  * \code 
+  * SparseLU<MatrixType, COLAMDOrdering<int> > solver;
+  * \endcode 
+  * 
+  * \code 
+  * SparseQR<MatrixType, COLAMDOrdering<int> > solver;
+  * \endcode
+  * 
+  * It is possible as well to call directly a particular ordering method for your own purpose, 
+  * \code 
+  * AMDOrdering<int> ordering;
+  * PermutationMatrix<Dynamic, Dynamic, int> perm;
+  * SparseMatrix<double> A; 
+  * //Fill the matrix ...
+  * 
+  * ordering(A, perm); // Call AMD
+  * \endcode
+  * 
+  * \note Some of these methods (like AMD or METIS), need the sparsity pattern 
+  * of the input matrix to be symmetric. When the matrix is structurally unsymmetric, 
+  * Eigen computes internally the pattern of \f$A^T*A\f$ before calling the method.
+  * If your matrix is already symmetric (at leat in structure), you can avoid that
+  * by calling the method with a SelfAdjointView type.
+  * 
+  * \code
+  *  // Call the ordering on the pattern of the lower triangular matrix A
+  * ordering(A.selfadjointView<Lower>(), perm);
+  * \endcode
   */
 
+#ifndef EIGEN_MPL2_ONLY
 #include "src/OrderingMethods/Amd.h"
+#endif
 
+#include "src/OrderingMethods/Ordering.h"
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_ORDERINGMETHODS_MODULE_H

pydensecrf/densecrf/include/Eigen/PaStiXSupport

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_PASTIXSUPPORT_MODULE_H
 #define EIGEN_PASTIXSUPPORT_MODULE_H
 
@@ -5,7 +12,6 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-#include <complex.h>
 extern "C" {
 #include <pastix_nompi.h>
 #include <pastix.h>
@@ -35,12 +41,8 @@ extern "C" {
   *
   */
 
-#include "src/misc/Solve.h"
-#include "src/misc/SparseSolve.h"
-
 #include "src/PaStiXSupport/PaStiXSupport.h"
 
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_PASTIXSUPPORT_MODULE_H

pydensecrf/densecrf/include/Eigen/PardisoSupport

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_PARDISOSUPPORT_MODULE_H
 #define EIGEN_PARDISOSUPPORT_MODULE_H
 
@@ -7,8 +14,6 @@
 
 #include <mkl_pardiso.h>
 
-#include <unsupported/Eigen/SparseExtra>
-
 /** \ingroup Support_modules
   * \defgroup PardisoSupport_Module PardisoSupport module
   *

pydensecrf/densecrf/include/Eigen/QR

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_QR_MODULE_H
 #define EIGEN_QR_MODULE_H
 
 #include "Core"
 
-#include "src/Core/util/DisableStupidWarnings.h"
-
 #include "Cholesky"
 #include "Jacobi"
 #include "Householder"
 
+#include "src/Core/util/DisableStupidWarnings.h"
+
 /** \defgroup QR_Module QR module
   *
   *
   *
   * This module provides various QR decompositions
   * This module also provides some MatrixBase methods, including:
-  *  - MatrixBase::qr(),
+  *  - MatrixBase::householderQr()
+  *  - MatrixBase::colPivHouseholderQr()
+  *  - MatrixBase::fullPivHouseholderQr()
   *
   * \code
   * #include <Eigen/QR>
   * \endcode
   */
 
-#include "src/misc/Solve.h"
 #include "src/QR/HouseholderQR.h"
 #include "src/QR/FullPivHouseholderQR.h"
 #include "src/QR/ColPivHouseholderQR.h"
+#include "src/QR/CompleteOrthogonalDecomposition.h"
 #ifdef EIGEN_USE_LAPACKE
-#include "src/QR/HouseholderQR_MKL.h"
-#include "src/QR/ColPivHouseholderQR_MKL.h"
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
+#include "src/misc/lapacke.h"
 #endif
-
-#ifdef EIGEN2_SUPPORT
-#include "src/Eigen2Support/QR.h"
+#include "src/QR/HouseholderQR_LAPACKE.h"
+#include "src/QR/ColPivHouseholderQR_LAPACKE.h"
 #endif
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 
-#ifdef EIGEN2_SUPPORT
-#include "Eigenvalues"
-#endif
-
 #endif // EIGEN_QR_MODULE_H
 /* vim: set filetype=cpp et sw=2 ts=2 ai: */

pydensecrf/densecrf/include/Eigen/QtAlignedMalloc

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
 
 #ifndef EIGEN_QTMALLOC_MODULE_H
 #define EIGEN_QTMALLOC_MODULE_H
@@ -8,7 +14,7 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-void *qMalloc(size_t size)
+void *qMalloc(std::size_t size)
 {
   return Eigen::internal::aligned_malloc(size);
 }
@@ -18,10 +24,10 @@ void qFree(void *ptr)
   Eigen::internal::aligned_free(ptr);
 }
 
-void *qRealloc(void *ptr, size_t size)
+void *qRealloc(void *ptr, std::size_t size)
 {
   void* newPtr = Eigen::internal::aligned_malloc(size);
-  memcpy(newPtr, ptr, size);
+  std::memcpy(newPtr, ptr, size);
   Eigen::internal::aligned_free(ptr);
   return newPtr;
 }

pydensecrf/densecrf/include/Eigen/SPQRSupport

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+#ifndef EIGEN_SPQRSUPPORT_MODULE_H
+#define EIGEN_SPQRSUPPORT_MODULE_H
+
+#include "SparseCore"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+#include "SuiteSparseQR.hpp"
+
+/** \ingroup Support_modules
+  * \defgroup SPQRSupport_Module SuiteSparseQR module
+  * 
+  * This module provides an interface to the SPQR library, which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
+  *
+  * \code
+  * #include <Eigen/SPQRSupport>
+  * \endcode
+  *
+  * In order to use this module, the SPQR headers must be accessible from the include paths, and your binary must be linked to the SPQR library and its dependencies (Cholmod, AMD, COLAMD,...).
+  * For a cmake based project, you can use our FindSPQR.cmake and FindCholmod.Cmake modules
+  *
+  */
+
+#include "src/CholmodSupport/CholmodSupport.h"
+#include "src/SPQRSupport/SuiteSparseQRSupport.h"
+
+#endif

pydensecrf/densecrf/include/Eigen/SVD

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_SVD_MODULE_H
 #define EIGEN_SVD_MODULE_H
 
@@ -12,23 +19,30 @@
   *
   *
   * This module provides SVD decomposition for matrices (both real and complex).
-  * This decomposition is accessible via the following MatrixBase method:
+  * Two decomposition algorithms are provided:
+  *  - JacobiSVD implementing two-sided Jacobi iterations is numerically very accurate, fast for small matrices, but very slow for larger ones.
+  *  - BDCSVD implementing a recursive divide & conquer strategy on top of an upper-bidiagonalization which remains fast for large problems.
+  * These decompositions are accessible via the respective classes and following MatrixBase methods:
   *  - MatrixBase::jacobiSvd()
+  *  - MatrixBase::bdcSvd()
   *
   * \code
   * #include <Eigen/SVD>
   * \endcode
   */
 
-#include "src/misc/Solve.h"
+#include "src/misc/RealSvd2x2.h"
+#include "src/SVD/UpperBidiagonalization.h"
+#include "src/SVD/SVDBase.h"
 #include "src/SVD/JacobiSVD.h"
+#include "src/SVD/BDCSVD.h"
 #if defined(EIGEN_USE_LAPACKE) && !defined(EIGEN_USE_LAPACKE_STRICT)
-#include "src/SVD/JacobiSVD_MKL.h"
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
+#include "src/misc/lapacke.h"
 #endif
-#include "src/SVD/UpperBidiagonalization.h"
-
-#ifdef EIGEN2_SUPPORT
-#include "src/Eigen2Support/SVD.h"
+#include "src/SVD/JacobiSVD_LAPACKE.h"
 #endif
 
 #include "src/Core/util/ReenableStupidWarnings.h"

pydensecrf/densecrf/include/Eigen/Sparse

+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
 #ifndef EIGEN_SPARSE_MODULE_H
 #define EIGEN_SPARSE_MODULE_H
 
-/** \defgroup Sparse_modules Sparse modules
+/** \defgroup Sparse_Module Sparse meta-module
   *
   * Meta-module including all related modules:
-  * - SparseCore
-  * - OrderingMethods
-  * - SparseCholesky
-  * - IterativeLinearSolvers
+  * - \ref SparseCore_Module
+  * - \ref OrderingMethods_Module
+  * - \ref SparseCholesky_Module
+  * - \ref SparseLU_Module
+  * - \ref SparseQR_Module
+  * - \ref IterativeLinearSolvers_Module
   *
-  * \code
-  * #include <Eigen/Sparse>
-  * \endcode
+    \code
+    #include <Eigen/Sparse>
+    \endcode
   */
 
 #include "SparseCore"
 #include "OrderingMethods"
+#ifndef EIGEN_MPL2_ONLY
 #include "SparseCholesky"
+#endif
+#include "SparseLU"
+#include "SparseQR"
 #include "IterativeLinearSolvers"
 
 #endif // EIGEN_SPARSE_MODULE_H