libs/README.md

-This folder contains the various required libraries for QGC to compile. They are distributed with the codebase to ease development.
+This folder contains the various required libraries for QGC to compile.
 
-# Qwt
-Qt Widgets for Technical Applications
-Version: 6.1
-Source obtained: `svn checkout svn://svn.code.sf.net/p/qwt/code/branches/qwt-6.1 qwt`
-
-Contents of `/libs/qwt` is the contents of the `/src` directory from the Qwt repository.
-qwt.pri file is custom made to compile all necessary Qwt code in with QGC.
+# eigen
+* Version 3.3.7
+* Pulled from http://bitbucket.org/eigen/eigen/get/3.3.7.zip

libs/eigen/.hg_archival.txt

+repo: 8a21fd850624c931e448cbcfb38168cb2717c790
+node: 323c052e17310984a40dda9426e0435bed7178fa
+branch: 3.3
+tag: 3.3.7

libs/eigen/.hgeol

+[patterns]
+*.sh = LF
+*.MINPACK = CRLF
+scripts/*.in = LF
+debug/msvc/*.dat = CRLF
+debug/msvc/*.natvis = CRLF
+unsupported/test/mpreal/*.* = CRLF
+** = native
+
+[repository]
+native = LF

libs/eigen/.hgignore

+syntax: glob
+qrc_*cxx
+*.orig
+*.pyc
+*.diff
+diff
+*.save
+save
+*.old
+*.gmo
+*.qm
+core
+core.*
+*.bak
+*~
+*build*
+*.moc.*
+*.moc
+ui_*
+CMakeCache.txt
+tags
+.*.swp
+activity.png
+*.out
+*.php*
+*.log
+*.orig
+*.rej
+log
+patch
+a
+a.*
+lapack/testing
+lapack/reference

libs/eigen/.hgtags

+2db9468678c6480c9633b6272ff0e3599d1e11a3 2.0-beta3
+375224817dce669b6fa31d920d4c895a63fabf32 2.0-beta1
+3b8120f077865e2a072e10f5be33e1d942b83a06 2.0-rc1
+19dfc0e7666bcee26f7a49eb42f39a0280a3485e 2.0-beta5
+7a7d8a9526f003ffa2430dfb0c2c535b5add3023 2.0-beta4
+7d14ad088ac23769c349518762704f0257f6a39b 2.0.1
+b9d48561579fd7d4c05b2aa42235dc9de6484bf2 2.0-beta6
+e17630a40408243cb1a51ad0fe3a99beb75b7450 before-hg-migration
+eda654d4cda2210ce80719addcf854773e6dec5a 2.0.0
+ee9a7c468a9e73fab12f38f02bac24b07f29ed71 2.0-beta2
+d49097c25d8049e730c254a2fed725a240ce4858 after-hg-migration
+655348878731bcb5d9bbe0854077b052e75e5237 actual-start-from-scratch
+12a658962d4e6dfdc9a1c350fe7b69e36e70675c 3.0-beta1
+5c4180ad827b3f869b13b1d82f5a6ce617d6fcee 3.0-beta2
+7ae24ca6f3891d5ac58ddc7db60ad413c8d6ec35 3.0-beta3
+c40708b9088d622567fecc9208ad4a426621d364 3.0-beta4
+b6456624eae74f49ae8683d8e7b2882a2ca0342a 3.0-rc1
+a810d5dbab47acfe65b3350236efdd98f67d4d8a 3.1.0-alpha1
+304c88ca3affc16dd0b008b1104873986edd77af 3.1.0-alpha2
+920fc730b5930daae0a6dbe296d60ce2e3808215 3.1.0-beta1
+8383e883ebcc6f14695ff0b5e20bb631abab43fb 3.1.0-rc1
+bf4cb8c934fa3a79f45f1e629610f0225e93e493 3.1.0-rc2
+da195914abcc1d739027cbee7c52077aab30b336 3.2-beta1
+a8e0d153fc5e239ef8b06e3665f1f9e8cb8d49c8 before-evaluators
+09a8e21866106b49c5dec1d6d543e5794e82efa0 3.3-alpha1
+ce5a455b34c0a0ac3545a1497cb4a16c38ed90e8 3.3-beta1
+69d418c0699907bcd0bf9e0b3ba0a112ed091d85 3.3-beta2
+bef509908b9da05d0d07ffc0da105e2c8c6d3996 3.3-rc1
+04ab5fa4b241754afcf631117572276444c67239 3.3-rc2
+26667be4f70baf4f0d39e96f330714c87b399090 3.3.0
+f562a193118d4f40514e2f4a0ace6e974926ef06 3.3.1
+da9b4e14c2550e0d11078a3c39e6d56eba9905df 3.3.2
+67e894c6cd8f5f1f604b27d37ed47fdf012674ff 3.3.3
+5a0156e40feb7c4136680b493c6e433d91a6f355 3.3.4
+b3f3d4950030e3fa2e8fde6b68405106ae5685e1 3.3.5
+b70bf4fad46787bce88d17d6f80d22f70ac882a1 3.3.6

libs/eigen/COPYING.BSD

+/*
+ Copyright (c) 2011, Intel Corporation. All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without modification,
+ are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of Intel Corporation nor the names of its contributors may
+   be used to endorse or promote products derived from this software without
+   specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
\ No newline at end of file

libs/eigen/COPYING.MINPACK

+Minpack Copyright Notice (1999) University of Chicago.  All rights reserved
+
+Redistribution and use in source and binary forms, with or
+without modification, are permitted provided that the
+following conditions are met:
+
+1. Redistributions of source code must retain the above
+copyright notice, this list of conditions and the following
+disclaimer.
+
+2. Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following
+disclaimer in the documentation and/or other materials
+provided with the distribution.
+
+3. The end-user documentation included with the
+redistribution, if any, must include the following
+acknowledgment:
+
+   "This product includes software developed by the
+   University of Chicago, as Operator of Argonne National
+   Laboratory.
+
+Alternately, this acknowledgment may appear in the software
+itself, if and wherever such third-party acknowledgments
+normally appear.
+
+4. WARRANTY DISCLAIMER. THE SOFTWARE IS SUPPLIED "AS IS"
+WITHOUT WARRANTY OF ANY KIND. THE COPYRIGHT HOLDER, THE
+UNITED STATES, THE UNITED STATES DEPARTMENT OF ENERGY, AND
+THEIR EMPLOYEES: (1) DISCLAIM ANY WARRANTIES, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO ANY IMPLIED WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE
+OR NON-INFRINGEMENT, (2) DO NOT ASSUME ANY LEGAL LIABILITY
+OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR
+USEFULNESS OF THE SOFTWARE, (3) DO NOT REPRESENT THAT USE OF
+THE SOFTWARE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS, (4)
+DO NOT WARRANT THAT THE SOFTWARE WILL FUNCTION
+UNINTERRUPTED, THAT IT IS ERROR-FREE OR THAT ANY ERRORS WILL
+BE CORRECTED.
+
+5. LIMITATION OF LIABILITY. IN NO EVENT WILL THE COPYRIGHT
+HOLDER, THE UNITED STATES, THE UNITED STATES DEPARTMENT OF
+ENERGY, OR THEIR EMPLOYEES: BE LIABLE FOR ANY INDIRECT,
+INCIDENTAL, CONSEQUENTIAL, SPECIAL OR PUNITIVE DAMAGES OF
+ANY KIND OR NATURE, INCLUDING BUT NOT LIMITED TO LOSS OF
+PROFITS OR LOSS OF DATA, FOR ANY REASON WHATSOEVER, WHETHER
+SUCH LIABILITY IS ASSERTED ON THE BASIS OF CONTRACT, TORT
+(INCLUDING NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE,
+EVEN IF ANY OF SAID PARTIES HAS BEEN WARNED OF THE
+POSSIBILITY OF SUCH LOSS OR DAMAGES.
+

libs/eigen/COPYING.README

+Eigen is primarily MPL2 licensed. See COPYING.MPL2 and these links:
+  http://www.mozilla.org/MPL/2.0/
+  http://www.mozilla.org/MPL/2.0/FAQ.html
+
+Some files contain third-party code under BSD or LGPL licenses, whence the other
+COPYING.* files here.
+
+All the LGPL code is either LGPL 2.1-only, or LGPL 2.1-or-later.
+For this reason, the COPYING.LGPL file contains the LGPL 2.1 text.
+
+If you want to guarantee that the Eigen code that you are #including is licensed
+under the MPL2 and possibly more permissive licenses (like BSD), #define this
+preprocessor symbol:
+  EIGEN_MPL2_ONLY
+For example, with most compilers, you could add this to your project CXXFLAGS:
+  -DEIGEN_MPL2_ONLY
+This will cause a compilation error to be generated if you #include any code that is
+LGPL licensed.

libs/eigen/Eigen/Array

-#ifndef EIGEN_ARRAY_MODULE_H
-#define EIGEN_ARRAY_MODULE_H
-
-// include Core first to handle Eigen2 support macros
-#include "Core"
-
-#ifndef EIGEN2_SUPPORT
-  #error The Eigen/Array header does no longer exist in Eigen3. All that functionality has moved to Eigen/Core.
-#endif
-
-#endif // EIGEN_ARRAY_MODULE_H

libs/eigen/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")

libs/eigen/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"

libs/eigen/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

libs/eigen/Eigen/Eigen

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

libs/eigen/Eigen/Eigen2Support

-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2009 Gael Guennebaud <gael.guennebaud@inria.fr>
-//
-// 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 EIGEN2SUPPORT_H
-#define EIGEN2SUPPORT_H
-
-#if (!defined(EIGEN2_SUPPORT)) || (!defined(EIGEN_CORE_H))
-#error Eigen2 support must be enabled by defining EIGEN2_SUPPORT before including any Eigen header
-#endif
-
-#ifndef EIGEN_NO_EIGEN2_DEPRECATED_WARNING
-
-#if defined(__GNUC__) || defined(__INTEL_COMPILER) || defined(__clang__)
-#warning "Eigen2 support is deprecated in Eigen 3.2.x and it will be removed in Eigen 3.3. (Define EIGEN_NO_EIGEN2_DEPRECATED_WARNING to disable this warning)"
-#else
-#pragma message ("Eigen2 support is deprecated in Eigen 3.2.x and it will be removed in Eigen 3.3. (Define EIGEN_NO_EIGEN2_DEPRECATED_WARNING to disable this warning)")
-#endif
-
-#endif // EIGEN_NO_EIGEN2_DEPRECATED_WARNING
-
-#include "src/Core/util/DisableStupidWarnings.h"
-
-/** \ingroup Support_modules
-  * \defgroup Eigen2Support_Module Eigen2 support module
-  *
-  * \warning Eigen2 support is deprecated in Eigen 3.2.x and it will be removed in Eigen 3.3.
-  *
-  * This module provides a couple of deprecated functions improving the compatibility with Eigen2.
-  * 
-  * To use it, define EIGEN2_SUPPORT before including any Eigen header
-  * \code
-  * #define EIGEN2_SUPPORT
-  * \endcode
-  *
-  */
-
-#include "src/Eigen2Support/Macros.h"
-#include "src/Eigen2Support/Memory.h"
-#include "src/Eigen2Support/Meta.h"
-#include "src/Eigen2Support/Lazy.h"
-#include "src/Eigen2Support/Cwise.h"
-#include "src/Eigen2Support/CwiseOperators.h"
-#include "src/Eigen2Support/TriangularSolver.h"
-#include "src/Eigen2Support/Block.h"
-#include "src/Eigen2Support/VectorBlock.h"
-#include "src/Eigen2Support/Minor.h"
-#include "src/Eigen2Support/MathFunctions.h"
-
-
-#include "src/Core/util/ReenableStupidWarnings.h"
-
-// Eigen2 used to include iostream
-#include<iostream>
-
-#define EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, SizeSuffix) \
-using Eigen::Matrix##SizeSuffix##TypeSuffix; \
-using Eigen::Vector##SizeSuffix##TypeSuffix; \
-using Eigen::RowVector##SizeSuffix##TypeSuffix;
-
-#define EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(TypeSuffix) \
-EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, 2) \
-EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, 3) \
-EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, 4) \
-EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, X) \
-
-#define EIGEN_USING_MATRIX_TYPEDEFS \
-EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(i) \
-EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(f) \
-EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(d) \
-EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(cf) \
-EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(cd)
-
-#define USING_PART_OF_NAMESPACE_EIGEN \
-EIGEN_USING_MATRIX_TYPEDEFS \
-using Eigen::Matrix; \
-using Eigen::MatrixBase; \
-using Eigen::ei_random; \
-using Eigen::ei_real; \
-using Eigen::ei_imag; \
-using Eigen::ei_conj; \
-using Eigen::ei_abs; \
-using Eigen::ei_abs2; \
-using Eigen::ei_sqrt; \
-using Eigen::ei_exp; \
-using Eigen::ei_log; \
-using Eigen::ei_sin; \
-using Eigen::ei_cos;
-
-#endif // EIGEN2SUPPORT_H

libs/eigen/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
 
@@ -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"
@@ -37,9 +45,14 @@
 #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"

libs/eigen/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
 
@@ -9,21 +16,17 @@
 #include "LU"
 #include <limits>
 
-#ifndef M_PI
-#define M_PI 3.14159265358979323846
-#endif
-
 /** \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"

libs/eigen/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
 

libs/eigen/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
 
@@ -12,28 +19,29 @@
   * 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"
 

libs/eigen/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
 

libs/eigen/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

libs/eigen/Eigen/LeastSquares

-#ifndef EIGEN_REGRESSION_MODULE_H
-#define EIGEN_REGRESSION_MODULE_H
-
-#ifndef EIGEN2_SUPPORT
-#error LeastSquares is only available in Eigen2 support mode (define EIGEN2_SUPPORT)
-#endif
-
-// exclude from normal eigen3-only documentation
-#ifdef EIGEN2_SUPPORT
-
-#include "Core"
-
-#include "src/Core/util/DisableStupidWarnings.h"
-
-#include "Eigenvalues"
-#include "Geometry"
-
-/** \defgroup LeastSquares_Module LeastSquares module
-  * This module provides linear regression and related features.
-  *
-  * \code
-  * #include <Eigen/LeastSquares>
-  * \endcode
-  */
-
-#include "src/Eigen2Support/LeastSquares.h"
-
-#include "src/Core/util/ReenableStupidWarnings.h"
-
-#endif // EIGEN2_SUPPORT
-
-#endif // EIGEN_REGRESSION_MODULE_H

libs/eigen/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
 

libs/eigen/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
 

libs/eigen/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

libs/eigen/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
   *

libs/eigen/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
 
@@ -15,31 +22,30 @@
   *
   * 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: */

libs/eigen/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;
 }

libs/eigen/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
 
@@ -10,7 +17,7 @@
 /** \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.cise.ufl.edu/research/sparse/SuiteSparse/">suitesparse</a> package.
+  * 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>
@@ -21,8 +28,6 @@
   *
   */
 
-#include "src/misc/Solve.h"
-#include "src/misc/SparseSolve.h"
 #include "src/CholmodSupport/CholmodSupport.h"
 #include "src/SPQRSupport/SuiteSparseQRSupport.h"
 

libs/eigen/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"

libs/eigen/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
 
@@ -11,14 +18,16 @@
   * - \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"

libs/eigen/Eigen/SparseCholesky

@@ -34,8 +34,6 @@
 #error The SparseCholesky module has nothing to offer in MPL2 only mode
 #endif
 
-#include "src/misc/Solve.h"
-#include "src/misc/SparseSolve.h"
 #include "src/SparseCholesky/SimplicialCholesky.h"
 
 #ifndef EIGEN_MPL2_ONLY

libs/eigen/Eigen/SparseCore

+// 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_SPARSECORE_MODULE_H
 #define EIGEN_SPARSECORE_MODULE_H
 
@@ -26,37 +33,35 @@
   * This module depends on: Core.
   */
 
-namespace Eigen {
-
-/** The type used to identify a general sparse storage. */
-struct Sparse {};
-
-}
-
 #include "src/SparseCore/SparseUtil.h"
 #include "src/SparseCore/SparseMatrixBase.h"
+#include "src/SparseCore/SparseAssign.h"
 #include "src/SparseCore/CompressedStorage.h"
 #include "src/SparseCore/AmbiVector.h"
+#include "src/SparseCore/SparseCompressedBase.h"
 #include "src/SparseCore/SparseMatrix.h"
+#include "src/SparseCore/SparseMap.h"
 #include "src/SparseCore/MappedSparseMatrix.h"
 #include "src/SparseCore/SparseVector.h"
-#include "src/SparseCore/SparseBlock.h"
-#include "src/SparseCore/SparseTranspose.h"
+#include "src/SparseCore/SparseRef.h"
 #include "src/SparseCore/SparseCwiseUnaryOp.h"
 #include "src/SparseCore/SparseCwiseBinaryOp.h"
+#include "src/SparseCore/SparseTranspose.h"
+#include "src/SparseCore/SparseBlock.h"
 #include "src/SparseCore/SparseDot.h"
-#include "src/SparseCore/SparsePermutation.h"
 #include "src/SparseCore/SparseRedux.h"
-#include "src/SparseCore/SparseFuzzy.h"
+#include "src/SparseCore/SparseView.h"
+#include "src/SparseCore/SparseDiagonalProduct.h"
 #include "src/SparseCore/ConservativeSparseSparseProduct.h"
 #include "src/SparseCore/SparseSparseProductWithPruning.h"
 #include "src/SparseCore/SparseProduct.h"
 #include "src/SparseCore/SparseDenseProduct.h"
-#include "src/SparseCore/SparseDiagonalProduct.h"
-#include "src/SparseCore/SparseTriangularView.h"
 #include "src/SparseCore/SparseSelfAdjointView.h"
+#include "src/SparseCore/SparseTriangularView.h"
 #include "src/SparseCore/TriangularSolver.h"
-#include "src/SparseCore/SparseView.h"
+#include "src/SparseCore/SparsePermutation.h"
+#include "src/SparseCore/SparseFuzzy.h"
+#include "src/SparseCore/SparseSolverBase.h"
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 

libs/eigen/Eigen/SparseLU

@@ -20,9 +20,6 @@
   * Please, see the documentation of the SparseLU class for more details.
   */
 
-#include "src/misc/Solve.h"
-#include "src/misc/SparseSolve.h"
-
 // Ordering interface
 #include "OrderingMethods"
 

libs/eigen/Eigen/SparseQR

+// 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_SPARSEQR_MODULE_H
 #define EIGEN_SPARSEQR_MODULE_H
 
@@ -21,9 +28,6 @@
   * 
   */
 
-#include "src/misc/Solve.h"
-#include "src/misc/SparseSolve.h"
-
 #include "OrderingMethods"
 #include "src/SparseCore/SparseColEtree.h"
 #include "src/SparseQR/SparseQR.h"

libs/eigen/Eigen/StdDeque

@@ -14,7 +14,7 @@
 #include "Core"
 #include <deque>
 
-#if (defined(_MSC_VER) && defined(_WIN64)) /* MSVC auto aligns in 64 bit builds */
+#if EIGEN_COMP_MSVC && EIGEN_OS_WIN64 && (EIGEN_MAX_STATIC_ALIGN_BYTES<=16) /* MSVC auto aligns up to 16 bytes in 64 bit builds */
 
 #define EIGEN_DEFINE_STL_DEQUE_SPECIALIZATION(...)
 

libs/eigen/Eigen/StdList

@@ -13,7 +13,7 @@
 #include "Core"
 #include <list>
 
-#if (defined(_MSC_VER) && defined(_WIN64)) /* MSVC auto aligns in 64 bit builds */    
+#if EIGEN_COMP_MSVC && EIGEN_OS_WIN64 && (EIGEN_MAX_STATIC_ALIGN_BYTES<=16) /* MSVC auto aligns up to 16 bytes in 64 bit builds */
 
 #define EIGEN_DEFINE_STL_LIST_SPECIALIZATION(...)
 

libs/eigen/Eigen/StdVector

@@ -14,7 +14,7 @@
 #include "Core"
 #include <vector>
 
-#if (defined(_MSC_VER) && defined(_WIN64)) /* MSVC auto aligns in 64 bit builds */
+#if EIGEN_COMP_MSVC && EIGEN_OS_WIN64 && (EIGEN_MAX_STATIC_ALIGN_BYTES<=16) /* MSVC auto aligns up to 16 bytes in 64 bit builds */
 
 #define EIGEN_DEFINE_STL_VECTOR_SPECIALIZATION(...)
 

libs/eigen/Eigen/SuperLUSupport

+// 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_SUPERLUSUPPORT_MODULE_H
 #define EIGEN_SUPERLUSUPPORT_MODULE_H
 
@@ -36,6 +43,8 @@ namespace Eigen { struct SluMatrix; }
   * - class SuperLU: a supernodal sequential LU factorization.
   * - class SuperILU: a supernodal sequential incomplete LU factorization (to be used as a preconditioner for iterative methods).
   *
+  * \warning This wrapper requires at least versions 4.0 of SuperLU. The 3.x versions are not supported.
+  *
   * \warning When including this module, you have to use SUPERLU_EMPTY instead of EMPTY which is no longer defined because it is too polluting.
   *
   * \code
@@ -48,12 +57,8 @@ namespace Eigen { struct SluMatrix; }
   *
   */
 
-#include "src/misc/Solve.h"
-#include "src/misc/SparseSolve.h"
-
 #include "src/SuperLUSupport/SuperLUSupport.h"
 
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_SUPERLUSUPPORT_MODULE_H

libs/eigen/Eigen/UmfPackSupport

+// 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_UMFPACKSUPPORT_MODULE_H
 #define EIGEN_UMFPACKSUPPORT_MODULE_H
 
@@ -12,7 +19,7 @@ extern "C" {
 /** \ingroup Support_modules
   * \defgroup UmfPackSupport_Module UmfPackSupport module
   *
-  * This module provides an interface to the UmfPack 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 UmfPack library which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
   * It provides the following factorization class:
   * - class UmfPackLU: a multifrontal sequential LU factorization.
   *
@@ -26,9 +33,6 @@ extern "C" {
   *
   */
 
-#include "src/misc/Solve.h"
-#include "src/misc/SparseSolve.h"
-
 #include "src/UmfPackSupport/UmfPackSupport.h"
 
 #include "src/Core/util/ReenableStupidWarnings.h"

libs/eigen/Eigen/src/CMakeLists.txt

-file(GLOB Eigen_src_subdirectories "*")
-escape_string_as_regex(ESCAPED_CMAKE_CURRENT_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
-foreach(f ${Eigen_src_subdirectories})
-  if(NOT f MATCHES "\\.txt" AND NOT f MATCHES "${ESCAPED_CMAKE_CURRENT_SOURCE_DIR}/[.].+" )
-    add_subdirectory(${f})
-  endif()
-endforeach()

libs/eigen/Eigen/src/Cholesky/CMakeLists.txt

-FILE(GLOB Eigen_Cholesky_SRCS "*.h")
-
-INSTALL(FILES
-  ${Eigen_Cholesky_SRCS}
-  DESTINATION ${INCLUDE_INSTALL_DIR}/Eigen/src/Cholesky COMPONENT Devel
-  )

libs/eigen/Eigen/src/Cholesky/LLT_MKL.h → libs/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h

@@ -25,41 +25,38 @@
  SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
  ********************************************************************************
- *   Content : Eigen bindings to Intel(R) MKL
+ *   Content : Eigen bindings to LAPACKe
  *     LLt decomposition based on LAPACKE_?potrf function.
  ********************************************************************************
 */
 
-#ifndef EIGEN_LLT_MKL_H
-#define EIGEN_LLT_MKL_H
-
-#include "Eigen/src/Core/util/MKL_support.h"
-#include <iostream>
+#ifndef EIGEN_LLT_LAPACKE_H
+#define EIGEN_LLT_LAPACKE_H
 
 namespace Eigen { 
 
 namespace internal {
 
-template<typename Scalar> struct mkl_llt;
+template<typename Scalar> struct lapacke_llt;
 
-#define EIGEN_MKL_LLT(EIGTYPE, MKLTYPE, MKLPREFIX) \
-template<> struct mkl_llt<EIGTYPE> \
+#define EIGEN_LAPACKE_LLT(EIGTYPE, BLASTYPE, LAPACKE_PREFIX) \
+template<> struct lapacke_llt<EIGTYPE> \
 { \
   template<typename MatrixType> \
-  static inline typename MatrixType::Index potrf(MatrixType& m, char uplo) \
+  static inline Index potrf(MatrixType& m, char uplo) \
   { \
     lapack_int matrix_order; \
     lapack_int size, lda, info, StorageOrder; \
     EIGTYPE* a; \
     eigen_assert(m.rows()==m.cols()); \
     /* Set up parameters for ?potrf */ \
-    size = m.rows(); \
+    size = convert_index<lapack_int>(m.rows()); \
     StorageOrder = MatrixType::Flags&RowMajorBit?RowMajor:ColMajor; \
     matrix_order = StorageOrder==RowMajor ? LAPACK_ROW_MAJOR : LAPACK_COL_MAJOR; \
     a = &(m.coeffRef(0,0)); \
-    lda = m.outerStride(); \
+    lda = convert_index<lapack_int>(m.outerStride()); \
 \
-    info = LAPACKE_##MKLPREFIX##potrf( matrix_order, uplo, size, (MKLTYPE*)a, lda ); \
+    info = LAPACKE_##LAPACKE_PREFIX##potrf( matrix_order, uplo, size, (BLASTYPE*)a, lda ); \
     info = (info==0) ? -1 : info>0 ? info-1 : size; \
     return info; \
   } \
@@ -67,36 +64,36 @@ template<> struct mkl_llt<EIGTYPE> \
 template<> struct llt_inplace<EIGTYPE, Lower> \
 { \
   template<typename MatrixType> \
-  static typename MatrixType::Index blocked(MatrixType& m) \
+  static Index blocked(MatrixType& m) \
   { \
-    return mkl_llt<EIGTYPE>::potrf(m, 'L'); \
+    return lapacke_llt<EIGTYPE>::potrf(m, 'L'); \
   } \
   template<typename MatrixType, typename VectorType> \
-  static typename MatrixType::Index rankUpdate(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) \
+  static Index rankUpdate(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) \
   { return Eigen::internal::llt_rank_update_lower(mat, vec, sigma); } \
 }; \
 template<> struct llt_inplace<EIGTYPE, Upper> \
 { \
   template<typename MatrixType> \
-  static typename MatrixType::Index blocked(MatrixType& m) \
+  static Index blocked(MatrixType& m) \
   { \
-    return mkl_llt<EIGTYPE>::potrf(m, 'U'); \
+    return lapacke_llt<EIGTYPE>::potrf(m, 'U'); \
   } \
   template<typename MatrixType, typename VectorType> \
-  static typename MatrixType::Index rankUpdate(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) \
+  static Index rankUpdate(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) \
   { \
     Transpose<MatrixType> matt(mat); \
     return llt_inplace<EIGTYPE, Lower>::rankUpdate(matt, vec.conjugate(), sigma); \
   } \
 };
 
-EIGEN_MKL_LLT(double, double, d)
-EIGEN_MKL_LLT(float, float, s)
-EIGEN_MKL_LLT(dcomplex, MKL_Complex16, z)
-EIGEN_MKL_LLT(scomplex, MKL_Complex8, c)
+EIGEN_LAPACKE_LLT(double, double, d)
+EIGEN_LAPACKE_LLT(float, float, s)
+EIGEN_LAPACKE_LLT(dcomplex, lapack_complex_double, z)
+EIGEN_LAPACKE_LLT(scomplex, lapack_complex_float, c)
 
 } // end namespace internal
 
 } // end namespace Eigen
 
-#endif // EIGEN_LLT_MKL_H
+#endif // EIGEN_LLT_LAPACKE_H

libs/eigen/Eigen/src/CholmodSupport/CMakeLists.txt

-FILE(GLOB Eigen_CholmodSupport_SRCS "*.h")
-
-INSTALL(FILES 
-  ${Eigen_CholmodSupport_SRCS}
-  DESTINATION ${INCLUDE_INSTALL_DIR}/Eigen/src/CholmodSupport COMPONENT Devel
-  )

libs/eigen/Eigen/src/Core/ArrayBase.h

@@ -32,7 +32,7 @@ template<typename ExpressionType> class MatrixWrapper;
   * \tparam Derived is the derived type, e.g., an array or an expression type.
   *
   * This class can be extended with the help of the plugin mechanism described on the page
-  * \ref TopicCustomizingEigen by defining the preprocessor symbol \c EIGEN_ARRAYBASE_PLUGIN.
+  * \ref TopicCustomizing_Plugins by defining the preprocessor symbol \c EIGEN_ARRAYBASE_PLUGIN.
   *
   * \sa class MatrixBase, \ref TopicClassHierarchy
   */
@@ -47,13 +47,11 @@ template<typename Derived> class ArrayBase
     typedef ArrayBase Eigen_BaseClassForSpecializationOfGlobalMathFuncImpl;
 
     typedef typename internal::traits<Derived>::StorageKind StorageKind;
-    typedef typename internal::traits<Derived>::Index Index;
     typedef typename internal::traits<Derived>::Scalar Scalar;
     typedef typename internal::packet_traits<Scalar>::type PacketScalar;
     typedef typename NumTraits<Scalar>::Real RealScalar;
 
     typedef DenseBase<Derived> Base;
-    using Base::operator*;
     using Base::RowsAtCompileTime;
     using Base::ColsAtCompileTime;
     using Base::SizeAtCompileTime;
@@ -62,8 +60,7 @@ template<typename Derived> class ArrayBase
     using Base::MaxSizeAtCompileTime;
     using Base::IsVectorAtCompileTime;
     using Base::Flags;
-    using Base::CoeffReadCost;
-
+    
     using Base::derived;
     using Base::const_cast_derived;
     using Base::rows;
@@ -83,25 +80,14 @@ template<typename Derived> class ArrayBase
 #endif // not EIGEN_PARSED_BY_DOXYGEN
 
 #ifndef EIGEN_PARSED_BY_DOXYGEN
-    /** \internal the plain matrix type corresponding to this expression. Note that is not necessarily
-      * exactly the return type of eval(): in the case of plain matrices, the return type of eval() is a const
-      * reference to a matrix, not a matrix! It is however guaranteed that the return type of eval() is either
-      * PlainObject or const PlainObject&.
-      */
-    typedef Array<typename internal::traits<Derived>::Scalar,
-                internal::traits<Derived>::RowsAtCompileTime,
-                internal::traits<Derived>::ColsAtCompileTime,
-                AutoAlign | (internal::traits<Derived>::Flags&RowMajorBit ? RowMajor : ColMajor),
-                internal::traits<Derived>::MaxRowsAtCompileTime,
-                internal::traits<Derived>::MaxColsAtCompileTime
-          > PlainObject;
-
+    typedef typename Base::PlainObject PlainObject;
 
     /** \internal Represents a matrix with all coefficients equal to one another*/
-    typedef CwiseNullaryOp<internal::scalar_constant_op<Scalar>,Derived> ConstantReturnType;
+    typedef CwiseNullaryOp<internal::scalar_constant_op<Scalar>,PlainObject> ConstantReturnType;
 #endif // not EIGEN_PARSED_BY_DOXYGEN
 
 #define EIGEN_CURRENT_STORAGE_BASE_CLASS Eigen::ArrayBase
+#define EIGEN_DOC_UNARY_ADDONS(X,Y)
 #   include "../plugins/CommonCwiseUnaryOps.h"
 #   include "../plugins/MatrixCwiseUnaryOps.h"
 #   include "../plugins/ArrayCwiseUnaryOps.h"
@@ -112,44 +98,62 @@ template<typename Derived> class ArrayBase
 #     include EIGEN_ARRAYBASE_PLUGIN
 #   endif
 #undef EIGEN_CURRENT_STORAGE_BASE_CLASS
+#undef EIGEN_DOC_UNARY_ADDONS
 
     /** Special case of the template operator=, in order to prevent the compiler
       * from generating a default operator= (issue hit with g++ 4.1)
       */
+    EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
     Derived& operator=(const ArrayBase& other)
     {
-      return internal::assign_selector<Derived,Derived>::run(derived(), other.derived());
+      internal::call_assignment(derived(), other.derived());
+      return derived();
     }
-
-    Derived& operator+=(const Scalar& scalar)
-    { return *this = derived() + scalar; }
-    Derived& operator-=(const Scalar& scalar)
-    { return *this = derived() - scalar; }
+    
+    /** Set all the entries to \a value.
+      * \sa DenseBase::setConstant(), DenseBase::fill() */
+    EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
+    Derived& operator=(const Scalar &value)
+    { Base::setConstant(value); return derived(); }
+
+    EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
+    Derived& operator+=(const Scalar& scalar);
+    EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
+    Derived& operator-=(const Scalar& scalar);
 
     template<typename OtherDerived>
+    EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
     Derived& operator+=(const ArrayBase<OtherDerived>& other);
     template<typename OtherDerived>
+    EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
     Derived& operator-=(const ArrayBase<OtherDerived>& other);
 
     template<typename OtherDerived>
+    EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
     Derived& operator*=(const ArrayBase<OtherDerived>& other);
 
     template<typename OtherDerived>
+    EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
     Derived& operator/=(const ArrayBase<OtherDerived>& other);
 
   public:
+    EIGEN_DEVICE_FUNC
     ArrayBase<Derived>& array() { return *this; }
+    EIGEN_DEVICE_FUNC
     const ArrayBase<Derived>& array() const { return *this; }
 
     /** \returns an \link Eigen::MatrixBase Matrix \endlink expression of this array
       * \sa MatrixBase::array() */
-    MatrixWrapper<Derived> matrix() { return derived(); }
-    const MatrixWrapper<const Derived> matrix() const { return derived(); }
+    EIGEN_DEVICE_FUNC
+    MatrixWrapper<Derived> matrix() { return MatrixWrapper<Derived>(derived()); }
+    EIGEN_DEVICE_FUNC
+    const MatrixWrapper<const Derived> matrix() const { return MatrixWrapper<const Derived>(derived()); }
 
 //     template<typename Dest>
 //     inline void evalTo(Dest& dst) const { dst = matrix(); }
 
   protected:
+    EIGEN_DEVICE_FUNC
     ArrayBase() : Base() {}
 
   private:
@@ -171,11 +175,10 @@ template<typename Derived> class ArrayBase
   */
 template<typename Derived>
 template<typename OtherDerived>
-EIGEN_STRONG_INLINE Derived &
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived &
 ArrayBase<Derived>::operator-=(const ArrayBase<OtherDerived> &other)
 {
-  SelfCwiseBinaryOp<internal::scalar_difference_op<Scalar>, Derived, OtherDerived> tmp(derived());
-  tmp = other.derived();
+  call_assignment(derived(), other.derived(), internal::sub_assign_op<Scalar,typename OtherDerived::Scalar>());
   return derived();
 }
 
@@ -185,11 +188,10 @@ ArrayBase<Derived>::operator-=(const ArrayBase<OtherDerived> &other)
   */
 template<typename Derived>
 template<typename OtherDerived>
-EIGEN_STRONG_INLINE Derived &
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived &
 ArrayBase<Derived>::operator+=(const ArrayBase<OtherDerived>& other)
 {
-  SelfCwiseBinaryOp<internal::scalar_sum_op<Scalar>, Derived, OtherDerived> tmp(derived());
-  tmp = other.derived();
+  call_assignment(derived(), other.derived(), internal::add_assign_op<Scalar,typename OtherDerived::Scalar>());
   return derived();
 }
 
@@ -199,11 +201,10 @@ ArrayBase<Derived>::operator+=(const ArrayBase<OtherDerived>& other)
   */
 template<typename Derived>
 template<typename OtherDerived>
-EIGEN_STRONG_INLINE Derived &
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived &
 ArrayBase<Derived>::operator*=(const ArrayBase<OtherDerived>& other)
 {
-  SelfCwiseBinaryOp<internal::scalar_product_op<Scalar>, Derived, OtherDerived> tmp(derived());
-  tmp = other.derived();
+  call_assignment(derived(), other.derived(), internal::mul_assign_op<Scalar,typename OtherDerived::Scalar>());
   return derived();
 }
 
@@ -213,11 +214,10 @@ ArrayBase<Derived>::operator*=(const ArrayBase<OtherDerived>& other)
   */
 template<typename Derived>
 template<typename OtherDerived>
-EIGEN_STRONG_INLINE Derived &
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived &
 ArrayBase<Derived>::operator/=(const ArrayBase<OtherDerived>& other)
 {
-  SelfCwiseBinaryOp<internal::scalar_quotient_op<Scalar>, Derived, OtherDerived> tmp(derived());
-  tmp = other.derived();
+  call_assignment(derived(), other.derived(), internal::div_assign_op<Scalar,typename OtherDerived::Scalar>());
   return derived();
 }
 

libs/eigen/Eigen/src/Core/ArrayWrapper.h

@@ -32,7 +32,8 @@ struct traits<ArrayWrapper<ExpressionType> >
   // Let's remove NestByRefBit
   enum {
     Flags0 = traits<typename remove_all<typename ExpressionType::Nested>::type >::Flags,
-    Flags = Flags0 & ~NestByRefBit
+    LvalueBitFlag = is_lvalue<ExpressionType>::value ? LvalueBit : 0,
+    Flags = (Flags0 & ~(NestByRefBit | LvalueBit)) | LvalueBitFlag
   };
 };
 }
@@ -44,6 +45,7 @@ class ArrayWrapper : public ArrayBase<ArrayWrapper<ExpressionType> >
     typedef ArrayBase<ArrayWrapper> Base;
     EIGEN_DENSE_PUBLIC_INTERFACE(ArrayWrapper)
     EIGEN_INHERIT_ASSIGNMENT_OPERATORS(ArrayWrapper)
+    typedef typename internal::remove_all<ExpressionType>::type NestedExpression;
 
     typedef typename internal::conditional<
                        internal::is_lvalue<ExpressionType>::value,
@@ -51,76 +53,45 @@ class ArrayWrapper : public ArrayBase<ArrayWrapper<ExpressionType> >
                        const Scalar
                      >::type ScalarWithConstIfNotLvalue;
 
-    typedef typename internal::nested<ExpressionType>::type NestedExpressionType;
+    typedef typename internal::ref_selector<ExpressionType>::non_const_type NestedExpressionType;
 
-    inline ArrayWrapper(ExpressionType& matrix) : m_expression(matrix) {}
+    using Base::coeffRef;
 
+    EIGEN_DEVICE_FUNC
+    explicit EIGEN_STRONG_INLINE ArrayWrapper(ExpressionType& matrix) : m_expression(matrix) {}
+
+    EIGEN_DEVICE_FUNC
     inline Index rows() const { return m_expression.rows(); }
+    EIGEN_DEVICE_FUNC
     inline Index cols() const { return m_expression.cols(); }
+    EIGEN_DEVICE_FUNC
     inline Index outerStride() const { return m_expression.outerStride(); }
+    EIGEN_DEVICE_FUNC
     inline Index innerStride() const { return m_expression.innerStride(); }
 
-    inline ScalarWithConstIfNotLvalue* data() { return m_expression.const_cast_derived().data(); }
+    EIGEN_DEVICE_FUNC
+    inline ScalarWithConstIfNotLvalue* data() { return m_expression.data(); }
+    EIGEN_DEVICE_FUNC
     inline const Scalar* data() const { return m_expression.data(); }
 
-    inline CoeffReturnType coeff(Index rowId, Index colId) const
-    {
-      return m_expression.coeff(rowId, colId);
-    }
-
-    inline Scalar& coeffRef(Index rowId, Index colId)
-    {
-      return m_expression.const_cast_derived().coeffRef(rowId, colId);
-    }
-
+    EIGEN_DEVICE_FUNC
     inline const Scalar& coeffRef(Index rowId, Index colId) const
     {
-      return m_expression.const_cast_derived().coeffRef(rowId, colId);
-    }
-
-    inline CoeffReturnType coeff(Index index) const
-    {
-      return m_expression.coeff(index);
-    }
-
-    inline Scalar& coeffRef(Index index)
-    {
-      return m_expression.const_cast_derived().coeffRef(index);
+      return m_expression.coeffRef(rowId, colId);
     }
 
+    EIGEN_DEVICE_FUNC
     inline const Scalar& coeffRef(Index index) const
     {
-      return m_expression.const_cast_derived().coeffRef(index);
-    }
-
-    template<int LoadMode>
-    inline const PacketScalar packet(Index rowId, Index colId) const
-    {
-      return m_expression.template packet<LoadMode>(rowId, colId);
-    }
-
-    template<int LoadMode>
-    inline void writePacket(Index rowId, Index colId, const PacketScalar& val)
-    {
-      m_expression.const_cast_derived().template writePacket<LoadMode>(rowId, colId, val);
-    }
-
-    template<int LoadMode>
-    inline const PacketScalar packet(Index index) const
-    {
-      return m_expression.template packet<LoadMode>(index);
-    }
-
-    template<int LoadMode>
-    inline void writePacket(Index index, const PacketScalar& val)
-    {
-      m_expression.const_cast_derived().template writePacket<LoadMode>(index, val);
+      return m_expression.coeffRef(index);
     }
 
     template<typename Dest>
+    EIGEN_DEVICE_FUNC
     inline void evalTo(Dest& dst) const { dst = m_expression; }
 
     const typename internal::remove_all<NestedExpressionType>::type& 
+    EIGEN_DEVICE_FUNC
     nestedExpression() const 
     {
       return m_expression;
@@ -128,10 +99,12 @@ class ArrayWrapper : public ArrayBase<ArrayWrapper<ExpressionType> >
 
     /** Forwards the resizing request to the nested expression
       * \sa DenseBase::resize(Index)  */
-    void resize(Index newSize) { m_expression.const_cast_derived().resize(newSize); }
+    EIGEN_DEVICE_FUNC
+    void resize(Index newSize) { m_expression.resize(newSize); }
     /** Forwards the resizing request to the nested expression
       * \sa DenseBase::resize(Index,Index)*/
-    void resize(Index nbRows, Index nbCols) { m_expression.const_cast_derived().resize(nbRows,nbCols); }
+    EIGEN_DEVICE_FUNC
+    void resize(Index rows, Index cols) { m_expression.resize(rows,cols); }
 
   protected:
     NestedExpressionType m_expression;
@@ -157,7 +130,8 @@ struct traits<MatrixWrapper<ExpressionType> >
   // Let's remove NestByRefBit
   enum {
     Flags0 = traits<typename remove_all<typename ExpressionType::Nested>::type >::Flags,
-    Flags = Flags0 & ~NestByRefBit
+    LvalueBitFlag = is_lvalue<ExpressionType>::value ? LvalueBit : 0,
+    Flags = (Flags0 & ~(NestByRefBit | LvalueBit)) | LvalueBitFlag
   };
 };
 }
@@ -169,6 +143,7 @@ class MatrixWrapper : public MatrixBase<MatrixWrapper<ExpressionType> >
     typedef MatrixBase<MatrixWrapper<ExpressionType> > Base;
     EIGEN_DENSE_PUBLIC_INTERFACE(MatrixWrapper)
     EIGEN_INHERIT_ASSIGNMENT_OPERATORS(MatrixWrapper)
+    typedef typename internal::remove_all<ExpressionType>::type NestedExpression;
 
     typedef typename internal::conditional<
                        internal::is_lvalue<ExpressionType>::value,
@@ -176,72 +151,40 @@ class MatrixWrapper : public MatrixBase<MatrixWrapper<ExpressionType> >
                        const Scalar
                      >::type ScalarWithConstIfNotLvalue;
 
-    typedef typename internal::nested<ExpressionType>::type NestedExpressionType;
+    typedef typename internal::ref_selector<ExpressionType>::non_const_type NestedExpressionType;
 
-    inline MatrixWrapper(ExpressionType& a_matrix) : m_expression(a_matrix) {}
+    using Base::coeffRef;
 
+    EIGEN_DEVICE_FUNC
+    explicit inline MatrixWrapper(ExpressionType& matrix) : m_expression(matrix) {}
+
+    EIGEN_DEVICE_FUNC
     inline Index rows() const { return m_expression.rows(); }
+    EIGEN_DEVICE_FUNC
     inline Index cols() const { return m_expression.cols(); }
+    EIGEN_DEVICE_FUNC
     inline Index outerStride() const { return m_expression.outerStride(); }
+    EIGEN_DEVICE_FUNC
     inline Index innerStride() const { return m_expression.innerStride(); }
 
-    inline ScalarWithConstIfNotLvalue* data() { return m_expression.const_cast_derived().data(); }
+    EIGEN_DEVICE_FUNC
+    inline ScalarWithConstIfNotLvalue* data() { return m_expression.data(); }
+    EIGEN_DEVICE_FUNC
     inline const Scalar* data() const { return m_expression.data(); }
 
-    inline CoeffReturnType coeff(Index rowId, Index colId) const
-    {
-      return m_expression.coeff(rowId, colId);
-    }
-
-    inline Scalar& coeffRef(Index rowId, Index colId)
-    {
-      return m_expression.const_cast_derived().coeffRef(rowId, colId);
-    }
-
+    EIGEN_DEVICE_FUNC
     inline const Scalar& coeffRef(Index rowId, Index colId) const
     {
       return m_expression.derived().coeffRef(rowId, colId);
     }
 
-    inline CoeffReturnType coeff(Index index) const
-    {
-      return m_expression.coeff(index);
-    }
-
-    inline Scalar& coeffRef(Index index)
-    {
-      return m_expression.const_cast_derived().coeffRef(index);
-    }
-
+    EIGEN_DEVICE_FUNC
     inline const Scalar& coeffRef(Index index) const
     {
-      return m_expression.const_cast_derived().coeffRef(index);
-    }
-
-    template<int LoadMode>
-    inline const PacketScalar packet(Index rowId, Index colId) const
-    {
-      return m_expression.template packet<LoadMode>(rowId, colId);
-    }
-
-    template<int LoadMode>
-    inline void writePacket(Index rowId, Index colId, const PacketScalar& val)
-    {
-      m_expression.const_cast_derived().template writePacket<LoadMode>(rowId, colId, val);
-    }
-
-    template<int LoadMode>
-    inline const PacketScalar packet(Index index) const
-    {
-      return m_expression.template packet<LoadMode>(index);
-    }
-
-    template<int LoadMode>
-    inline void writePacket(Index index, const PacketScalar& val)
-    {
-      m_expression.const_cast_derived().template writePacket<LoadMode>(index, val);
+      return m_expression.coeffRef(index);
     }
 
+    EIGEN_DEVICE_FUNC
     const typename internal::remove_all<NestedExpressionType>::type& 
     nestedExpression() const 
     {
@@ -250,10 +193,12 @@ class MatrixWrapper : public MatrixBase<MatrixWrapper<ExpressionType> >
 
     /** Forwards the resizing request to the nested expression
       * \sa DenseBase::resize(Index)  */
-    void resize(Index newSize) { m_expression.const_cast_derived().resize(newSize); }
+    EIGEN_DEVICE_FUNC
+    void resize(Index newSize) { m_expression.resize(newSize); }
     /** Forwards the resizing request to the nested expression
       * \sa DenseBase::resize(Index,Index)*/
-    void resize(Index nbRows, Index nbCols) { m_expression.const_cast_derived().resize(nbRows,nbCols); }
+    EIGEN_DEVICE_FUNC
+    void resize(Index rows, Index cols) { m_expression.resize(rows,cols); }
 
   protected:
     NestedExpressionType m_expression;

libs/eigen/Eigen/src/Core/BandMatrix.h

@@ -32,7 +32,7 @@ class BandMatrixBase : public EigenBase<Derived>
     };
     typedef typename internal::traits<Derived>::Scalar Scalar;
     typedef Matrix<Scalar,RowsAtCompileTime,ColsAtCompileTime> DenseMatrixType;
-    typedef typename DenseMatrixType::Index Index;
+    typedef typename DenseMatrixType::StorageIndex StorageIndex;
     typedef typename internal::traits<Derived>::CoefficientsType CoefficientsType;
     typedef EigenBase<Derived> Base;
 
@@ -161,15 +161,15 @@ class BandMatrixBase : public EigenBase<Derived>
   *
   * \brief Represents a rectangular matrix with a banded storage
   *
-  * \param _Scalar Numeric type, i.e. float, double, int
-  * \param Rows Number of rows, or \b Dynamic
-  * \param Cols Number of columns, or \b Dynamic
-  * \param Supers Number of super diagonal
-  * \param Subs Number of sub diagonal
-  * \param _Options A combination of either \b #RowMajor or \b #ColMajor, and of \b #SelfAdjoint
-  *                 The former controls \ref TopicStorageOrders "storage order", and defaults to
-  *                 column-major. The latter controls whether the matrix represents a selfadjoint 
-  *                 matrix in which case either Supers of Subs have to be null.
+  * \tparam _Scalar Numeric type, i.e. float, double, int
+  * \tparam _Rows Number of rows, or \b Dynamic
+  * \tparam _Cols Number of columns, or \b Dynamic
+  * \tparam _Supers Number of super diagonal
+  * \tparam _Subs Number of sub diagonal
+  * \tparam _Options A combination of either \b #RowMajor or \b #ColMajor, and of \b #SelfAdjoint
+  *                  The former controls \ref TopicStorageOrders "storage order", and defaults to
+  *                  column-major. The latter controls whether the matrix represents a selfadjoint
+  *                  matrix in which case either Supers of Subs have to be null.
   *
   * \sa class TridiagonalMatrix
   */
@@ -179,7 +179,7 @@ struct traits<BandMatrix<_Scalar,_Rows,_Cols,_Supers,_Subs,_Options> >
 {
   typedef _Scalar Scalar;
   typedef Dense StorageKind;
-  typedef DenseIndex Index;
+  typedef Eigen::Index StorageIndex;
   enum {
     CoeffReadCost = NumTraits<Scalar>::ReadCost,
     RowsAtCompileTime = _Rows,
@@ -201,10 +201,10 @@ class BandMatrix : public BandMatrixBase<BandMatrix<_Scalar,Rows,Cols,Supers,Sub
   public:
 
     typedef typename internal::traits<BandMatrix>::Scalar Scalar;
-    typedef typename internal::traits<BandMatrix>::Index Index;
+    typedef typename internal::traits<BandMatrix>::StorageIndex StorageIndex;
     typedef typename internal::traits<BandMatrix>::CoefficientsType CoefficientsType;
 
-    inline BandMatrix(Index rows=Rows, Index cols=Cols, Index supers=Supers, Index subs=Subs)
+    explicit inline BandMatrix(Index rows=Rows, Index cols=Cols, Index supers=Supers, Index subs=Subs)
       : m_coeffs(1+supers+subs,cols),
         m_rows(rows), m_supers(supers), m_subs(subs)
     {
@@ -241,7 +241,7 @@ struct traits<BandMatrixWrapper<_CoefficientsType,_Rows,_Cols,_Supers,_Subs,_Opt
 {
   typedef typename _CoefficientsType::Scalar Scalar;
   typedef typename _CoefficientsType::StorageKind StorageKind;
-  typedef typename _CoefficientsType::Index Index;
+  typedef typename _CoefficientsType::StorageIndex StorageIndex;
   enum {
     CoeffReadCost = internal::traits<_CoefficientsType>::CoeffReadCost,
     RowsAtCompileTime = _Rows,
@@ -264,9 +264,9 @@ class BandMatrixWrapper : public BandMatrixBase<BandMatrixWrapper<_CoefficientsT
 
     typedef typename internal::traits<BandMatrixWrapper>::Scalar Scalar;
     typedef typename internal::traits<BandMatrixWrapper>::CoefficientsType CoefficientsType;
-    typedef typename internal::traits<BandMatrixWrapper>::Index Index;
+    typedef typename internal::traits<BandMatrixWrapper>::StorageIndex StorageIndex;
 
-    inline BandMatrixWrapper(const CoefficientsType& coeffs, Index rows=_Rows, Index cols=_Cols, Index supers=_Supers, Index subs=_Subs)
+    explicit inline BandMatrixWrapper(const CoefficientsType& coeffs, Index rows=_Rows, Index cols=_Cols, Index supers=_Supers, Index subs=_Subs)
       : m_coeffs(coeffs),
         m_rows(rows), m_supers(supers), m_subs(subs)
     {
@@ -302,9 +302,9 @@ class BandMatrixWrapper : public BandMatrixBase<BandMatrixWrapper<_CoefficientsT
   *
   * \brief Represents a tridiagonal matrix with a compact banded storage
   *
-  * \param _Scalar Numeric type, i.e. float, double, int
-  * \param Size Number of rows and cols, or \b Dynamic
-  * \param _Options Can be 0 or \b SelfAdjoint
+  * \tparam Scalar Numeric type, i.e. float, double, int
+  * \tparam Size Number of rows and cols, or \b Dynamic
+  * \tparam Options Can be 0 or \b SelfAdjoint
   *
   * \sa class BandMatrix
   */
@@ -312,9 +312,9 @@ template<typename Scalar, int Size, int Options>
 class TridiagonalMatrix : public BandMatrix<Scalar,Size,Size,Options&SelfAdjoint?0:1,1,Options|RowMajor>
 {
     typedef BandMatrix<Scalar,Size,Size,Options&SelfAdjoint?0:1,1,Options|RowMajor> Base;
-    typedef typename Base::Index Index;
+    typedef typename Base::StorageIndex StorageIndex;
   public:
-    TridiagonalMatrix(Index size = Size) : Base(size,size,Options&SelfAdjoint?0:1,1) {}
+    explicit TridiagonalMatrix(Index size = Size) : Base(size,size,Options&SelfAdjoint?0:1,1) {}
 
     inline typename Base::template DiagonalIntReturnType<1>::Type super()
     { return Base::template diagonal<1>(); }
@@ -327,6 +327,25 @@ class TridiagonalMatrix : public BandMatrix<Scalar,Size,Size,Options&SelfAdjoint
   protected:
 };
 
+
+struct BandShape {};
+
+template<typename _Scalar, int _Rows, int _Cols, int _Supers, int _Subs, int _Options>
+struct evaluator_traits<BandMatrix<_Scalar,_Rows,_Cols,_Supers,_Subs,_Options> >
+  : public evaluator_traits_base<BandMatrix<_Scalar,_Rows,_Cols,_Supers,_Subs,_Options> >
+{
+  typedef BandShape Shape;
+};
+
+template<typename _CoefficientsType,int _Rows, int _Cols, int _Supers, int _Subs,int _Options>
+struct evaluator_traits<BandMatrixWrapper<_CoefficientsType,_Rows,_Cols,_Supers,_Subs,_Options> >
+  : public evaluator_traits_base<BandMatrixWrapper<_CoefficientsType,_Rows,_Cols,_Supers,_Subs,_Options> >
+{
+  typedef BandShape Shape;
+};
+
+template<> struct AssignmentKind<DenseShape,BandShape> { typedef EigenBase2EigenBase Kind; };
+
 } // end namespace internal
 
 } // end namespace Eigen

libs/eigen/Eigen/src/Core/BooleanRedux.h

@@ -17,9 +17,10 @@ namespace internal {
 template<typename Derived, int UnrollCount>
 struct all_unroller
 {
+  typedef typename Derived::ExpressionTraits Traits;
   enum {
-    col = (UnrollCount-1) / Derived::RowsAtCompileTime,
-    row = (UnrollCount-1) % Derived::RowsAtCompileTime
+    col = (UnrollCount-1) / Traits::RowsAtCompileTime,
+    row = (UnrollCount-1) % Traits::RowsAtCompileTime
   };
 
   static inline bool run(const Derived &mat)
@@ -43,11 +44,12 @@ struct all_unroller<Derived, Dynamic>
 template<typename Derived, int UnrollCount>
 struct any_unroller
 {
+  typedef typename Derived::ExpressionTraits Traits;
   enum {
-    col = (UnrollCount-1) / Derived::RowsAtCompileTime,
-    row = (UnrollCount-1) % Derived::RowsAtCompileTime
+    col = (UnrollCount-1) / Traits::RowsAtCompileTime,
+    row = (UnrollCount-1) % Traits::RowsAtCompileTime
   };
-
+  
   static inline bool run(const Derived &mat)
   {
     return any_unroller<Derived, UnrollCount-1>::run(mat) || mat.coeff(row, col);
@@ -78,19 +80,19 @@ struct any_unroller<Derived, Dynamic>
 template<typename Derived>
 inline bool DenseBase<Derived>::all() const
 {
+  typedef internal::evaluator<Derived> Evaluator;
   enum {
     unroll = SizeAtCompileTime != Dynamic
-          && CoeffReadCost != Dynamic
-          && NumTraits<Scalar>::AddCost != Dynamic
-          && SizeAtCompileTime * (CoeffReadCost + NumTraits<Scalar>::AddCost) <= EIGEN_UNROLLING_LIMIT
+          && SizeAtCompileTime * (Evaluator::CoeffReadCost + NumTraits<Scalar>::AddCost) <= EIGEN_UNROLLING_LIMIT
   };
+  Evaluator evaluator(derived());
   if(unroll)
-    return internal::all_unroller<Derived, unroll ? int(SizeAtCompileTime) : Dynamic>::run(derived());
+    return internal::all_unroller<Evaluator, unroll ? int(SizeAtCompileTime) : Dynamic>::run(evaluator);
   else
   {
     for(Index j = 0; j < cols(); ++j)
       for(Index i = 0; i < rows(); ++i)
-        if (!coeff(i, j)) return false;
+        if (!evaluator.coeff(i, j)) return false;
     return true;
   }
 }
@@ -102,19 +104,19 @@ inline bool DenseBase<Derived>::all() const
 template<typename Derived>
 inline bool DenseBase<Derived>::any() const
 {
+  typedef internal::evaluator<Derived> Evaluator;
   enum {
     unroll = SizeAtCompileTime != Dynamic
-          && CoeffReadCost != Dynamic
-          && NumTraits<Scalar>::AddCost != Dynamic
-          && SizeAtCompileTime * (CoeffReadCost + NumTraits<Scalar>::AddCost) <= EIGEN_UNROLLING_LIMIT
+          && SizeAtCompileTime * (Evaluator::CoeffReadCost + NumTraits<Scalar>::AddCost) <= EIGEN_UNROLLING_LIMIT
   };
+  Evaluator evaluator(derived());
   if(unroll)
-    return internal::any_unroller<Derived, unroll ? int(SizeAtCompileTime) : Dynamic>::run(derived());
+    return internal::any_unroller<Evaluator, unroll ? int(SizeAtCompileTime) : Dynamic>::run(evaluator);
   else
   {
     for(Index j = 0; j < cols(); ++j)
       for(Index i = 0; i < rows(); ++i)
-        if (coeff(i, j)) return true;
+        if (evaluator.coeff(i, j)) return true;
     return false;
   }
 }
@@ -124,7 +126,7 @@ inline bool DenseBase<Derived>::any() const
   * \sa all(), any()
   */
 template<typename Derived>
-inline typename DenseBase<Derived>::Index DenseBase<Derived>::count() const
+inline Eigen::Index DenseBase<Derived>::count() const
 {
   return derived().template cast<bool>().template cast<Index>().sum();
 }
@@ -136,7 +138,11 @@ inline typename DenseBase<Derived>::Index DenseBase<Derived>::count() const
 template<typename Derived>
 inline bool DenseBase<Derived>::hasNaN() const
 {
+#if EIGEN_COMP_MSVC || (defined __FAST_MATH__)
+  return derived().array().isNaN().any();
+#else
   return !((derived().array()==derived().array()).all());
+#endif
 }
 
 /** \returns true if \c *this contains only finite numbers, i.e., no NaN and no +/-INF values.
@@ -146,7 +152,11 @@ inline bool DenseBase<Derived>::hasNaN() const
 template<typename Derived>
 inline bool DenseBase<Derived>::allFinite() const
 {
+#if EIGEN_COMP_MSVC || (defined __FAST_MATH__)
+  return derived().array().isFinite().all();
+#else
   return !((derived()-derived()).hasNaN());
+#endif
 }
     
 } // end namespace Eigen

libs/eigen/Eigen/src/Core/CMakeLists.txt

-FILE(GLOB Eigen_Core_SRCS "*.h")
-
-INSTALL(FILES
-  ${Eigen_Core_SRCS}
-  DESTINATION ${INCLUDE_INSTALL_DIR}/Eigen/src/Core COMPONENT Devel
-  )
-
-ADD_SUBDIRECTORY(products)
-ADD_SUBDIRECTORY(util)
-ADD_SUBDIRECTORY(arch)