Fix numerous doxygen issues in auto-link generation

Eigen/src/CholmodSupport/CholmodSupport.h

@@ -358,7 +358,7 @@ class CholmodBase : public SparseSolverBase<Derived>
   *
   * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; compressed or non compressed.
   *
-  * \sa \ref TutorialSparseDirectSolvers, class CholmodSupernodalLLT, class SimplicialLLT
+  * \sa \ref TutorialSparseSolverConcept, class CholmodSupernodalLLT, class SimplicialLLT
   */
 template<typename _MatrixType, int _UpLo = Lower>
 class CholmodSimplicialLLT : public CholmodBase<_MatrixType, _UpLo, CholmodSimplicialLLT<_MatrixType, _UpLo> >
@@ -407,7 +407,7 @@ class CholmodSimplicialLLT : public CholmodBase<_MatrixType, _UpLo, CholmodSimpl
   *
   * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; compressed or non compressed.
   *
-  * \sa \ref TutorialSparseDirectSolvers, class CholmodSupernodalLLT, class SimplicialLDLT
+  * \sa \ref TutorialSparseSolverConcept, class CholmodSupernodalLLT, class SimplicialLDLT
   */
 template<typename _MatrixType, int _UpLo = Lower>
 class CholmodSimplicialLDLT : public CholmodBase<_MatrixType, _UpLo, CholmodSimplicialLDLT<_MatrixType, _UpLo> >
@@ -454,7 +454,7 @@ class CholmodSimplicialLDLT : public CholmodBase<_MatrixType, _UpLo, CholmodSimp
   *
   * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; compressed or non compressed.
   *
-  * \sa \ref TutorialSparseDirectSolvers
+  * \sa \ref TutorialSparseSolverConcept
   */
 template<typename _MatrixType, int _UpLo = Lower>
 class CholmodSupernodalLLT : public CholmodBase<_MatrixType, _UpLo, CholmodSupernodalLLT<_MatrixType, _UpLo> >
@@ -503,7 +503,7 @@ class CholmodSupernodalLLT : public CholmodBase<_MatrixType, _UpLo, CholmodSuper
   *
   * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; compressed or non compressed.
   *
-  * \sa \ref TutorialSparseDirectSolvers
+  * \sa \ref TutorialSparseSolverConcept
   */
 template<typename _MatrixType, int _UpLo = Lower>
 class CholmodDecomposition : public CholmodBase<_MatrixType, _UpLo, CholmodDecomposition<_MatrixType, _UpLo> >

Eigen/src/Core/CwiseNullaryOp.h

@@ -328,7 +328,7 @@ EIGEN_STRONG_INLINE void DenseBase<Derived>::fill(const Scalar& val)
   setConstant(val);
 }
 
-/** Sets all coefficients in this expression to \a value.
+/** Sets all coefficients in this expression to value \a val.
   *
   * \sa fill(), setConstant(Index,const Scalar&), setConstant(Index,Index,const Scalar&), setZero(), setOnes(), Constant(), class CwiseNullaryOp, setZero(), setOnes()
   */
@@ -338,7 +338,7 @@ EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setConstant(const Scalar& val)
   return derived() = Constant(rows(), cols(), val);
 }
 
-/** Resizes to the given \a size, and sets all coefficients in this expression to the given \a value.
+/** Resizes to the given \a size, and sets all coefficients in this expression to the given value \a val.
   *
   * \only_for_vectors
   *
@@ -355,7 +355,7 @@ PlainObjectBase<Derived>::setConstant(Index size, const Scalar& val)
   return setConstant(val);
 }
 
-/** Resizes to the given size, and sets all coefficients in this expression to the given \a value.
+/** Resizes to the given size, and sets all coefficients in this expression to the given value \a val.
   *
   * \param rows the new number of rows
   * \param cols the new number of columns

Eigen/src/Core/Dot.h

@@ -82,7 +82,7 @@ MatrixBase<Derived>::dot(const MatrixBase<OtherDerived>& other) const
   * In both cases, it consists in the sum of the square of all the matrix entries.
   * For vectors, this is also equals to the dot product of \c *this with itself.
   *
-  * \sa dot(), norm()
+  * \sa dot(), norm(), lpNorm()
   */
 template<typename Derived>
 EIGEN_STRONG_INLINE typename NumTraits<typename internal::traits<Derived>::Scalar>::Real MatrixBase<Derived>::squaredNorm() const
@@ -94,7 +94,7 @@ EIGEN_STRONG_INLINE typename NumTraits<typename internal::traits<Derived>::Scala
   * In both cases, it consists in the square root of the sum of the square of all the matrix entries.
   * For vectors, this is also equals to the square root of the dot product of \c *this with itself.
   *
-  * \sa dot(), squaredNorm()
+  * \sa lpNorm(), dot(), squaredNorm()
   */
 template<typename Derived>
 inline typename NumTraits<typename internal::traits<Derived>::Scalar>::Real MatrixBase<Derived>::norm() const
@@ -188,7 +188,11 @@ struct lpNorm_selector<Derived, Infinity>
   */
 template<typename Derived>
 template<int p>
+#ifndef EIGEN_PARSED_BY_DOXYGEN
 inline typename NumTraits<typename internal::traits<Derived>::Scalar>::Real
+#else
+MatrixBase<Derived>::RealScalar
+#endif
 MatrixBase<Derived>::lpNorm() const
 {
   return internal::lpNorm_selector<Derived, p>::run(*this);

Eigen/src/Core/MatrixBase.h

@@ -386,7 +386,11 @@ template<typename Derived> class MatrixBase
     #endif // EIGEN_PARSED_BY_DOXYGEN
     template<typename OtherDerived>
     EIGEN_DEVICE_FUNC
+#ifndef EIGEN_PARSED_BY_DOXYGEN
     inline typename cross_product_return_type<OtherDerived>::type
+#else
+    inline PlainObject
+#endif
     cross(const MatrixBase<OtherDerived>& other) const;
     
     template<typename OtherDerived>

Eigen/src/Core/PlainObjectBase.h

@@ -533,7 +533,7 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
 
   public:
 
-    /** \copydoc MatrixBase::operator=(const EigenBase<OtherDerived>&)
+    /** \copydoc DenseBase::operator=(const EigenBase<OtherDerived>&)
       */
     template<typename OtherDerived>
     EIGEN_DEVICE_FUNC 
@@ -618,8 +618,8 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
     //@}
 
     using Base::setConstant;
-    EIGEN_DEVICE_FUNC Derived& setConstant(Index size, const Scalar& value);
-    EIGEN_DEVICE_FUNC Derived& setConstant(Index rows, Index cols, const Scalar& value);
+    EIGEN_DEVICE_FUNC Derived& setConstant(Index size, const Scalar& val);
+    EIGEN_DEVICE_FUNC Derived& setConstant(Index rows, Index cols, const Scalar& val);
 
     using Base::setZero;
     EIGEN_DEVICE_FUNC Derived& setZero(Index size);

Eigen/src/Core/util/Constants.h

@@ -224,7 +224,7 @@ enum {
 
 /** \ingroup enums
   * Enum for indicating whether a buffer is aligned or not. */
-enum { 
+enum Foo {
   Unaligned=0,        /**< Data pointer has no specific alignment. */
   Aligned8=8,         /**< Data pointer is aligned on a 8 bytes boundary. */
   Aligned16=16,       /**< Data pointer is aligned on a 16 bytes boundary. */

Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h

@@ -228,6 +228,7 @@ template<typename _MatrixType> class SelfAdjointEigenSolver
       *
       * \param[in] diag The vector containing the diagonal of the matrix.
       * \param[in] subdiag The subdiagonal of the matrix.
+      * \param[in] options Can be #ComputeEigenvectors (default) or #EigenvaluesOnly.
       * \returns Reference to \c *this
       *
       * This function assumes that the matrix has been reduced to tridiagonal form.
@@ -299,8 +300,7 @@ template<typename _MatrixType> class SelfAdjointEigenSolver
       * Example: \include SelfAdjointEigenSolver_operatorSqrt.cpp
       * Output: \verbinclude SelfAdjointEigenSolver_operatorSqrt.out
       *
-      * \sa operatorInverseSqrt(),
-      *     \ref MatrixFunctions_Module "MatrixFunctions Module"
+      * \sa operatorInverseSqrt(), <a href="unsupported/group__MatrixFunctions__Module.html">MatrixFunctions Module</a>
       */
     EIGEN_DEVICE_FUNC
     MatrixType operatorSqrt() const
@@ -325,8 +325,7 @@ template<typename _MatrixType> class SelfAdjointEigenSolver
       * Example: \include SelfAdjointEigenSolver_operatorInverseSqrt.cpp
       * Output: \verbinclude SelfAdjointEigenSolver_operatorInverseSqrt.out
       *
-      * \sa operatorSqrt(), MatrixBase::inverse(),
-      *     \ref MatrixFunctions_Module "MatrixFunctions Module"
+      * \sa operatorSqrt(), MatrixBase::inverse(), <a href="unsupported/group__MatrixFunctions__Module.html">MatrixFunctions Module</a>
       */
     EIGEN_DEVICE_FUNC
     MatrixType operatorInverseSqrt() const

Eigen/src/Geometry/Homogeneous.h

@@ -112,7 +112,7 @@ template<typename MatrixType,int _Direction> class Homogeneous
     typename MatrixType::Nested m_matrix;
 };
 
-/** \geometry_module
+/** \geometry_module \ingroup Geometry_Module
   *
   * \return an expression of the equivalent homogeneous vector
   *
@@ -131,7 +131,7 @@ MatrixBase<Derived>::homogeneous() const
   return HomogeneousReturnType(derived());
 }
 
-/** \geometry_module
+/** \geometry_module \ingroup Geometry_Module
   *
   * \returns a matrix expression of homogeneous column (or row) vectors
   *
@@ -146,7 +146,7 @@ VectorwiseOp<ExpressionType,Direction>::homogeneous() const
   return HomogeneousReturnType(_expression());
 }
 
-/** \geometry_module
+/** \geometry_module \ingroup Geometry_Module
   *
   * \returns an expression of the homogeneous normalized vector of \c *this
   *
@@ -164,7 +164,7 @@ MatrixBase<Derived>::hnormalized() const
     ColsAtCompileTime==1?1:size()-1) / coeff(size()-1);
 }
 
-/** \geometry_module
+/** \geometry_module \ingroup Geometry_Module
   *
   * \returns an expression of the homogeneous normalized vector of \c *this
   *

Eigen/src/Geometry/OrthoMethods.h

@@ -13,7 +13,7 @@
 
 namespace Eigen { 
 
-/** \geometry_module
+/** \geometry_module \ingroup Geometry_Module
   *
   * \returns the cross product of \c *this and \a other
   *
@@ -26,7 +26,11 @@ namespace Eigen {
   */
 template<typename Derived>
 template<typename OtherDerived>
+#ifndef EIGEN_PARSED_BY_DOXYGEN
 inline typename MatrixBase<Derived>::template cross_product_return_type<OtherDerived>::type
+#else
+inline typename MatrixBase<Derived>::PlainObject
+#endif
 MatrixBase<Derived>::cross(const MatrixBase<OtherDerived>& other) const
 {
   EIGEN_STATIC_ASSERT_VECTOR_SPECIFIC_SIZE(Derived,3)
@@ -63,7 +67,7 @@ struct cross3_impl {
 
 }
 
-/** \geometry_module
+/** \geometry_module \ingroup Geometry_Module
   *
   * \returns the cross product of \c *this and \a other using only the x, y, and z coefficients
   *
@@ -90,14 +94,14 @@ MatrixBase<Derived>::cross3(const MatrixBase<OtherDerived>& other) const
                         typename internal::remove_all<OtherDerivedNested>::type>::run(lhs,rhs);
 }
 
-/** \returns a matrix expression of the cross product of each column or row
+/** \geometry_module \ingroup Geometry_Module
+  *
+  * \returns a matrix expression of the cross product of each column or row
   * of the referenced expression with the \a other vector.
   *
   * The referenced matrix must have one dimension equal to 3.
   * The result matrix has the same dimensions than the referenced one.
   *
-  * \geometry_module
-  *
   * \sa MatrixBase::cross() */
 template<typename ExpressionType, int Direction>
 template<typename OtherDerived>
@@ -207,7 +211,9 @@ struct unitOrthogonal_selector<Derived,2>
 
 } // end namespace internal
 
-/** \returns a unit vector which is orthogonal to \c *this
+/** \geometry_module \ingroup Geometry_Module
+  *
+  * \returns a unit vector which is orthogonal to \c *this
   *
   * The size of \c *this must be at least 2. If the size is exactly 2,
   * then the returned vector is a counter clock wise rotation of \c *this, i.e., (-y,x).normalized().

Eigen/src/Geometry/Scaling.h

@@ -104,6 +104,9 @@ public:
 
 };
 
+/** \addtogroup Geometry_Module */
+//@{
+
 /** Concatenates a linear transformation matrix and a uniform scaling */
 // NOTE this operator is defiend in MatrixBase and not as a friend function
 // of UniformScaling to fix an internal crash of Intel's ICC
@@ -136,8 +139,6 @@ template<typename Derived>
 static inline const DiagonalWrapper<const Derived> Scaling(const MatrixBase<Derived>& coeffs)
 { return coeffs.asDiagonal(); }
 
-/** \addtogroup Geometry_Module */
-//@{
 /** \deprecated */
 typedef DiagonalMatrix<float, 2> AlignedScaling2f;
 /** \deprecated */

Eigen/src/PaStiXSupport/PaStiXSupport.h

@@ -405,7 +405,7 @@ bool PastixBase<Base>::_solve_impl(const MatrixBase<Rhs> &b, MatrixBase<Dest> &x
   *
   * \implsparsesolverconcept
   *
-  * \sa \ref TutorialSparseDirectSolvers
+  * \sa \ref TutorialSparseSolverConcept, class SparseLU
   * 
   */
 template<typename _MatrixType, bool IsStrSym>
@@ -518,7 +518,7 @@ class PastixLU : public PastixBase< PastixLU<_MatrixType> >
   *
   * \implsparsesolverconcept
   *
-  * \sa \ref TutorialSparseDirectSolvers
+  * \sa \ref TutorialSparseSolverConcept, class SimplicialLLT
   */
 template<typename _MatrixType, int _UpLo>
 class PastixLLT : public PastixBase< PastixLLT<_MatrixType, _UpLo> >
@@ -601,7 +601,7 @@ class PastixLLT : public PastixBase< PastixLLT<_MatrixType, _UpLo> >
   *
   * \implsparsesolverconcept
   *
-  * \sa \ref TutorialSparseDirectSolvers
+  * \sa \ref TutorialSparseSolverConcept, class SimplicialLDLT
   */
 template<typename _MatrixType, int _UpLo>
 class PastixLDLT : public PastixBase< PastixLDLT<_MatrixType, _UpLo> >

Eigen/src/PardisoSupport/PardisoSupport.h

@@ -375,7 +375,7 @@ void PardisoImpl<Derived>::_solve_impl(const MatrixBase<BDerived> &b, MatrixBase
   *
   * \implsparsesolverconcept
   *
-  * \sa \ref TutorialSparseDirectSolvers
+  * \sa \ref TutorialSparseSolverConcept, class SparseLU
   */
 template<typename MatrixType>
 class PardisoLU : public PardisoImpl< PardisoLU<MatrixType> >
@@ -427,7 +427,7 @@ class PardisoLU : public PardisoImpl< PardisoLU<MatrixType> >
   *
   * \implsparsesolverconcept
   *
-  * \sa \ref TutorialSparseDirectSolvers
+  * \sa \ref TutorialSparseSolverConcept, class SimplicialLLT
   */
 template<typename MatrixType, int _UpLo>
 class PardisoLLT : public PardisoImpl< PardisoLLT<MatrixType,_UpLo> >
@@ -487,7 +487,7 @@ class PardisoLLT : public PardisoImpl< PardisoLLT<MatrixType,_UpLo> >
   *
   * \implsparsesolverconcept
   *
-  * \sa \ref TutorialSparseDirectSolvers
+  * \sa \ref TutorialSparseSolverConcept, class SimplicialLDLT
   */
 template<typename MatrixType, int Options>
 class PardisoLDLT : public PardisoImpl< PardisoLDLT<MatrixType,Options> >

Eigen/src/SVD/SVDBase.h

@@ -42,7 +42,7 @@ namespace Eigen {
  *  
  * If the input matrix has inf or nan coefficients, the result of the computation is undefined, but the computation is guaranteed to
  * terminate in finite (and reasonable) time.
- * \sa MatrixBase::genericSvd()
+ * \sa class BDCSVD, class JacobiSVD
  */
 template<typename Derived>
 class SVDBase
@@ -74,7 +74,7 @@ public:
   /** \returns the \a U matrix.
    *
    * For the SVD decomposition of a n-by-p matrix, letting \a m be the minimum of \a n and \a p,
-   * the U matrix is n-by-n if you asked for #ComputeFullU, and is n-by-m if you asked for #ComputeThinU.
+   * the U matrix is n-by-n if you asked for \link Eigen::ComputeFullU ComputeFullU \endlink, and is n-by-m if you asked for \link Eigen::ComputeThinU ComputeThinU \endlink.
    *
    * The \a m first columns of \a U are the left singular vectors of the matrix being decomposed.
    *
@@ -90,7 +90,7 @@ public:
   /** \returns the \a V matrix.
    *
    * For the SVD decomposition of a n-by-p matrix, letting \a m be the minimum of \a n and \a p,
-   * the V matrix is p-by-p if you asked for #ComputeFullV, and is p-by-m if you asked for ComputeThinV.
+   * the V matrix is p-by-p if you asked for \link Eigen::ComputeFullV ComputeFullV \endlink, and is p-by-m if you asked for \link Eigen::ComputeThinV ComputeThinV \endlink.
    *
    * The \a m first columns of \a V are the right singular vectors of the matrix being decomposed.
    *

Eigen/src/SparseCore/SparseRef.h

@@ -13,7 +13,7 @@
 namespace Eigen {
 
 enum {
-  StandardCompressedFormat = 2
+  StandardCompressedFormat = 2 /**< used by Ref<SparseMatrix> to specify whether the input storage must be in standard compressed form */
 };
   
 namespace internal {

Eigen/src/SparseLU/SparseLU.h

@@ -67,7 +67,7 @@ template <typename MatrixLType, typename MatrixUType> struct SparseLUMatrixURetu
   *
   * \implsparsesolverconcept
   * 
-  * \sa \ref TutorialSparseDirectSolvers
+  * \sa \ref TutorialSparseSolverConcept
   * \sa \ref OrderingMethods_Module
   */
 template <typename _MatrixType, typename _OrderingType>

Eigen/src/SuperLUSupport/SuperLUSupport.h

@@ -456,7 +456,7 @@ class SuperLUBase : public SparseSolverBase<Derived>
   *
   * \implsparsesolverconcept
   *
-  * \sa \ref TutorialSparseDirectSolvers
+  * \sa \ref TutorialSparseSolverConcept, class SparseLU
   */
 template<typename _MatrixType>
 class SuperLU : public SuperLUBase<_MatrixType,SuperLU<_MatrixType> >
@@ -809,7 +809,7 @@ typename SuperLU<MatrixType>::Scalar SuperLU<MatrixType>::determinant() const
   *
   * \implsparsesolverconcept
   *
-  * \sa \ref TutorialSparseDirectSolvers, class ConjugateGradient, class BiCGSTAB
+  * \sa \ref TutorialSparseSolverConcept, class IncompleteLUT, class ConjugateGradient, class BiCGSTAB
   */
 
 template<typename _MatrixType>

Eigen/src/UmfPackSupport/UmfPackSupport.h

@@ -126,7 +126,9 @@ inline int umfpack_get_determinant(std::complex<double> *Mx, double *Ex, void *N
   * Otherwise an expensive copy will be made. You can call the inexpensive makeCompressed() to get a compressed matrix.
   * \tparam _MatrixType the type of the sparse matrix A, it must be a SparseMatrix<>
   *
-  * \sa \ref TutorialSparseDirectSolvers
+  * \implsparsesolverconcept
+  *
+  * \sa \ref TutorialSparseSolverConcept, class SparseLU
   */
 template<typename _MatrixType>
 class UmfPackLU : public SparseSolverBase<UmfPackLU<_MatrixType> >