fix some documentation issues

Eigen/src/Cholesky/Cholesky.h

@@ -51,9 +51,10 @@ template<typename MatrixType> class Cholesky
       compute(matrix);
     }
 
+		/** \deprecated */
     inline Part<MatrixType, Lower> matrixL(void) const { return m_matrix; }
 
-    /** \returns true if the matrix is positive definite */
+    /** \deprecated */
     inline bool isPositiveDefinite(void) const { return m_isPositiveDefinite; }
 
     template<typename Derived>
@@ -76,8 +77,7 @@ template<typename MatrixType> class Cholesky
     bool m_isPositiveDefinite;
 };
 
-/** Computes / recomputes the Cholesky decomposition A = LL^* = U^*U of \a matrix
-  */
+/** \deprecated */
 template<typename MatrixType>
 void Cholesky<MatrixType>::compute(const MatrixType& a)
 {
@@ -128,20 +128,7 @@ typename Derived::Eval Cholesky<MatrixType>::solve(const MatrixBase<Derived> &b)
   return x;
 }
 
-/** Computes the solution x of \f$ A x = b \f$ using the current decomposition of A.
-  * The result is stored in \a bAndx
-  *
-  * \returns true in case of success, false otherwise.
-  *
-  * In other words, it computes \f$ b = A^{-1} b \f$ with
-  * \f$ {L^{*}}^{-1} L^{-1} b \f$ from right to left.
-  * \param bAndX stores both the matrix \f$ b \f$ and the result \f$ x \f$
-  *
-  * Example: \include Cholesky_solve.cpp
-  * Output: \verbinclude Cholesky_solve.out
-  *
-  * \sa MatrixBase::cholesky(), Cholesky::solveInPlace()
-  */
+/** \deprecated */
 template<typename MatrixType>
 template<typename RhsDerived, typename ResDerived>
 bool Cholesky<MatrixType>::solve(const MatrixBase<RhsDerived> &b, MatrixBase<ResDerived> *result) const
@@ -151,15 +138,7 @@ bool Cholesky<MatrixType>::solve(const MatrixBase<RhsDerived> &b, MatrixBase<Res
   return solveInPlace((*result) = b);
 }
 
-/** This is the \em in-place version of solve().
-  *
-  * \param bAndX represents both the right-hand side matrix b and result x.
-  *
-  * This version avoids a copy when the right hand side matrix b is not
-  * needed anymore.
-  *
-  * \sa Cholesky::solve(), MatrixBase::cholesky()
-  */
+/** \deprecated */
 template<typename MatrixType>
 template<typename Derived>
 bool Cholesky<MatrixType>::solveInPlace(MatrixBase<Derived> &bAndX) const

Eigen/src/Cholesky/CholeskyWithoutSquareRoot.h

@@ -77,8 +77,7 @@ template<typename MatrixType> class CholeskyWithoutSquareRoot
     bool m_isPositiveDefinite;
 };
 
-/** Compute / recompute the Cholesky decomposition A = L D L^* = U^* D U of \a matrix
-  */
+/** \deprecated */
 template<typename MatrixType>
 void CholeskyWithoutSquareRoot<MatrixType>::compute(const MatrixType& a)
 {
@@ -145,20 +144,7 @@ typename Derived::Eval CholeskyWithoutSquareRoot<MatrixType>::solve(const Matrix
      );
 }
 
-/** Computes the solution x of \f$ A x = b \f$ using the current decomposition of A.
-  * The result is stored in \a bAndx
-  *
-  * \returns true in case of success, false otherwise.
-  *
-  * In other words, it computes \f$ b = A^{-1} b \f$ with
-  * \f$ {L^{*}}^{-1} D^{-1} L^{-1} b \f$ from right to left.
-  * \param bAndX stores both the matrix \f$ b \f$ and the result \f$ x \f$
-  *
-  * Example: \include CholeskyCholeskyWithoutSquareRoot_solve.cpp
-  * Output: \verbinclude CholeskyCholeskyWithoutSquareRoot_solve.out
-  *
-  * \sa CholeskyWithoutSquareRoot::solveInPlace(), MatrixBase::choleskyNoSqrt()
-  */
+/** \deprecated */
 template<typename MatrixType>
 template<typename RhsDerived, typename ResDerived>
 bool CholeskyWithoutSquareRoot<MatrixType>
@@ -170,15 +156,7 @@ bool CholeskyWithoutSquareRoot<MatrixType>
   return solveInPlace(*result);
 }
 
-/** This is the \em in-place version of solve().
-  *
-  * \param bAndX represents both the right-hand side matrix b and result x.
-  *
-  * This version avoids a copy when the right hand side matrix b is not
-  * needed anymore.
-  *
-  * \sa CholeskyWithoutSquareRoot::solve(), MatrixBase::choleskyNoSqrt()
-  */
+/** \deprecated */
 template<typename MatrixType>
 template<typename Derived>
 bool CholeskyWithoutSquareRoot<MatrixType>::solveInPlace(MatrixBase<Derived> &bAndX) const
@@ -193,7 +171,7 @@ bool CholeskyWithoutSquareRoot<MatrixType>::solveInPlace(MatrixBase<Derived> &bA
   return true;
 }
 
-/** \deprecated \cholesky_module
+/** \cholesky_module
   * \deprecated has been renamed ldlt()
   */
 template<typename Derived>

Eigen/src/Cholesky/LDLT.h

@@ -142,16 +142,12 @@ void LDLT<MatrixType>::compute(const MatrixType& a)
 }
 
 /** Computes the solution x of \f$ A x = b \f$ using the current decomposition of A.
-  * The result is stored in \a bAndx
+  * The result is stored in \a result
   *
   * \returns true in case of success, false otherwise.
   *
   * In other words, it computes \f$ b = A^{-1} b \f$ with
   * \f$ {L^{*}}^{-1} D^{-1} L^{-1} b \f$ from right to left.
-  * \param bAndX stores both the matrix \f$ b \f$ and the result \f$ x \f$
-  *
-  * Example: \include LLTLDLT_solve.cpp
-  * Output: \verbinclude LLTLDLT_solve.out
   *
   * \sa LDLT::solveInPlace(), MatrixBase::ldlt()
   */

Eigen/src/Cholesky/LLT.h

@@ -66,6 +66,7 @@ template<typename MatrixType> class LLT
       compute(matrix);
     }
 
+    /** \returns the lower triangular matrix L */
     inline Part<MatrixType, Lower> matrixL(void) const { return m_matrix; }
 
     /** \returns true if the matrix is positive definite */
@@ -129,13 +130,12 @@ void LLT<MatrixType>::compute(const MatrixType& a)
 }
 
 /** Computes the solution x of \f$ A x = b \f$ using the current decomposition of A.
-  * The result is stored in \a bAndx
+  * The result is stored in \a result
   *
   * \returns true in case of success, false otherwise.
   *
   * In other words, it computes \f$ b = A^{-1} b \f$ with
   * \f$ {L^{*}}^{-1} L^{-1} b \f$ from right to left.
-  * \param bAndX stores both the matrix \f$ b \f$ and the result \f$ x \f$
   *
   * Example: \include LLT_solve.cpp
   * Output: \verbinclude LLT_solve.out

doc/QuickStartGuide.dox

@@ -24,6 +24,7 @@ namespace Eigen {
   - \ref TutorialCoreTriangularMatrix
   - \ref TutorialLazyEvaluation
 \n
+
 <hr>
 
 <a href="#" class="top">top</a>\section TutorialCoreGettingStarted Getting started
@@ -256,7 +257,6 @@ scalar product</td><td>\code
 mat3 = mat1 * s1;   mat3 = s1 * mat1;   mat3 *= s1;
 mat3 = mat1 / s1;   mat3 /= s1;\endcode
 </td></tr>
-<tr><td>
 </table>
 
 In Eigen, only traditional mathematical operators can be used right away.
@@ -424,11 +424,13 @@ Read-write access to sub-matrices:</td><td></td><td></td></tr>
 <tr><td>\code
 mat4x4.minor(i,j) = mat3x3;
 mat3x3 = mat4x4.minor(i,j);\endcode
-</td><td>
+</td><td></td><td>
 \link MatrixBase::minor() minor \endlink (read-write)</td>
 </tr>
 </table>
 
+
+
 <a href="#" class="top">top</a>\section TutorialCoreDiagonalMatrices Diagonal matrices
 
 <table class="tutorial_code">

doc/TutorialLinearAlgebra.dox

@@ -2,7 +2,7 @@
 namespace Eigen {
 
 /** \page TutorialAdvancedLinearAlgebra Tutorial 3/3 - Advanced linear algebra
-    \in group Tutorial
+    \ingroup Tutorial
 
 <div class="eimainmenu">\ref index "Overview"
   | \ref TutorialCore "Core features"

doc/eigendoxy.css

@@ -479,6 +479,7 @@ th {
 
 
 TABLE.noborder {
+  border-collapse: separate;
   border-bottom-style : none;
   border-left-style   : none;
   border-right-style  : none;
@@ -499,16 +500,22 @@ TABLE.noborder TD {
 
 table.tutorial_code {
   border-collapse: collapse;
-  empty-cells : show;
+  border-width: 1px;
+  border-style: dotted;
+  border-color: #888888;
+  empty-cells : hide;
   margin: 4pt 0 0 0;
   padding: 0 0 0 0;
 }
 table.tutorial_code tr {
-   border-style: none dashed none dashed;
+   border-style: dashed;
    border-width: 1px;
+   border-color: #888888;
 }
 table.tutorial_code td {
-  border-style: dashed none dashed none;
+  border-style: none dotted none dotted;
+  border-width: 0 1px 0 1px;
+  border-color: transparent;
   empty-cells : show;
   margin: 0 0 0 0;
   padding: 2pt 5pt 2pt 5pt;