Fix and workaround several doxygen issues/warnings

Eigen/src/Core/Dot.h

@@ -51,7 +51,8 @@ struct dot_nocheck<T, U, true>
 
 } // end namespace internal
 
-/** \returns the dot product of *this with other.
+/** \fn MatrixBase::dot
+  * \returns the dot product of *this with other.
   *
   * \only_for_vectors
   *

Eigen/src/Core/PlainObjectBase.h

@@ -560,7 +560,8 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
 
   public:
 
-    /** \copydoc DenseBase::operator=(const EigenBase<OtherDerived>&)
+    /** \brief Copies the generic expression \a other into *this.
+      * \copydetails DenseBase::operator=(const EigenBase<OtherDerived> &other)
       */
     template<typename OtherDerived>
     EIGEN_DEVICE_FUNC 

Eigen/src/Core/SolveTriangular.h

@@ -161,6 +161,7 @@ struct triangular_solver_selector<Lhs,Rhs,OnTheRight,Mode,CompleteUnrolling,1> {
 * TriangularView methods
 ***************************************************************************/
 
+#ifndef EIGEN_PARSED_BY_DOXYGEN
 template<typename MatrixType, unsigned int Mode>
 template<int Side, typename OtherDerived>
 void TriangularViewImpl<MatrixType,Mode,Dense>::solveInPlace(const MatrixBase<OtherDerived>& _other) const
@@ -188,6 +189,7 @@ TriangularViewImpl<Derived,Mode,Dense>::solve(const MatrixBase<Other>& other) co
 {
   return internal::triangular_solve_retval<Side,TriangularViewType,Other>(derived(), other.derived());
 }
+#endif
 
 namespace internal {
 

Eigen/src/Core/TriangularMatrix.h

@@ -470,6 +470,8 @@ template<typename _MatrixType, unsigned int _Mode> class TriangularViewImpl<_Mat
       * \a Side==OnTheLeft (the default), or the right-inverse-multiply  \a other * inverse(\c *this) if
       * \a Side==OnTheRight.
       *
+      * Note that the template parameter \c Side can be ommitted, in which case \c Side==OnTheLeft
+      *
       * The matrix \c *this must be triangular and invertible (i.e., all the coefficients of the
       * diagonal must be non zero). It works as a forward (resp. backward) substitution if \c *this
       * is an upper (resp. lower) triangular matrix.
@@ -495,6 +497,8 @@ template<typename _MatrixType, unsigned int _Mode> class TriangularViewImpl<_Mat
       * \warning The parameter is only marked 'const' to make the C++ compiler accept a temporary expression here.
       * This function will const_cast it, so constness isn't honored here.
       *
+      * Note that the template parameter \c Side can be ommitted, in which case \c Side==OnTheLeft
+      *
       * See TriangularView:solve() for the details.
       */
     template<int Side, typename OtherDerived>
@@ -546,6 +550,7 @@ template<typename _MatrixType, unsigned int _Mode> class TriangularViewImpl<_Mat
 * Implementation of triangular evaluation/assignment
 ***************************************************************************/
 
+#ifndef EIGEN_PARSED_BY_DOXYGEN
 // FIXME should we keep that possibility
 template<typename MatrixType, unsigned int Mode>
 template<typename OtherDerived>
@@ -583,6 +588,7 @@ void TriangularViewImpl<MatrixType, Mode, Dense>::lazyAssign(const TriangularBas
   eigen_assert(Mode == int(OtherDerived::Mode));
   internal::call_assignment_no_alias(derived(), other.derived());
 }
+#endif
 
 /***************************************************************************
 * Implementation of TriangularBase methods

Eigen/src/Core/Visitor.h

@@ -194,7 +194,8 @@ struct functor_traits<max_coeff_visitor<Scalar> > {
 
 } // end namespace internal
 
-/** \returns the minimum of all coefficients of *this and puts in *row and *col its location.
+/** \fn DenseBase<Derived>::minCoeff(IndexType* rowId, IndexType* colId) const
+  * \returns the minimum of all coefficients of *this and puts in *row and *col its location.
   * \warning the result is undefined if \c *this contains NaN.
   *
   * \sa DenseBase::minCoeff(Index*), DenseBase::maxCoeff(Index*,Index*), DenseBase::visit(), DenseBase::minCoeff()
@@ -230,7 +231,8 @@ DenseBase<Derived>::minCoeff(IndexType* index) const
   return minVisitor.res;
 }
 
-/** \returns the maximum of all coefficients of *this and puts in *row and *col its location.
+/** \fn DenseBase<Derived>::maxCoeff(IndexType* rowId, IndexType* colId) const
+  * \returns the maximum of all coefficients of *this and puts in *row and *col its location.
   * \warning the result is undefined if \c *this contains NaN. 
   *
   * \sa DenseBase::minCoeff(IndexType*,IndexType*), DenseBase::visit(), DenseBase::maxCoeff()

Eigen/src/QR/CompleteOrthogonalDecomposition.h

@@ -138,7 +138,7 @@ class CompleteOrthogonalDecomposition {
    * problem \f[\mathrm{minimize} \|A X - B\|, \f] where \b A is the matrix of
    * which \c *this is the complete orthogonal decomposition.
    *
-   * \param B the right-hand sides of the problem to solve.
+   * \param b the right-hand sides of the problem to solve.
    *
    * \returns a solution.
    *

Eigen/src/SparseCore/TriangularSolver.h

@@ -171,6 +171,8 @@ struct sparse_solve_triangular_selector<Lhs,Rhs,Mode,Upper,ColMajor>
 
 } // end namespace internal
 
+#ifndef EIGEN_PARSED_BY_DOXYGEN
+
 template<typename ExpressionType,unsigned int Mode>
 template<typename OtherDerived>
 void TriangularViewImpl<ExpressionType,Mode,Sparse>::solveInPlace(MatrixBase<OtherDerived>& other) const
@@ -189,6 +191,7 @@ void TriangularViewImpl<ExpressionType,Mode,Sparse>::solveInPlace(MatrixBase<Oth
   if (copy)
     other = otherCopy;
 }
+#endif
 
 // pure sparse path
 
@@ -286,6 +289,7 @@ struct sparse_solve_triangular_sparse_selector<Lhs,Rhs,Mode,UpLo,ColMajor>
 
 } // end namespace internal
 
+#ifndef EIGEN_PARSED_BY_DOXYGEN
 template<typename ExpressionType,unsigned int Mode>
 template<typename OtherDerived>
 void TriangularViewImpl<ExpressionType,Mode,Sparse>::solveInPlace(SparseMatrixBase<OtherDerived>& other) const
@@ -304,6 +308,7 @@ void TriangularViewImpl<ExpressionType,Mode,Sparse>::solveInPlace(SparseMatrixBa
 //   if (copy)
 //     other = otherCopy;
 }
+#endif
 
 } // end namespace Eigen
 

Eigen/src/SuperLUSupport/SuperLUSupport.h

@@ -967,6 +967,7 @@ void SuperILU<MatrixType>::factorize(const MatrixType& a)
   m_factorizationIsOk = true;
 }
 
+#ifndef EIGEN_PARSED_BY_DOXYGEN
 template<typename MatrixType>
 template<typename Rhs,typename Dest>
 void SuperILU<MatrixType>::_solve_impl(const MatrixBase<Rhs> &b, MatrixBase<Dest>& x) const
@@ -1019,6 +1020,8 @@ void SuperILU<MatrixType>::_solve_impl(const MatrixBase<Rhs> &b, MatrixBase<Dest
 }
 #endif
 
+#endif
+
 } // end namespace Eigen
 
 #endif // EIGEN_SUPERLUSUPPORT_H

Eigen/src/plugins/BlockMethods.h

@@ -818,7 +818,7 @@ inline typename FixedBlockXpr<NRows,NCols>::Type block(Index startRow, Index sta
   return typename FixedBlockXpr<NRows,NCols>::Type(derived(), startRow, startCol, blockRows, blockCols);
 }
 
-/// This is the const version of block<>(Index, Index, Index, Index). */
+/// This is the const version of block<>(Index, Index, Index, Index).
 template<int NRows, int NCols>
 inline const typename ConstFixedBlockXpr<NRows,NCols>::Type block(Index startRow, Index startCol,
                                                               Index blockRows, Index blockCols) const
@@ -832,15 +832,15 @@ inline const typename ConstFixedBlockXpr<NRows,NCols>::Type block(Index startRow
 /// Output: \verbinclude MatrixBase_col.out
 ///
 EIGEN_DOC_BLOCK_ADDONS_INNER_PANEL_IF(column-major)
-///
+/**
-/// \sa row(), class Block */
+  * \sa row(), class Block */
 EIGEN_DEVICE_FUNC
 inline ColXpr col(Index i)
 {
   return ColXpr(derived(), i);
 }
 
-/// This is the const version of col(). */
+/// This is the const version of col().
 EIGEN_DEVICE_FUNC
 inline ConstColXpr col(Index i) const
 {
@@ -853,8 +853,8 @@ inline ConstColXpr col(Index i) const
 /// Output: \verbinclude MatrixBase_row.out
 ///
 EIGEN_DOC_BLOCK_ADDONS_INNER_PANEL_IF(row-major)
-///
+/**
-/// \sa col(), class Block */
+  * \sa col(), class Block */
 EIGEN_DEVICE_FUNC
 inline RowXpr row(Index i)
 {

doc/CoeffwiseMathFunctionsTable.dox

@@ -366,7 +366,7 @@ This also means that, unless specified, if the function \c std::foo is available
 <tr>
   <td class="code">
   \anchor cwisetable_isfinite
-  a.\link ArrayBase::isfinite isfinite\endlink(); \n
+  a.\link ArrayBase::isFinite isFinite\endlink(); \n
   \link Eigen::isfinite isfinite\endlink(a);
   </td>
   <td>checks if the given number has finite value</td>
@@ -377,7 +377,7 @@ This also means that, unless specified, if the function \c std::foo is available
 <tr>
   <td class="code">
   \anchor cwisetable_isinf
-  a.\link ArrayBase::isinf isinf\endlink(); \n
+  a.\link ArrayBase::isInf isInf\endlink(); \n
   \link Eigen::isinf isinf\endlink(a);
   </td>
   <td>checks if the given number is infinite</td>
@@ -388,7 +388,7 @@ This also means that, unless specified, if the function \c std::foo is available
 <tr>
   <td class="code">
   \anchor cwisetable_isnan
-  a.\link ArrayBase::isnan isnan\endlink(); \n
+  a.\link ArrayBase::isNaN isNaN\endlink(); \n
   \link Eigen::isnan isnan\endlink(a);
   </td>
   <td>checks if the given number is not a number</td>
@@ -399,7 +399,7 @@ This also means that, unless specified, if the function \c std::foo is available
 <tr>
 <th colspan="4">Error and gamma functions</th>
 </tr>
-<tr> <td colspan="4">  Require \c #include \c <unsupported/Eigen/SpecialFunctions> </td></tr>
+<tr> <td colspan="4">  Require \c \#include \c <unsupported/Eigen/SpecialFunctions> </td></tr>
 <tr>
   <td class="code">
   \anchor cwisetable_erf
@@ -478,7 +478,7 @@ This also means that, unless specified, if the function \c std::foo is available
 <tr>
 <th colspan="4">Special functions</th>
 </tr>
-<tr> <td colspan="4">  Require \c #include \c <unsupported/Eigen/SpecialFunctions> </td></tr>
+<tr> <td colspan="4">  Require \c \#include \c <unsupported/Eigen/SpecialFunctions> </td></tr>
 <tr>
   <td class="code">
   \anchor cwisetable_polygamma
@@ -522,4 +522,4 @@ This also means that, unless specified, if the function \c std::foo is available
 
 */
 
-}
+}

doc/Doxyfile.in

@@ -727,7 +727,8 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = "${Eigen_SOURCE_DIR}/Eigen/Eigen2Support" \
+EXCLUDE                = "${Eigen_SOURCE_DIR}/Eigen/src/Core/products" \
+                         "${Eigen_SOURCE_DIR}/Eigen/Eigen2Support" \
                          "${Eigen_SOURCE_DIR}/Eigen/src/Eigen2Support" \
                          "${Eigen_SOURCE_DIR}/doc/examples" \
                          "${Eigen_SOURCE_DIR}/doc/special_examples" \

doc/PreprocessorDirectives.dox

@@ -129,7 +129,7 @@ run time. However, these assertions do cost time and can thus be turned off.
 \section TopicPreprocessorDirectivesPlugins Plugins
 
 It is possible to add new methods to many fundamental classes in %Eigen by writing a plugin. As explained in
-the section \ref ExtendingMatrixBase, the plugin is specified by defining a \c EIGEN_xxx_PLUGIN macro. The
+the section \ref TopicCustomizing_Plugins, the plugin is specified by defining a \c EIGEN_xxx_PLUGIN macro. The
 following macros are supported; none of them are defined by default.
 
  - \b EIGEN_ARRAY_PLUGIN - filename of plugin for extending the Array class.

doc/QuickReference.dox

@@ -340,7 +340,7 @@ mat1 = mat2.adjoint();        mat1.adjointInPlace();
 \endcode
 </td></tr>
 <tr><td>
-\link MatrixBase::dot() dot \endlink product \n inner product \matrixworld</td><td>\code
+\link MatrixBase::dot dot \endlink product \n inner product \matrixworld</td><td>\code
 scalar = vec1.dot(vec2);
 scalar = col1.adjoint() * col2;
 scalar = (col1.adjoint() * col2).value();\endcode