Fix most Doxygen warnings. Also add links to stable documentation from unsupported modules (by using the corresponding Doxytags file).

Eigen/src/Core/MatrixBase.h

@@ -444,16 +444,24 @@ template<typename Derived> class MatrixBase
 ///////// MatrixFunctions module /////////
 
     typedef typename internal::stem_function<Scalar>::type StemFunction;
-    const MatrixExponentialReturnValue<Derived> exp() const;
+#define EIGEN_MATRIX_FUNCTION(ReturnType, Name, Description) \
+    /** \returns an expression of the matrix Description of \c *this. \brief This function requires the <a href="unsupported/group__MatrixFunctions__Module.html"> unsupported MatrixFunctions module</a>. To compute the coefficient-wise Description use ArrayBase::##Name . */ \
+    const ReturnType<Derived> Name() const;
+#define EIGEN_MATRIX_FUNCTION_1(ReturnType, Name, Description, Argument) \
+    /** \returns an expression of the matrix Description of \c *this. \brief This function requires the <a href="unsupported/group__MatrixFunctions__Module.html"> unsupported MatrixFunctions module</a>. To compute the coefficient-wise Description use ArrayBase::##Name . */ \
+    const ReturnType<Derived> Name(Argument) const;
+
+    EIGEN_MATRIX_FUNCTION(MatrixExponentialReturnValue, exp, exponential)
+    /** \brief Helper function for the <a href="unsupported/group__MatrixFunctions__Module.html"> unsupported MatrixFunctions module</a>.*/
     const MatrixFunctionReturnValue<Derived> matrixFunction(StemFunction f) const;
-    const MatrixFunctionReturnValue<Derived> cosh() const;
+    EIGEN_MATRIX_FUNCTION(MatrixFunctionReturnValue, cosh, hyperbolic cosine)
-    const MatrixFunctionReturnValue<Derived> sinh() const;
+    EIGEN_MATRIX_FUNCTION(MatrixFunctionReturnValue, sinh, hyperbolic sine)
-    const MatrixFunctionReturnValue<Derived> cos() const;
+    EIGEN_MATRIX_FUNCTION(MatrixFunctionReturnValue, cos, cosine)
-    const MatrixFunctionReturnValue<Derived> sin() const;
+    EIGEN_MATRIX_FUNCTION(MatrixFunctionReturnValue, sin, sine)
-    const MatrixSquareRootReturnValue<Derived> sqrt() const;
+    EIGEN_MATRIX_FUNCTION(MatrixSquareRootReturnValue, sqrt, square root)
-    const MatrixLogarithmReturnValue<Derived> log() const;
+    EIGEN_MATRIX_FUNCTION(MatrixLogarithmReturnValue, log, logarithm)
-    const MatrixPowerReturnValue<Derived> pow(const RealScalar& p) const;
+    EIGEN_MATRIX_FUNCTION_1(MatrixPowerReturnValue,        pow, power to \c p, const RealScalar& p)
-    const MatrixComplexPowerReturnValue<Derived> pow(const std::complex<RealScalar>& p) const;
+    EIGEN_MATRIX_FUNCTION_1(MatrixComplexPowerReturnValue, pow, power to \c p, const std::complex<RealScalar>& p)
 
   protected:
     EIGEN_DEVICE_FUNC MatrixBase() : Base() {}

doc/CMakeLists.txt

@@ -34,8 +34,8 @@ set(EIGEN_DOXY_PROJECT_NAME             "Eigen-unsupported")
 set(EIGEN_DOXY_OUTPUT_DIRECTORY_SUFFIX  "/unsupported")
 set(EIGEN_DOXY_INPUT                    "\"${Eigen_SOURCE_DIR}/unsupported/Eigen\" \"${Eigen_SOURCE_DIR}/unsupported/doc\"")
 set(EIGEN_DOXY_HTML_COLORSTYLE_HUE      "0")
-# set(EIGEN_DOXY_TAGFILES                 "\"${Eigen_BINARY_DIR}/doc/eigen.doxytags =../\"")
+set(EIGEN_DOXY_TAGFILES                 "\"${Eigen_BINARY_DIR}/doc/Eigen.doxytags=..\"")
-set(EIGEN_DOXY_TAGFILES                 "")
+#set(EIGEN_DOXY_TAGFILES                 "")
 
 configure_file(
   ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in

doc/CoeffwiseMathFunctionsTable.dox

@@ -63,7 +63,7 @@ This also means that, unless specified, if the function \c std::foo is available
   \anchor cwisetable_conj
   a.\link ArrayBase::conjugate conjugate\endlink(); \n
   \link Eigen::conj conj\endlink(a); \n
-  m.\link MatrixBase::conjugate conjugate();
+  m.\link MatrixBase::conjugate conjugate\endlink();
   </td>
   <td><a href="https://en.wikipedia.org/wiki/Complex_conjugate">complex conjugate</a> (\f$ \bar{a_i} \f$),\n
   no-op for real </td>
@@ -133,8 +133,9 @@ This also means that, unless specified, if the function \c std::foo is available
   <td class="code">
   \anchor cwisetable_pow
   a.\link ArrayBase::pow pow\endlink(b); \n
-  \link Eigen::pow pow\endlink(a,b);
+  \link ArrayBase::pow(const Eigen::ArrayBase< Derived > &x, const Eigen::ArrayBase< ExponentDerived > &exponents) pow\endlink(a,b);
   </td>
+  <!-- For some reason Doxygen thinks that pow is in ArrayBase namespace -->
   <td>raises a number to the given power (\f$ a_i ^ {b_i} \f$) \n \c a and \c b can be either an array or scalar.</td>
   <td class="code">
   using <a href="http://en.cppreference.com/w/cpp/numeric/math/pow">std::pow</a>; \n

doc/Doxyfile.in

@@ -1596,6 +1596,7 @@ PREDEFINED             = EIGEN_EMPTY_STRUCT \
                          "EIGEN_CAT2(a,b)= a ## b"\
                          "EIGEN_CAT(a,b)=EIGEN_CAT2(a,b)"\
                          "EIGEN_CWISE_BINARY_RETURN_TYPE(LHS,RHS,OPNAME)=CwiseBinaryOp<EIGEN_CAT(EIGEN_CAT(internal::scalar_,OPNAME),_op)<LHS::Scalar, RHS::Scalar>, const LHS, const RHS>"\
+                         "EIGEN_ALIGN_TO_BOUNDARY(x)="\
                          DOXCOMMA=,
 
 
@@ -1618,6 +1619,9 @@ EXPAND_AS_DEFINED      = EIGEN_MAKE_TYPEDEFS \
                          EIGEN_EULER_ANGLES_TYPEDEFS \
                          EIGEN_EULER_ANGLES_SINGLE_TYPEDEF \
                          EIGEN_EULER_SYSTEM_TYPEDEF \
+                         EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY \
+                         EIGEN_MATRIX_FUNCTION \
+                         EIGEN_MATRIX_FUNCTION_1 \
                          EIGEN_DOC_UNARY_ADDONS \
                          EIGEN_DOC_BLOCK_ADDONS_NOT_INNER_PANEL \
                          EIGEN_DOC_BLOCK_ADDONS_INNER_PANEL_IF
@@ -1665,7 +1669,7 @@ ALLEXTERNALS           = NO
 # in the modules index. If set to NO, only the current project's groups will
 # be listed.
 
-EXTERNAL_GROUPS        = YES
+EXTERNAL_GROUPS        = NO
 
 # The PERL_PATH should be the absolute path and name of the perl script
 # interpreter (i.e. the result of `which perl').

unsupported/Eigen/CXX11/src/Tensor/Tensor.h

@@ -23,12 +23,12 @@ namespace Eigen {
   * The %Tensor class encompasses only dynamic-size objects so far.
   *
   * The first two template parameters are required:
-  * \tparam Scalar_ \anchor tensor_tparam_scalar Numeric type, e.g. float, double, int or std::complex<float>.
+  * \tparam Scalar_  Numeric type, e.g. float, double, int or `std::complex<float>`.
   *                 User defined scalar types are supported as well (see \ref user_defined_scalars "here").
   * \tparam NumIndices_ Number of indices (i.e. rank of the tensor)
   *
   * The remaining template parameters are optional -- in most cases you don't have to worry about them.
-  * \tparam Options_ \anchor tensor_tparam_options A combination of either \b #RowMajor or \b #ColMajor, and of either
+  * \tparam Options_  A combination of either \b #RowMajor or \b #ColMajor, and of either
   *                 \b #AutoAlign or \b #DontAlign.
   *                 The former controls \ref TopicStorageOrders "storage order", and defaults to column-major. The latter controls alignment, which is required
   *                 for vectorization. It defaults to aligning tensors. Note that tensors currently do not support any operations that profit from vectorization.
@@ -42,13 +42,13 @@ namespace Eigen {
   * \endcode
   *
   * 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_TENSOR_PLUGIN.
+  * \ref TopicCustomizing_Plugins by defining the preprocessor symbol \c EIGEN_TENSOR_PLUGIN.
   *
   * <i><b>Some notes:</b></i>
   *
   * <dl>
   * <dt><b>Relation to other parts of Eigen:</b></dt>
-  * <dd>The midterm developement goal for this class is to have a similar hierarchy as Eigen uses for matrices, so that
+  * <dd>The midterm development goal for this class is to have a similar hierarchy as Eigen uses for matrices, so that
   * taking blocks or using tensors in expressions is easily possible, including an interface with the vector/matrix code
   * by providing .asMatrix() and .asVector() (or similar) methods for rank 2 and 1 tensors. However, currently, the %Tensor
   * class does not provide any of these features and is only available as a stand-alone class that just allows for

unsupported/Eigen/CXX11/src/Tensor/TensorForcedEval.h

@@ -12,19 +12,6 @@
 
 namespace Eigen {
 
-/** \class TensorForcedEval
-  * \ingroup CXX11_Tensor_Module
-  *
-  * \brief Tensor reshaping class.
-  *
-  *
-  */
-/// template <class> class MakePointer_ is added to convert the host pointer to the device pointer.
-/// It is added due to the fact that for our device compiler T* is not allowed.
-/// If we wanted to use the same Evaluator functions we have to convert that type to our pointer T.
-/// This is done through our MakePointer_ class. By default the Type in the MakePointer_<T> is T* .
-/// Therefore, by adding the default value, we managed to convert the type and it does not break any
-/// existing code as its default value is T*.
 namespace internal {
 template<typename XprType, template <class> class MakePointer_>
 struct traits<TensorForcedEvalOp<XprType, MakePointer_> >
@@ -65,6 +52,21 @@ struct nested<TensorForcedEvalOp<XprType, MakePointer_>, 1, typename eval<Tensor
 
 
 
+// FIXME use proper doxygen documentation (e.g. \tparam MakePointer_)
+
+/** \class TensorForcedEvalOp
+  * \ingroup CXX11_Tensor_Module
+  *
+  * \brief Tensor reshaping class.
+  *
+  *
+  */
+/// `template <class> class MakePointer_` is added to convert the host pointer to the device pointer.
+/// It is added due to the fact that for our device compiler `T*` is not allowed.
+/// If we wanted to use the same Evaluator functions we have to convert that type to our pointer `T`.
+/// This is done through our `MakePointer_` class. By default the Type in the `MakePointer_<T>` is `T*` .
+/// Therefore, by adding the default value, we managed to convert the type and it does not break any
+/// existing code as its default value is `T*`.
 template<typename XprType, template <class> class MakePointer_>
 class TensorForcedEvalOp : public TensorBase<TensorForcedEvalOp<XprType, MakePointer_>, ReadOnlyAccessors>
 {

unsupported/Eigen/CXX11/src/Tensor/TensorMap.h

@@ -12,18 +12,20 @@
 
 namespace Eigen {
 
+// FIXME use proper doxygen documentation (e.g. \tparam MakePointer_)
+
 /** \class TensorMap
   * \ingroup CXX11_Tensor_Module
   *
   * \brief A tensor expression mapping an existing array of data.
   *
   */
-/// template <class> class MakePointer_ is added to convert the host pointer to the device pointer.
+/// `template <class> class MakePointer_` is added to convert the host pointer to the device pointer.
-/// It is added due to the fact that for our device compiler T* is not allowed.
+/// It is added due to the fact that for our device compiler `T*` is not allowed.
-/// If we wanted to use the same Evaluator functions we have to convert that type to our pointer T.
+/// If we wanted to use the same Evaluator functions we have to convert that type to our pointer `T`.
-/// This is done through our MakePointer_ class. By default the Type in the MakePointer_<T> is T* .
+/// This is done through our `MakePointer_` class. By default the Type in the `MakePointer_<T>` is `T*` .
 /// Therefore, by adding the default value, we managed to convert the type and it does not break any
-/// existing code as its default value is T*.
+/// existing code as its default value is `T*`.
 template<typename PlainObjectType, int Options_, template <class> class MakePointer_> class TensorMap : public TensorBase<TensorMap<PlainObjectType, Options_, MakePointer_> >
 {
   public:

unsupported/Eigen/CXX11/src/Tensor/TensorSyclExtractAccessor.h

@@ -35,7 +35,7 @@
 namespace Eigen {
 namespace TensorSycl {
 namespace internal {
-/// \struct ExtractAccessor: Extract Accessor Class is used to extract the
+/// struct ExtractAccessor: Extract Accessor Class is used to extract the
 /// accessor from a buffer.
 /// Depending on the type of the leaf node we can get a read accessor or a
 /// read_write accessor

unsupported/Eigen/CXX11/src/Tensor/TensorSyclTuple.h

@@ -147,6 +147,8 @@ struct IndexList {};
 template <size_t MIN, size_t N, size_t... Is>
 struct RangeBuilder;
 
+// FIXME Doxygen has problems with recursive inheritance
+#ifndef EIGEN_PARSED_BY_DOXYGEN
 /// \brief base Step: Specialisation of the \ref RangeBuilder when the
 /// MIN==MAX. In this case the Is... is [0 to sizeof...(tuple elements))
 /// \tparam MIN is the starting index of the tuple
@@ -164,6 +166,7 @@ struct RangeBuilder<MIN, MIN, Is...> {
 /// \tparam Is... are the list of generated index so far
 template <size_t MIN, size_t N, size_t... Is>
 struct RangeBuilder : public RangeBuilder<MIN, N - 1, N - 1, Is...> {};
+#endif // EIGEN_PARSED_BY_DOXYGEN
 
 /// \brief IndexRange that returns a [MIN, MAX) index range
 /// \tparam MIN is the starting index in the tuple

unsupported/Eigen/CXX11/src/TensorSymmetry/util/TemplateGroupTheory.h

@@ -167,7 +167,9 @@ template<
   typename elements,
   bool dont_add_current_element   // = false
 >
-struct dimino_first_step_elements_helper :
+struct dimino_first_step_elements_helper
+#ifndef EIGEN_PARSED_BY_DOXYGEN
+  : // recursive inheritance is too difficult for Doxygen
   public dimino_first_step_elements_helper<
     Multiply,
     Equality,
@@ -187,6 +189,7 @@ template<
   typename elements
 >
 struct dimino_first_step_elements_helper<Multiply, Equality, id, g, current_element, elements, true>
+#endif // EIGEN_PARSED_BY_DOXYGEN
 {
   typedef elements type;
   constexpr static int global_flags = Equality<current_element, id>::global_flags;

unsupported/Eigen/MatrixFunctions

@@ -161,8 +161,8 @@ the z-axis.
 \include MatrixExponential.cpp
 Output: \verbinclude MatrixExponential.out
 
-\note \p M has to be a matrix of \c float, \c double, \c long double
+\note \p M has to be a matrix of \c float, \c double, `long double`
-\c complex<float>, \c complex<double>, or \c complex<long double> .
+\c complex<float>, \c complex<double>, or `complex<long double>` .
 
 
 \subsection matrixbase_log MatrixBase::log()
@@ -219,9 +219,8 @@ documentation of \ref matrixbase_exp "exp()".
 \include MatrixLogarithm.cpp
 Output: \verbinclude MatrixLogarithm.out
 
-\note \p M has to be a matrix of \c float, \c double, <tt>long
+\note \p M has to be a matrix of \c float, \c double, `long
-double</tt>, \c complex<float>, \c complex<double>, or \c complex<long
+double`, \c complex<float>, \c complex<double>, or `complex<long double>`.
-double> .
 
 \sa MatrixBase::exp(), MatrixBase::matrixFunction(), 
     class MatrixLogarithmAtomic, MatrixBase::sqrt().
@@ -326,9 +325,9 @@ Example:
 \include MatrixPower_optimal.cpp
 Output: \verbinclude MatrixPower_optimal.out
 
-\note \p M has to be a matrix of \c float, \c double, <tt>long
+\note \p M has to be a matrix of \c float, \c double, `long
-double</tt>, \c complex<float>, \c complex<double>, or \c complex<long
+double`, \c complex<float>, \c complex<double>, or
-double> .
+\c complex<long double> .
 
 \sa MatrixBase::exp(), MatrixBase::log(), class MatrixPower.
 

unsupported/Eigen/src/IterativeSolvers/GMRES.h

@@ -21,7 +21,7 @@ namespace internal {
 *
 * Parameters:
 *  \param mat       matrix of linear system of equations
-*  \param Rhs       right hand side vector of linear system of equations
+*  \param rhs       right hand side vector of linear system of equations
 *  \param x         on input: initial guess, on output: solution
 *  \param precond   preconditioner used
 *  \param iters     on input: maximum number of iterations to perform

unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h

@@ -7,8 +7,8 @@
 // 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_MATRIX_FUNCTION
+#ifndef EIGEN_MATRIX_FUNCTION_H
-#define EIGEN_MATRIX_FUNCTION
+#define EIGEN_MATRIX_FUNCTION_H
 
 #include "StemFunction.h"
 
@@ -577,4 +577,4 @@ const MatrixFunctionReturnValue<Derived> MatrixBase<Derived>::cosh() const
 
 } // end namespace Eigen
 
-#endif // EIGEN_MATRIX_FUNCTION
+#endif // EIGEN_MATRIX_FUNCTION_H

unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h

@@ -324,7 +324,7 @@ public:
   
   /** \brief Compute the matrix logarithm.
     *
-    * \param[out]  result  Logarithm of \p A, where \A is as specified in the constructor.
+    * \param[out]  result  Logarithm of \c A, where \c A is as specified in the constructor.
     */
   template <typename ResultType>
   inline void evalTo(ResultType& result) const

unsupported/Eigen/src/MatrixFunctions/MatrixPower.h

@@ -57,8 +57,8 @@ class MatrixPowerParenthesesReturnValue : public ReturnByValue< MatrixPowerParen
      * \param[out] result
      */
     template<typename ResultType>
-    inline void evalTo(ResultType& res) const
+    inline void evalTo(ResultType& result) const
-    { m_pow.compute(res, m_p); }
+    { m_pow.compute(result, m_p); }
 
     Index rows() const { return m_pow.rows(); }
     Index cols() const { return m_pow.cols(); }
@@ -618,8 +618,8 @@ class MatrixPowerReturnValue : public ReturnByValue< MatrixPowerReturnValue<Deri
      * constructor.
      */
     template<typename ResultType>
-    inline void evalTo(ResultType& res) const
+    inline void evalTo(ResultType& result) const
-    { MatrixPower<PlainObject>(m_A.eval()).compute(res, m_p); }
+    { MatrixPower<PlainObject>(m_A.eval()).compute(result, m_p); }
 
     Index rows() const { return m_A.rows(); }
     Index cols() const { return m_A.cols(); }
@@ -669,8 +669,8 @@ class MatrixComplexPowerReturnValue : public ReturnByValue< MatrixComplexPowerRe
      * constructor.
      */
     template<typename ResultType>
-    inline void evalTo(ResultType& res) const
+    inline void evalTo(ResultType& result) const
-    { res = (m_p * m_A.log()).exp(); }
+    { result = (m_p * m_A.log()).exp(); }
 
     Index rows() const { return m_A.rows(); }
     Index cols() const { return m_A.cols(); }

unsupported/Eigen/src/Polynomials/PolynomialUtils.h

@@ -20,8 +20,8 @@ namespace Eigen {
  *  e.g. \f$ 1 + 3x^2 \f$ is stored as a vector \f$ [ 1, 0, 3 ] \f$.
  * \param[in] x : the value to evaluate the polynomial at.
  *
- * <i><b>Note for stability:</b></i>
+ * \note for stability:
- *  <dd> \f$ |x| \le 1 \f$ </dd>
+ *   \f$ |x| \le 1 \f$
  */
 template <typename Polynomials, typename T>
 inline
@@ -67,8 +67,8 @@ T poly_eval( const Polynomials& poly, const T& x )
  *  by degrees i.e. poly[i] is the coefficient of degree i of the polynomial
  *  e.g. \f$ 1 + 3x^2 \f$ is stored as a vector \f$ [ 1, 0, 3 ] \f$.
  *
- *  <i><b>Precondition:</b></i>
+ *  \pre
- *  <dd> the leading coefficient of the input polynomial poly must be non zero </dd>
+ *   the leading coefficient of the input polynomial poly must be non zero
  */
 template <typename Polynomial>
 inline

unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h

@@ -931,7 +931,7 @@ class BlockSparseMatrix : public SparseMatrixBase<BlockSparseMatrix<_Scalar,_Blo
     }
 
     /**
-      * \returns the starting position of the block <id> in the array of values
+      * \returns the starting position of the block \p id in the array of values
       */
     Index blockPtr(Index id) const
     {