Adds doxygen modules to OpenCL and write more documentation

doxygen/doxygen.cfg

@@ -133,7 +133,7 @@ ALWAYS_DETAILED_SEC    = NO
 # operators of the base classes will not be shown.
 # The default value is: NO.
 
-INLINE_INHERITED_MEMB  = NO
+INLINE_INHERITED_MEMB  = YES
 
 # If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
 # before files name in the file list and in the header files. If set to NO the
@@ -341,14 +341,14 @@ IDL_PROPERTY_SUPPORT   = YES
 # all members of a group must be documented explicitly.
 # The default value is: NO.
 
-DISTRIBUTE_GROUP_DOC   = NO
+DISTRIBUTE_GROUP_DOC   = YES
 
 # If one adds a struct or class to a group and this option is enabled, then also
 # any nested class or struct is added to the same group. By default this option
 # is disabled and one has to add nested compounds explicitly via \ingroup.
 # The default value is: NO.
 
-GROUP_NESTED_COMPOUNDS = NO
+GROUP_NESTED_COMPOUNDS = YES
 
 # Set the SUBGROUPING tag to YES to allow class member groups of the same type
 # (for instance a group of public functions) to be put as a subgroup of that
@@ -378,7 +378,7 @@ INLINE_GROUPED_CLASSES = NO
 # Man pages) or section (for LaTeX and RTF).
 # The default value is: NO.
 
-INLINE_SIMPLE_STRUCTS  = NO
+INLINE_SIMPLE_STRUCTS  = YES
 
 # When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
 # enum is documented as struct, union, or enum with the name of the typedef. So
@@ -422,7 +422,7 @@ EXTRACT_ALL            = YES
 # be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PRIVATE        = NO
+EXTRACT_PRIVATE        = YES
 
 # If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
 # scope will be included in the documentation.
@@ -743,7 +743,7 @@ WARN_NO_PARAMDOC       = NO
 # a warning is encountered.
 # The default value is: NO.
 
-WARN_AS_ERROR          = NO
+WARN_AS_ERROR          = YES
 
 # The WARN_FORMAT tag determines the format of the warning messages that doxygen
 # can produce. The string should contain the $file, $line, and $text tags, which
@@ -845,8 +845,7 @@ EXCLUDE_PATTERNS       =
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories use the pattern */test/*
 
-EXCLUDE_SYMBOLS        = std::* \
-                         Eigen::*
+EXCLUDE_SYMBOLS        =
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or directories
 # that contain example code fragments that are included (see the \include

stan/math/memory/stack_alloc.hpp

@@ -88,7 +88,7 @@ class stack_alloc {
    * if necessary, and allocates len bytes of memory within that
    * block.
    *
-   * @param size_t $len Number of bytes to allocate.
+   * @param len Number of bytes to allocate.
    * @return A pointer to the allocated memory.
    */
   char* move_to_next_block(size_t len) {

stan/math/opencl/buffer_types.hpp

@@ -9,20 +9,26 @@
 namespace stan {
 namespace math {
 namespace opencl_kernels {
-
-// An in_buffer signifies a cl::Buffer argument used as input.
+/** \ingroup kernel_executor_opencl
+ * An in_buffer signifies a cl::Buffer argument used as input.
+ */
 struct in_buffer {};
 
-// An out_buffer signifies a cl::Buffer argument used as output.
+/** \ingroup kernel_executor_opencl
+ * An out_buffer signifies a cl::Buffer argument used as output.
+ */
 struct out_buffer {};
 
-// An in_out_buffer signifies a cl::Buffer argument used as both input and
-// output.
+/** \ingroup kernel_executor_opencl
+ * An in_out_buffer signifies a cl::Buffer argument used as both input and
+ * output.
+ */
 struct in_out_buffer {};
 
 namespace internal {
 
-/** \ingroup opencl
+/**  kernel_executor_opencl
+ * @internal
  * meta template struct for changing read/write buffer argument types to
  * cl::Buffer types.
  * @tparam T A template typename that for cases of non-read/write buffers
@@ -49,7 +55,9 @@ struct to_buffer<in_out_buffer> {
   using type = cl::Buffer;
 };
 
-// Alias for making const cl::Buffer argument types
+/**  kernel_executor_opencl
+ * Alias for making const cl::Buffer argument types
+ */
 template <typename T>
 using to_const_buffer_t = const typename internal::to_buffer<T>::type;
 }  // namespace internal

stan/math/opencl/copy.hpp

@@ -72,7 +72,6 @@ inline matrix_cl<Vec_scalar> to_matrix_cl(Vec&& src) {
  * @param src source matrix on the OpenCL device
  * @return Eigen matrix with a copy of the data in the source matrix
  */
-
 template <int R = Eigen::Dynamic, int C = Eigen::Dynamic, typename T,
           typename = require_arithmetic_t<T>>
 inline Eigen::Matrix<T, R, C> from_matrix_cl(const matrix_cl<T>& src) {

stan/math/opencl/err/check_diagonal_zeros.hpp

@@ -13,7 +13,7 @@
 
 namespace stan {
 namespace math {
-/** \ingroup opencl
+/** \ingroup error_checks_opencl
  * Check if the <code>matrix_cl</code> has zeros on the diagonal
  *
  * @param function Function name (for error messages)

stan/math/opencl/err/check_invalid_matrix_view.hpp

@@ -9,7 +9,7 @@
 namespace stan {
 namespace math {
 
-/** \ingroup opencl
+/** \ingroup error_checks_opencl
  * Check if the <code>matrix_cl</code> has an invalid view.
  *
  * @param function Function name (for error messages)

stan/math/opencl/err/check_mat_size_one.hpp

@@ -9,7 +9,7 @@
 namespace stan {
 namespace math {
 
-/** \ingroup opencl
+/** \ingroup error_checks_opencl
  * Check if the <code>matrix_cl</code> has a single element.
  *
  * @param function Function name (for error messages)
@@ -27,7 +27,7 @@ inline void check_mat_size_one(const char* function, const char* name,
   }
 }
 
-/** \ingroup opencl
+/** \ingroup error_checks_opencl
  * Check if the <code>matrix_cl</code> has a single element.
  *
  * @param function Function name (for error messages)

stan/math/opencl/err/check_matching_dims.hpp

@@ -7,7 +7,7 @@
 
 namespace stan {
 namespace math {
-/** \ingroup opencl
+/** \ingroup error_checks_opencl
  * Check if two <code>matrix_cl</code>s have the same dimensions.
  *
  * @param function Function name (for error messages)

stan/math/opencl/err/check_nan.hpp

@@ -12,7 +12,7 @@
 
 namespace stan {
 namespace math {
-/** \ingroup opencl
+/** \ingroup error_checks_opencl
  * Check if the <code>matrix_cl</code> has NaN values
  *
  * @param function Function name (for error messages)

stan/math/opencl/err/check_opencl.hpp

@@ -12,7 +12,7 @@
 namespace stan {
 namespace math {
 
-/** \ingroup opencl
+/** \ingroup error_checks_opencl
  * Throws the domain error with specifying the OpenCL error that
  * occurred. It outputs the OpenCL errors that are specified
  * in OpenCL 2.0. If no matching error number is found,

stan/math/opencl/err/check_square.hpp

@@ -7,7 +7,7 @@
 
 namespace stan {
 namespace math {
-/** \ingroup opencl
+/** \ingroup error_checks_opencl
  * Check if the <code>matrix_cl</code> is square.
  *
  * @param function Function name (for error messages)

stan/math/opencl/err/check_symmetric.hpp

@@ -13,7 +13,7 @@
 
 namespace stan {
 namespace math {
-/** \ingroup opencl
+/** \ingroup error_checks_opencl
  * Check if the <code>matrix_cl</code> is symmetric
  *
  * @param function Function name (for error messages)

stan/math/opencl/err/check_triangular.hpp

@@ -8,7 +8,7 @@
 namespace stan {
 namespace math {
 
-/** \ingroup opencl
+/** \ingroup error_checks_opencl
  * Check if the <code>matrix_cl</code> is either upper triangular or lower
  * triangular.
  *

stan/math/opencl/err/check_vector.hpp

@@ -12,7 +12,7 @@
 namespace stan {
 namespace math {
 
-/** \ingroup opencl
+/** \ingroup error_checks_opencl
  * Check if the matrix is either a row vector or column vector.
  * This function checks the runtime size of the matrix to check
  * whether it is a row or column vector.

stan/math/opencl/is_matrix_cl.hpp

@@ -8,7 +8,10 @@
 namespace stan {
 
 namespace math {
-// Dummy class to instantiate matrix_cl to enable for specific types.
+/**
+ * Dummy class to instantiate matrix_cl to enable for specific types.
+ * @ingroup matrix_cl_group
+ */
 template <typename T, typename = void>
 class matrix_cl {
  public:
@@ -19,13 +22,15 @@ class matrix_cl {
 
 namespace internal {
 
-/** \ingroup opencl
+/** \ingroup type_traits
+ * @internal
  * This underlying implementation is used when the type is not an std vector.
  */
 template <typename T>
 struct is_matrix_cl_impl : std::false_type {};
 
-/** \ingroup opencl
+/** \ingroup type_traits
+ * @internal
  * This specialization implementation has a static member named value when the
  * template type is an std vector.
  */
@@ -37,16 +42,16 @@ struct is_matrix_cl_impl<stan::math::matrix_cl<Args...>> : std::true_type {};
 template <typename T, typename = void>
 struct is_matrix_cl : std::false_type {};
 
-/** \ingroup opencl
+/** \ingroup type_traits
  * Checks if the decayed type of T is a matrix_cl.
  */
 template <typename T>
 struct is_matrix_cl<
     T, std::enable_if_t<internal::is_matrix_cl_impl<std::decay_t<T>>::value>>
     : std::true_type {};
 
-STAN_ADD_REQUIRE_UNARY(matrix_cl, is_matrix_cl, opencl);
-STAN_ADD_REQUIRE_CONTAINER(matrix_cl, is_matrix_cl, opencl);
+STAN_ADD_REQUIRE_UNARY(matrix_cl, is_matrix_cl, matrix_cl_group);
+STAN_ADD_REQUIRE_CONTAINER(matrix_cl, is_matrix_cl, matrix_cl_group);
 
 }  // namespace stan
 #endif