[FIX] Groups

include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp

@@ -26,7 +26,7 @@ namespace seqan3::detail
 {
 
 /*!\brief               Create the formatted alignment output and add it to the provided debug_stream.
- * \ingroup             aligned_sequence
+ * \ingroup             alignment_aligned_sequence
  * \tparam alignment_t  The type of the alignment; must model seqan3::tuple_like.
  * \tparam idx          An index sequence.
  * \param[in] stream    The output stream that receives the formatted alignment.

include/seqan3/alignment/matrix/all.hpp

@@ -6,18 +6,15 @@
 // -----------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Meta-header for the \cond DEV \link alignment_matrix Alignment / Matrix submodule \endlink \endcond.
+ * \brief Meta-header for the \link alignment_matrix Alignment / Matrix submodule \endlink.
  * \author Marcel Ehrhardt <marcel.ehrhardt AT fu-berlin.de>
  */
 
-//!\cond DEV
-
 /*!\defgroup alignment_matrix Matrix
  * \brief Provides data structures for representing alignment coordinates and alignments as a matrix.
  * \ingroup alignment
  * \see alignment
  */
-//!\endcond
 
 #pragma once
 

include/seqan3/alignment/pairwise/alignment_algorithm.hpp

@@ -62,8 +62,8 @@ namespace seqan3::detail
  * using SIMD operations or scalar operations, computing the traceback or only the score etc.. These configurations
  * are inherited using so-called `alignment policies`. An alignment policy is a type that implements a specific
  * functionality through a common interface that is used by the alignment algorithm. These policies are also
- * the customisation points of the algorithm which will be used to implement a specific behaviour. You can read more
- * about the policies in \ref alignment_pairwise_policy.
+ * the customisation points of the algorithm which will be used to implement a specific behaviour. \if DEV You can read
+ * more about the policies in \ref alignment_pairwise_policy. \endif
  *
  * Since some of the policies are augmented with traits to further refine the policy execution during the configuration,
  * it is necessary to defer the template instantiation of the policies, which are modelled as CRTP-base classes.

include/seqan3/utility/simd/all.hpp

@@ -7,25 +7,20 @@
 
 /*!\file
  * \author Marcel Ehrhardt <marcel.ehrhardt AT fu-berlin.de>
- * \brief Meta-header for the \cond DEV \link utility_simd Utility / SIMD submodule \endlink \endcond.
+ * \brief Meta-header for the \link utility_simd Utility / SIMD submodule \endlink.
  */
 
-//!\cond DEV
-
 /*!\defgroup utility_simd SIMD
  * \brief The simd module contains a unified interface to provide simd types and functions used in seqan3.
  * \ingroup utility
  * \see utility
  * \see https://en.wikipedia.org/wiki/SIMD
  *
- * \todo Make this public again. We made this documentation internal-documentation only for the 3.0.0 release, because
- * the API was not in shape yet. Remove the `cond DEV` and `todo` commands and remove `seqan3::simd` from
- * SEQAN3_DOXYGEN_EXCLUDE_SYMBOLS in `seqan3-doxygen.cmake`.
- *
  * There are different simd implementations (backends), which are auto-selected by seqan3::simd::simd_type_t.
- * \if DEV
  * Namely seqan3::detail::builtin_simd.
- * \endif
+ *
+ * \todo Make this public again. We made this documentation internal-documentation only for the 3.0.0 release, because
+ * the API was not in shape yet. Remove /utility/simd/ exclusion from EXCLUDE_PATTERNS.
  *
  * \todo Describe more what SIMD is and how to use it.
  */
@@ -35,7 +30,6 @@
  * \sa https://en.wikipedia.org/wiki/SIMD What is SIMD conceptually?
  * \sa https://en.wikipedia.org/wiki/Streaming_SIMD_Extensions Which SIMD architectures exist?
  */
-//!\endcond
 
 #pragma once
 

include/seqan3/utility/simd/detail/debug_stream_simd.hpp

@@ -22,10 +22,6 @@ namespace seqan3
 
 /*!\brief Overload for debug_stream for simd types.
  * \ingroup utility_simd
- * \private
- * \todo Make this public again. We made this documentation internal-documentation only for the 3.0.0 release, because
- * the API was not in shape yet. Remove the `private` and `todo` commands and remove `seqan3::simd` from
- * SEQAN3_DOXYGEN_EXCLUDE_SYMBOLS in `seqan3-doxygen.cmake`.
  */
 template <typename char_t, typename simd_t>
     requires simd::simd_concept<std::remove_cvref_t<simd_t>>

include/seqan3/utility/simd/views/all.hpp

@@ -6,20 +6,16 @@
 // -----------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Meta-header for the \cond DEV \link utility_simd_views Utility / SIMD / Views submodule \endlink \endcond.
+ * \brief Meta-header for the \link utility_simd_views Utility / SIMD / Views submodule \endlink.
  * \author Marcel Ehrhardt <marcel.ehrhardt AT fu-berlin.de>
  */
 
-//!\cond DEV
-
 /*!\defgroup utility_simd_views Views
  * \brief SIMD related views.
  * \ingroup utility_simd
  * \see utility_simd
  */
 
-//!\endcond
-
 #pragma once
 
 #include <seqan3/utility/simd/views/iota_simd.hpp>

test/documentation/doc_usr/CMakeLists.txt

@@ -8,7 +8,7 @@
 message (STATUS "Configuring user doc.")
 
 set (SEQAN3_DOXYGEN_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}")
-set (SEQAN3_DOXYGEN_EXCLUDE_SYMBOLS "detail seqan3::simd") #/""
+set (SEQAN3_DOXYGEN_EXCLUDE_SYMBOLS "")
 set (SEQAN3_DOXYGEN_PREDEFINED_NDEBUG "-NDEBUG") #/""
 set (SEQAN3_DOXYGEN_ENABLED_SECTIONS "") #/"DEV"
 set (SEQAN3_SHOW_DEV_DOCS "NO") #/"YES"

test/documentation/seqan3_doxygen_cfg.in

@@ -155,7 +155,8 @@ RECURSIVE              = YES
 EXCLUDE                =
 EXCLUDE_SYMLINKS       = NO
 EXCLUDE_PATTERNS       = */doc/*.cpp \
-                         */contrib/std/*.hpp
+                         */contrib/std/*.hpp \
+                         */utility/simd/*.hpp
 EXCLUDE_SYMBOLS        = seqan3::contrib \
                          ${SEQAN3_DOXYGEN_EXCLUDE_SYMBOLS}
 EXAMPLE_PATH           = ${SEQAN3_DOXYGEN_SOURCE_DIR}