diff --git a/include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp b/include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp index 5c8396ff83..ed8bcac612 100644 --- a/include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp +++ b/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. diff --git a/include/seqan3/alignment/matrix/all.hpp b/include/seqan3/alignment/matrix/all.hpp index 617b17ebb9..d1d70e2103 100644 --- a/include/seqan3/alignment/matrix/all.hpp +++ b/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 */ -//!\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 diff --git a/include/seqan3/alignment/pairwise/alignment_algorithm.hpp b/include/seqan3/alignment/pairwise/alignment_algorithm.hpp index 74b25999f2..60b4dd113d 100644 --- a/include/seqan3/alignment/pairwise/alignment_algorithm.hpp +++ b/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. diff --git a/include/seqan3/utility/simd/all.hpp b/include/seqan3/utility/simd/all.hpp index 922838c26f..c7984ecd86 100644 --- a/include/seqan3/utility/simd/all.hpp +++ b/include/seqan3/utility/simd/all.hpp @@ -7,25 +7,20 @@ /*!\file * \author Marcel Ehrhardt - * \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 diff --git a/include/seqan3/utility/simd/detail/debug_stream_simd.hpp b/include/seqan3/utility/simd/detail/debug_stream_simd.hpp index 59ffb168d8..30fbd9d5bb 100644 --- a/include/seqan3/utility/simd/detail/debug_stream_simd.hpp +++ b/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 requires simd::simd_concept> diff --git a/include/seqan3/utility/simd/views/all.hpp b/include/seqan3/utility/simd/views/all.hpp index 002f1f54e8..6864e7323d 100644 --- a/include/seqan3/utility/simd/views/all.hpp +++ b/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 */ -//!\cond DEV - /*!\defgroup utility_simd_views Views * \brief SIMD related views. * \ingroup utility_simd * \see utility_simd */ -//!\endcond - #pragma once #include diff --git a/test/documentation/doc_usr/CMakeLists.txt b/test/documentation/doc_usr/CMakeLists.txt index b1d2c46fbc..972c92f09f 100644 --- a/test/documentation/doc_usr/CMakeLists.txt +++ b/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" diff --git a/test/documentation/seqan3_doxygen_cfg.in b/test/documentation/seqan3_doxygen_cfg.in index 8f2b2dbd72..c1859ccf06 100644 --- a/test/documentation/seqan3_doxygen_cfg.in +++ b/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}