diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml index 3bdbdd24c4..85e5567325 100644 --- a/.github/workflows/ci_documentation.yml +++ b/.github/workflows/ci_documentation.yml @@ -50,7 +50,7 @@ jobs: - name: Install Doxygen uses: seqan/actions/setup-doxygen@main with: - doxygen: 1.9.6 + doxygen: 1.9.8 - name: Configure tests run: | diff --git a/.github/workflows/deploy_documentation.yaml b/.github/workflows/deploy_documentation.yaml index a5d8222ddb..d34781be0b 100644 --- a/.github/workflows/deploy_documentation.yaml +++ b/.github/workflows/deploy_documentation.yaml @@ -36,13 +36,13 @@ jobs: - name: Install Doxygen uses: seqan/actions/setup-doxygen@main with: - doxygen: 1.9.6 + doxygen: 1.9.8 - name: Load cached documentation uses: actions/cache@v3 with: path: doc-build - key: ${{ runner.os }}-documentation-1.9.6 + key: ${{ runner.os }}-documentation-1.9.8 - name: Build documentation run: | diff --git a/CHANGELOG.md b/CHANGELOG.md index 918393daf2..fa091949c8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,17 @@ The following API changes should be documented as such: If possible, provide tooling that performs the changes, e.g. a shell-script. --> +# 3.3.1 + +## New features + +## Notable Bug-fixes + +## API changes + +#### Dependencies + * We now use Doxygen version 1.9.8 to build our documentation ([\#3197](https://github.com/seqan/seqan3/pull/3197)). + # 3.3.0 ## New features 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/.vercel/install.sh b/test/documentation/.vercel/install.sh index 68e20b8f88..0b89492dc8 100755 --- a/test/documentation/.vercel/install.sh +++ b/test/documentation/.vercel/install.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash set -exo pipefail -DOXYGEN_VERSION=1.9.6 +DOXYGEN_VERSION=1.9.8 SOURCE_DIR=`pwd` CACHE_DIR="${SOURCE_DIR}/node_modules" diff --git a/test/documentation/DoxygenLayout.xml b/test/documentation/DoxygenLayout.xml index 765b228d85..c20d745fd4 100644 --- a/test/documentation/DoxygenLayout.xml +++ b/test/documentation/DoxygenLayout.xml @@ -1,5 +1,6 @@ + - + @@ -21,8 +22,12 @@ - + + + + + @@ -201,6 +206,7 @@ + @@ -246,6 +252,25 @@ + + + + + + + + + + + + + + + + + + + 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..892cdefa53 100644 --- a/test/documentation/seqan3_doxygen_cfg.in +++ b/test/documentation/seqan3_doxygen_cfg.in @@ -1,4 +1,4 @@ -# Doxyfile 1.9.6 +# Doxyfile 1.9.8 #--------------------------------------------------------------------------- # Project related configuration options @@ -69,6 +69,7 @@ OPTIMIZE_OUTPUT_SLICE = NO EXTENSION_MAPPING = .no_extension=C++ MARKDOWN_SUPPORT = YES TOC_INCLUDE_HEADINGS = 2 +MARKDOWN_ID_STYLE = DOXYGEN AUTOLINK_SUPPORT = YES BUILTIN_STL_SUPPORT = NO CPP_CLI_SUPPORT = NO @@ -82,6 +83,7 @@ INLINE_SIMPLE_STRUCTS = NO TYPEDEF_HIDES_STRUCT = NO LOOKUP_CACHE_SIZE = 0 NUM_PROC_THREADS = 1 +TIMESTAMP = YES #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- @@ -155,7 +157,8 @@ 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} @@ -210,9 +213,9 @@ HTML_COLORSTYLE = LIGHT HTML_COLORSTYLE_HUE = 209 HTML_COLORSTYLE_SAT = 255 HTML_COLORSTYLE_GAMMA = 113 -HTML_TIMESTAMP = YES HTML_DYNAMIC_MENUS = YES HTML_DYNAMIC_SECTIONS = YES +HTML_CODE_FOLDING = YES HTML_INDEX_NUM_ENTRIES = 100 GENERATE_DOCSET = NO DOCSET_FEEDNAME = "Doxygen generated docs" @@ -227,6 +230,7 @@ GENERATE_CHI = NO CHM_INDEX_ENCODING = BINARY_TOC = NO TOC_EXPAND = NO +SITEMAP_URL = GENERATE_QHP = NO QCH_FILE = QHP_NAMESPACE = org.doxygen.Project @@ -280,7 +284,6 @@ USE_PDFLATEX = YES LATEX_BATCHMODE = NO LATEX_HIDE_INDICES = NO LATEX_BIB_STYLE = plain -LATEX_TIMESTAMP = NO LATEX_EMOJI_DIRECTORY = #--------------------------------------------------------------------------- # Configuration options related to the RTF output @@ -316,6 +319,12 @@ DOCBOOK_OUTPUT = docbook #--------------------------------------------------------------------------- GENERATE_AUTOGEN_DEF = NO #--------------------------------------------------------------------------- +# Configuration options related to Sqlite3 output +#--------------------------------------------------------------------------- +GENERATE_SQLITE3 = NO +SQLITE3_OUTPUT = sqlite3 +SQLITE3_RECREATE_DB = YES +#--------------------------------------------------------------------------- # Configuration options related to the Perl module output #--------------------------------------------------------------------------- GENERATE_PERLMOD = NO @@ -352,9 +361,8 @@ ALLEXTERNALS = NO EXTERNAL_GROUPS = YES EXTERNAL_PAGES = YES #--------------------------------------------------------------------------- -# Configuration options related to the dot tool +# Configuration options related to diagram generator tools #--------------------------------------------------------------------------- -DIA_PATH = HIDE_UNDOC_RELATIONS = YES ## DOT SUPPORT HAVE_DOT = ${SEQAN3_DOXYGEN_HAVE_DOT} @@ -382,7 +390,7 @@ DOT_IMAGE_FORMAT = svg INTERACTIVE_SVG = ${SEQAN3_DOXYGEN_HAVE_DOT} DOT_PATH = DOTFILE_DIRS = -MSCFILE_DIRS = +DIA_PATH = DIAFILE_DIRS = PLANTUML_JAR_PATH = PLANTUML_CFG_FILE = @@ -392,6 +400,8 @@ MAX_DOT_GRAPH_DEPTH = 0 DOT_MULTI_TARGETS = NO GENERATE_LEGEND = YES DOT_CLEANUP = YES +MSCGEN_TOOL = +MSCFILE_DIRS = #--------------------------------------------------------------------------- # Configuration options related to the deployment by Vercel #--------------------------------------------------------------------------- diff --git a/test/documentation/seqan3_footer.html.in b/test/documentation/seqan3_footer.html.in index 18e56af7ca..84ddec3f9f 100644 --- a/test/documentation/seqan3_footer.html.in +++ b/test/documentation/seqan3_footer.html.in @@ -1,4 +1,4 @@ - + diff --git a/test/documentation/seqan3_header.html b/test/documentation/seqan3_header.html index 58a75dbf18..9e11917db4 100644 --- a/test/documentation/seqan3_header.html +++ b/test/documentation/seqan3_header.html @@ -1,4 +1,4 @@ - +