From 7f899cfd0adaa485615e0c43facbad0f779924a8 Mon Sep 17 00:00:00 2001
From: Enrico Seiler <enrico.seiler@hotmail.de>
Date: Sun, 15 Oct 2023 13:51:59 +0200
Subject: [PATCH] [DOC,INFRA] Doxygen groups

---
 .../aligned_sequence_concept.hpp              |  4 ++--
 include/seqan3/std/new                        | 24 +++++++++++++++++++
 test/documentation/doc_dev/CMakeLists.txt     |  1 +
 test/documentation/doc_usr/CMakeLists.txt     |  3 ++-
 test/documentation/seqan3_doxygen_cfg.in      |  2 +-
 5 files changed, 30 insertions(+), 4 deletions(-)

diff --git a/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp b/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp
index 849deb955e..15d293f5ca 100644
--- a/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp
+++ b/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp
@@ -85,7 +85,7 @@ namespace seqan3
 /*!\interface seqan3::aligned_sequence <>
  * \extends   seqan3::sequence
  * \brief     The generic concept for an aligned sequence.
- * \ingroup   aligned_sequence
+ * \ingroup   alignment_aligned_sequence
  *
  * This concept describes the requirements a sequence must fulfil in order to represent a sequence in an alignment.
  *
@@ -111,7 +111,7 @@ concept aligned_sequence = sequence<t> && std::equality_comparable_with<std::ran
  * \extends   seqan3::aligned_sequence
  * \extends   std::ranges::forward_range
  * \brief     The generic concept for an aligned sequence that is writable.
- * \ingroup   aligned_sequence
+ * \ingroup   alignment_aligned_sequence
  *
  * This concept describes the requirements a sequence must fulfill in order to be used inside of the alignment algorithm
  * to store the final alignment.
diff --git a/include/seqan3/std/new b/include/seqan3/std/new
index 4bbaad7abc..a02a986328 100644
--- a/include/seqan3/std/new
+++ b/include/seqan3/std/new
@@ -19,6 +19,30 @@
 
 #ifndef __cpp_lib_hardware_interference_size
 
+/*!\defgroup std std
+ * \brief A subset of the C++20 standard library made available in pre-C++20 contexts.
+ *
+ * \details
+ *
+ * This module provides many parts of the C++20 standard library (and some parts of the C++17 standard library
+ * not available in GCC). They are only defined if not found in the compiler's standard library and are called exactly
+ * like the originals so they can be used interchangeably.
+ *
+ * \attention All of this sub-module is subject to change!
+ *
+ * In particular:
+ *
+ *   * We do not provide all C++20 library features, only those that are used by SeqAn.
+ *   * All of these might change or be removed once C++20 is published.
+ *   * The documentation of this module will likely be removed entirely in favour of links to
+ *     https://en.cppreference.com
+ *
+ * It is best you consider every entity in this module as:
+ *
+ * \noapi
+ *
+ */
+
 /*!\defgroup std_new new
  * \ingroup std
  * \brief The [\<new\> header](https://en.cppreference.com/w/cpp/header/new) from C++17's standard library.
diff --git a/test/documentation/doc_dev/CMakeLists.txt b/test/documentation/doc_dev/CMakeLists.txt
index b1cfb18d28..23f38be5af 100644
--- a/test/documentation/doc_dev/CMakeLists.txt
+++ b/test/documentation/doc_dev/CMakeLists.txt
@@ -9,6 +9,7 @@ message (STATUS "Configuring devel doc.")
 
 set (SEQAN3_DOXYGEN_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}")
 set (SEQAN3_DOXYGEN_EXCLUDE_SYMBOLS "")
+set (SEQAN3_DOXYGEN_EXCLUDE_PATTERNS "")
 set (SEQAN3_DOXYGEN_PREDEFINED_NDEBUG "")
 set (SEQAN3_DOXYGEN_ENABLED_SECTIONS "DEV")
 set (SEQAN3_SHOW_DEV_DOCS "YES")
diff --git a/test/documentation/doc_usr/CMakeLists.txt b/test/documentation/doc_usr/CMakeLists.txt
index 972c92f09f..0f9c4fe149 100644
--- a/test/documentation/doc_usr/CMakeLists.txt
+++ b/test/documentation/doc_usr/CMakeLists.txt
@@ -8,7 +8,8 @@
 message (STATUS "Configuring user doc.")
 
 set (SEQAN3_DOXYGEN_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}")
-set (SEQAN3_DOXYGEN_EXCLUDE_SYMBOLS "")
+set (SEQAN3_DOXYGEN_EXCLUDE_SYMBOLS "seqan3::detail seqan3::simd")
+set (SEQAN3_DOXYGEN_EXCLUDE_PATTERNS "*/utility/parallel/*.hpp */utility/simd/*.hpp */alignment/pairwise/policy/*.hpp")
 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 892cdefa53..5d893ad7d1 100644
--- a/test/documentation/seqan3_doxygen_cfg.in
+++ b/test/documentation/seqan3_doxygen_cfg.in
@@ -158,7 +158,7 @@ EXCLUDE                =
 EXCLUDE_SYMLINKS       = NO
 EXCLUDE_PATTERNS       = */doc/*.cpp \
                          */contrib/std/*.hpp \
-                         */utility/simd/*.hpp
+                         ${SEQAN3_DOXYGEN_EXCLUDE_PATTERNS}
 EXCLUDE_SYMBOLS        = seqan3::contrib \
                          ${SEQAN3_DOXYGEN_EXCLUDE_SYMBOLS}
 EXAMPLE_PATH           = ${SEQAN3_DOXYGEN_SOURCE_DIR}