seqan · eseiler · Jan 30, 2024 · Jan 30, 2024 · Jan 30, 2024
diff --git a/doc/about/api/index.md b/doc/about/api/index.md
@@ -1,10 +1,10 @@
+# Stability and long-term promises {#about_api}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Stability and long-term promises {#about_api}
-
 [TOC]
 
 SeqAn3 adheres to [semantic versioning](https://semver.org) and provides a stable API within

diff --git a/doc/about/citing/index.md b/doc/about/citing/index.md
@@ -1,10 +1,10 @@
+# Citing {#about_citing}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Citing {#about_citing}
-
 [TOC]
 
 SeqAn is a research project and depends strongly on being correctly attributed.

diff --git a/doc/about/customisation/index.md b/doc/about/customisation/index.md
@@ -1,10 +1,10 @@
+# Customisation {#about_customisation}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Customisation {#about_customisation}
-
 SeqAn clearly documents which of its interfaces are designed to be used with user-provided types and how
 this can be realised.
 

diff --git a/doc/cookbook/index.md b/doc/cookbook/index.md
@@ -1,10 +1,10 @@
+# The SeqAn Cookbook {#cookbook}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# The SeqAn Cookbook {#cookbook}
-
 [TOC]
 
 This document provides example recipes on how to carry out particular tasks using the SeqAn functionalities in C++.

diff --git a/doc/howto/porting/index.md b/doc/howto/porting/index.md
@@ -1,10 +1,10 @@
+# Porting from SeqAn2 {#howto_porting}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Porting from SeqAn2 {#howto_porting}
-
 SeqAn3 is a completely new library so there is no easy or automated way of porting applications from SeqAn2.
 We recommend that everyone go through the tutorial, learn the new idioms and then re-write their application.
 We know this is a big burden and we promise that next major versions will be incremental updates again.

diff --git a/doc/howto/subcommand_argument_parser/index.md b/doc/howto/subcommand_argument_parser/index.md
@@ -1,10 +1,10 @@
+# How to write an argument parser with subcommands {#subcommand_arg_parse}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# How to write an argument parser with subcommands {#subcommand_arg_parse}
-
 [TOC]
 
 This HowTo shows you how to write an argument parser with subcommand like `git push` using SeqAn.

diff --git a/doc/howto/use_cereal/index.md b/doc/howto/use_cereal/index.md
@@ -1,10 +1,10 @@
+# How to serialise SeqAn data structures {#howto_use_cereal}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# How to serialise SeqAn data structures {#howto_use_cereal}
-
 [TOC]
 
 This HowTo shows how to serialise data structures with [cereal](https://uscilab.github.io/cereal/). Every SeqAn data

diff --git a/doc/howto/write_a_view/index.md b/doc/howto/write_a_view/index.md
@@ -1,10 +1,10 @@
+# How to write a view {#howto_write_a_view}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# How to write a view {#howto_write_a_view}
-
 [TOC]
 
 This HowTo documents how to write a view using the standard library and some helpers from SeqAn.

diff --git a/doc/howto/write_an_alphabet/index.md b/doc/howto/write_an_alphabet/index.md
@@ -1,10 +1,10 @@
+# How to write your own alphabet {#howto_write_an_alphabet}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# How to write your own alphabet {#howto_write_an_alphabet}
-
 [TOC]
 
 This HowTo documents how to write a custom alphabet that can be used with the algorithms and data structures in SeqAn.

diff --git a/doc/main_page.md b/doc/main_page.md
@@ -1,10 +1,10 @@
+# Welcome {#mainpage}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Welcome {#mainpage}
-
 Welcome to the documentation of the SeqAn library.
 This web-site contains the API reference (documentation of our interfaces) and more elaborate Tutorials and
 How-Tos.

diff --git a/doc/setup/library_tests/index.md b/doc/setup/library_tests/index.md
@@ -1,10 +1,10 @@
+# Setting up library tests {#setup_tests}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Setting up library tests {#setup_tests}
-
 <b>Learning Objective:</b><br>
 In this guide you will learn to set up SeqAn3's library tests to make sure that your contributions don't break anything.
 

diff --git a/doc/setup/quickstart_cmake/index.md b/doc/setup/quickstart_cmake/index.md
@@ -1,10 +1,10 @@
+# Quick Setup (using CMake) {#setup}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Quick Setup (using CMake) {#setup}
-
 <b>Learning Objective:</b><br>
 In this short guide you will learn how to set up SeqAn and how to compile a small example to test whether everything
 works.

diff --git a/doc/tutorial/01_introduction/index.md b/doc/tutorial/01_introduction/index.md
@@ -1,10 +1,10 @@
+# First steps with SeqAn {#tutorial_first_example}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# First steps with SeqAn {#tutorial_first_example}
-
 ***Learning Objective:***
 
 This tutorial walks you through small SeqAn programs. It is intended to give you a short overview

diff --git a/doc/tutorial/02_argument_parser/index.md b/doc/tutorial/02_argument_parser/index.md
@@ -1,10 +1,10 @@
+# Parsing command line arguments with Sharg {#tutorial_argument_parser}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Parsing command line arguments with Sharg {#tutorial_argument_parser}
-
 We have separated the feature of parsing command line arguments to its own project:
 
 ### [![sharg_logo][sharg_logo_link]][sharg_link] The Sharg Parser

diff --git a/doc/tutorial/03_concepts/index.md b/doc/tutorial/03_concepts/index.md
@@ -1,10 +1,10 @@
+# C++ Concepts {#tutorial_concepts}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# C++ Concepts {#tutorial_concepts}
-
 ***Learning Objective:***
 
 This tutorial introduces "C++ Concepts", a feature of C++20 (and available to some extent in older GCC versions).

diff --git a/doc/tutorial/04_alphabet/index.md b/doc/tutorial/04_alphabet/index.md
@@ -1,10 +1,10 @@
+# Alphabets in SeqAn {#tutorial_alphabets}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Alphabets in SeqAn {#tutorial_alphabets}
-
 ***Learning Objective:***
 
 In this tutorial, we look at alphabets and you will learn how to work with nucleotides and amino acids in SeqAn.

diff --git a/doc/tutorial/05_ranges/index.md b/doc/tutorial/05_ranges/index.md
@@ -1,10 +1,10 @@
+# Ranges {#tutorial_ranges}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Ranges {#tutorial_ranges}
-
 [TOC]
 
 This tutorial introduces the notion of *ranges*, a C++20 feature that SeqAn3 makes strong use of.

diff --git a/doc/tutorial/06_minimisers/index.md b/doc/tutorial/06_minimisers/index.md
@@ -1,10 +1,10 @@
+# Minimisers {#tutorial_minimiser}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Minimisers {#tutorial_minimiser}
-
 [TOC]
 
 This tutorial introduces minimisers. Minimisers are a compact representation of a DNA or RNA sequence that is closely

diff --git a/doc/tutorial/07_sequence_file/index.md b/doc/tutorial/07_sequence_file/index.md
@@ -1,10 +1,10 @@
+# Sequence File Input and Output {#tutorial_sequence_file}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Sequence File Input and Output {#tutorial_sequence_file}
-
 <b>Learning Objective:</b> <br/>
 You will get an overview of how Input/Output files are handled in SeqAn and learn how to read and write
 sequence files. This tutorial is a walk-through with links into the API documentation and also meant as a

diff --git a/doc/tutorial/08_pairwise_alignment/index.md b/doc/tutorial/08_pairwise_alignment/index.md
@@ -1,10 +1,10 @@
+# Pairwise Alignment {#tutorial_pairwise_alignment}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Pairwise Alignment {#tutorial_pairwise_alignment}
-
 <b>Learning Objective:</b> <br/>
 
 In this tutorial, you will learn how to compute pairwise sequence alignments with SeqAn.

diff --git a/doc/tutorial/09_search/index.md b/doc/tutorial/09_search/index.md
@@ -1,10 +1,10 @@
+# Indexing and searching with SeqAn {#tutorial_index_search}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Indexing and searching with SeqAn {#tutorial_index_search}
-
 <b>Learning Objective:</b><br>
 In this tutorial, you will learn how to construct an index and conduct searches.
 

diff --git a/doc/tutorial/10_sam_file/index.md b/doc/tutorial/10_sam_file/index.md
@@ -1,10 +1,10 @@
+# SAM Input and Output in SeqAn {#tutorial_sam_file}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# SAM Input and Output in SeqAn {#tutorial_sam_file}
-
 ***Learning Objective:***
 
 <b>Learning Objective:</b> <br/>

diff --git a/doc/tutorial/11_read_mapper/index.md b/doc/tutorial/11_read_mapper/index.md
@@ -1,10 +1,10 @@
+# Implementing your own read mapper with SeqAn {#tutorial_read_mapper}
+
 <!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
      SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
      SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Implementing your own read mapper with SeqAn {#tutorial_read_mapper}
-
 <b>Learning Objective:</b><br>
 In this tutorial, you will learn how to combine the components of previous tutorials to create your very first
 SeqAn application: a read mapper!

diff --git a/include/seqan3/alphabet/aminoacid/aa10li.hpp b/include/seqan3/alphabet/aminoacid/aa10li.hpp
@@ -21,7 +21,7 @@ namespace seqan3
  * \ingroup alphabet_aminoacid
  * \implements seqan3::aminoacid_alphabet
  * \implements seqan3::writable_alphabet
- * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif
+ * \implements seqan3::detail::writable_constexpr_alphabet
  * \implements seqan3::trivially_copyable
  * \implements seqan3::standard_layout
  * \implements std::regular

diff --git a/include/seqan3/alphabet/aminoacid/aa10murphy.hpp b/include/seqan3/alphabet/aminoacid/aa10murphy.hpp
@@ -22,7 +22,7 @@ namespace seqan3
  * \ingroup alphabet_aminoacid
  * \implements seqan3::aminoacid_alphabet
  * \implements seqan3::writable_alphabet
- * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif
+ * \implements seqan3::detail::writable_constexpr_alphabet
  * \implements seqan3::trivially_copyable
  * \implements seqan3::standard_layout
  * \implements std::regular

diff --git a/include/seqan3/alphabet/aminoacid/aa20.hpp b/include/seqan3/alphabet/aminoacid/aa20.hpp
@@ -22,7 +22,7 @@ namespace seqan3
  * \ingroup alphabet_aminoacid
  * \implements seqan3::aminoacid_alphabet
  * \implements seqan3::writable_alphabet
- * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif
+ * \implements seqan3::detail::writable_constexpr_alphabet
  * \implements seqan3::trivially_copyable
  * \implements seqan3::standard_layout
  * \implements std::regular

diff --git a/include/seqan3/alphabet/aminoacid/aa27.hpp b/include/seqan3/alphabet/aminoacid/aa27.hpp
@@ -21,7 +21,7 @@ namespace seqan3
  * \ingroup alphabet_aminoacid
  * \implements seqan3::aminoacid_alphabet
  * \implements seqan3::writable_alphabet
- * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif
+ * \implements seqan3::detail::writable_constexpr_alphabet
  * \implements seqan3::trivially_copyable
  * \implements seqan3::standard_layout
  * \implements std::regular

diff --git a/include/seqan3/alphabet/cigar/exposition_only/cigar_operation.hpp b/include/seqan3/alphabet/cigar/exposition_only/cigar_operation.hpp
@@ -20,7 +20,7 @@ namespace seqan3::exposition_only
 
 /*!\brief The actual implementation of seqan3::cigar::operation for documentation purposes only.
  * \implements seqan3::writable_alphabet
- * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif
+ * \implements seqan3::detail::writable_constexpr_alphabet
  * \implements seqan3::trivially_copyable
  * \implements seqan3::standard_layout
  * \implements std::regular

diff --git a/include/seqan3/alphabet/gap/gap.hpp b/include/seqan3/alphabet/gap/gap.hpp
@@ -20,7 +20,7 @@ namespace seqan3
 /*!\brief The alphabet of a gap character '-'
  * \ingroup alphabet_gap
  * \implements seqan3::writable_alphabet
- * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif
+ * \implements seqan3::detail::writable_constexpr_alphabet
  * \implements seqan3::trivially_copyable
  * \implements seqan3::standard_layout
  * \implements std::regular

diff --git a/include/seqan3/alphabet/mask/mask.hpp b/include/seqan3/alphabet/mask/mask.hpp
@@ -18,7 +18,7 @@ namespace seqan3
 /*!\brief Implementation of a masked alphabet to be used for tuple composites.
  * \ingroup alphabet_mask
  * \implements seqan3::writable_semialphabet
- * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif
+ * \implements seqan3::detail::writable_constexpr_alphabet
  *
  * \details
  *

diff --git a/include/seqan3/alphabet/mask/masked.hpp b/include/seqan3/alphabet/mask/masked.hpp
@@ -19,7 +19,7 @@ namespace seqan3
 /*!\brief Implementation of a masked composite, which extends a given alphabet with a mask.
  * \ingroup alphabet_mask
  * \implements seqan3::writable_alphabet
- * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif
+ * \implements seqan3::detail::writable_constexpr_alphabet
  *
  * \tparam sequence_alphabet_t Type of the first letter; must satisfy seqan3::writable_alphabet and std::regular.
  *

diff --git a/include/seqan3/alphabet/nucleotide/dna15.hpp b/include/seqan3/alphabet/nucleotide/dna15.hpp
@@ -27,7 +27,7 @@ class rna15;
  * \ingroup alphabet_nucleotide
  * \implements seqan3::nucleotide_alphabet
  * \implements seqan3::writable_alphabet
- * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif
+ * \implements seqan3::detail::writable_constexpr_alphabet
  * \implements seqan3::trivially_copyable
  * \implements seqan3::standard_layout
  * \implements std::regular

diff --git a/include/seqan3/alphabet/nucleotide/dna16sam.hpp b/include/seqan3/alphabet/nucleotide/dna16sam.hpp
@@ -20,7 +20,7 @@ namespace seqan3
  * \implements seqan3::nucleotide_alphabet
  * \implements seqan3::trivially_copyable
  * \implements seqan3::standard_layout
- * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif
+ * \implements seqan3::detail::writable_constexpr_alphabet
  *
  * \details
  *

diff --git a/include/seqan3/alphabet/nucleotide/dna3bs.hpp b/include/seqan3/alphabet/nucleotide/dna3bs.hpp
@@ -24,7 +24,7 @@ namespace seqan3
  * \ingroup alphabet_nucleotide
  * \implements seqan3::nucleotide_alphabet
  * \implements seqan3::writable_alphabet
- * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif
+ * \implements seqan3::detail::writable_constexpr_alphabet
  * \implements seqan3::trivially_copyable
  * \implements seqan3::standard_layout
  * \implements std::regular