Merge pull request #2327 from eseiler/infra/new_doxy

[INFRA] Use doxygen 1.9.1

.github/workflows/ci.yml

@@ -11,7 +11,7 @@ on:
 
 env:
   CMAKE_VERSION: 3.8.2
-  DOXYGEN_VERSION: 1.8.20
+  DOXYGEN_VERSION: 1.9.1
   SEQAN3_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 

.github/workflows/documentation.yaml

@@ -7,7 +7,7 @@ on:
 
 env:
   CMAKE_VERSION: 3.7.2
-  DOXYGEN_VERSION: 1.8.20
+  DOXYGEN_VERSION: 1.9.1
   TZ: Europe/Berlin
 
 defaults:

CHANGELOG.md

@@ -43,6 +43,10 @@ If possible, provide tooling that performs the changes, e.g. a shell-script.
 * The subcommand of the `seqan3::argument_parser` may contain a dash
   ([\#2306](https://github.com/seqan/seqan3/pull/2306)).
 
+#### Build system
+
+* We now use Doxygen version 1.9.1 to build our documentation ([\#2327](https://github.com/seqan/seqan3/pull/2327)).
+
 #### Search
 
 * The `seqan3::fm_index_cursor` exposes its suffix array interval ([\#2076](https://github.com/seqan/seqan3/pull/2076)).

include/seqan3/alignment/matrix/detail/alignment_matrix_column_major_range_base.hpp

@@ -368,9 +368,8 @@ class alignment_matrix_column_major_range_base
             return column_index == me_ptr->num_cols;
         }
 
-        //!\copydoc operator==
-        friend constexpr bool operator==(std::default_sentinel_t const & lhs, iterator_type const & rhs)
-            noexcept
+        //!\copydoc seqan3::detail::alignment_matrix_column_major_range_base::alignment_column_type::iterator_type::operator==
+        friend constexpr bool operator==(std::default_sentinel_t const & lhs, iterator_type const & rhs) noexcept
         {
             return rhs == lhs;
         }
@@ -381,9 +380,8 @@ class alignment_matrix_column_major_range_base
             return !(*this == rhs);
         }
 
-        //!\copydoc operator!=
-        friend constexpr bool operator!=(std::default_sentinel_t const & lhs, iterator_type const & rhs)
-            noexcept
+        //!\copydoc seqan3::detail::alignment_matrix_column_major_range_base::alignment_column_type::iterator_type::operator!=
+        friend constexpr bool operator!=(std::default_sentinel_t const & lhs, iterator_type const & rhs) noexcept
         {
             return rhs != lhs;
         }

include/seqan3/alphabet/composite/alphabet_tuple_base.hpp

@@ -150,7 +150,7 @@ class alphabet_tuple_base :
     private:
         //!\brief The base type.
         using base_t = alphabet_proxy<component_proxy<alphabet_type, index>, alphabet_type>;
-        //!\brief Befriend the base type so it can call our #on_update().
+        //!\brief Befriend the base type so it can call our seqan3::alphabet_tuple_base::component_proxy::on_update().
         friend base_t;
 
         //!\brief Store a pointer to the parent object so we can update it.
@@ -199,67 +199,67 @@ class alphabet_tuple_base :
             return get<index>(lhs) == static_cast<alphabet_type>(rhs);
         }
 
-        //!\copydoc operator==(derived_type const lhs, component_proxy const rhs)
+        //!\copydoc seqan3::alphabet_tuple_base::component_proxy::operator==(derived_type const, component_proxy const)
         friend constexpr bool operator==(component_proxy<alphabet_type, index> const lhs, derived_type const rhs) noexcept
         {
             return rhs == lhs;
         }
 
-        //!\copydoc operator==(derived_type const lhs, component_proxy const rhs)
+        //!\copydoc seqan3::alphabet_tuple_base::component_proxy::operator==(derived_type const, component_proxy const)
         friend constexpr bool operator!=(derived_type const lhs, component_proxy const rhs) noexcept
         {
             return get<index>(lhs) != static_cast<alphabet_type>(rhs);
         }
 
-        //!\copydoc operator==(derived_type const lhs, component_proxy const rhs)
+        //!\copydoc seqan3::alphabet_tuple_base::component_proxy::operator==(derived_type const, component_proxy const)
         friend constexpr bool operator!=(component_proxy<alphabet_type, index> const lhs, derived_type const rhs) noexcept
         {
             return rhs != lhs;
         }
 
-        //!\copydoc operator==(derived_type const lhs, component_proxy const rhs)
+        //!\copydoc seqan3::alphabet_tuple_base::component_proxy::operator==(derived_type const, component_proxy const)
         friend constexpr bool operator<(derived_type const lhs, component_proxy const rhs) noexcept
         {
             return get<index>(lhs) < static_cast<alphabet_type>(rhs);
         }
 
-        //!\copydoc operator==(derived_type const lhs, component_proxy const rhs)
+        //!\copydoc seqan3::alphabet_tuple_base::component_proxy::operator==(derived_type const, component_proxy const)
         friend constexpr bool operator<(component_proxy<alphabet_type, index> const lhs, derived_type const rhs) noexcept
         {
             return rhs > lhs;
         }
 
-        //!\copydoc operator==(derived_type const lhs, component_proxy const rhs)
+        //!\copydoc seqan3::alphabet_tuple_base::component_proxy::operator==(derived_type const, component_proxy const)
         friend constexpr bool operator<=(derived_type const lhs, component_proxy const rhs) noexcept
         {
             return get<index>(lhs) <= static_cast<alphabet_type>(rhs);
         }
 
-        //!\copydoc operator==(derived_type const lhs, component_proxy const rhs)
+        //!\copydoc seqan3::alphabet_tuple_base::component_proxy::operator==(derived_type const, component_proxy const)
         friend constexpr bool operator<=(component_proxy<alphabet_type, index> const lhs, derived_type const rhs) noexcept
         {
             return rhs >= lhs;
         }
 
-        //!\copydoc operator==(derived_type const lhs, component_proxy const rhs)
+        //!\copydoc seqan3::alphabet_tuple_base::component_proxy::operator==(derived_type const, component_proxy const)
         friend constexpr bool operator>(derived_type const lhs, component_proxy const rhs) noexcept
         {
             return get<index>(lhs) > static_cast<alphabet_type>(rhs);
         }
 
-        //!\copydoc operator==(derived_type const lhs, component_proxy const rhs)
+        //!\copydoc seqan3::alphabet_tuple_base::component_proxy::operator==(derived_type const, component_proxy const)
         friend constexpr bool operator>(component_proxy<alphabet_type, index> const lhs, derived_type const rhs) noexcept
         {
             return rhs < lhs;
         }
 
-        //!\copydoc operator==(derived_type const lhs, component_proxy const rhs)
+        //!\copydoc seqan3::alphabet_tuple_base::component_proxy::operator==(derived_type const, component_proxy const)
         friend constexpr bool operator>=(derived_type const lhs, component_proxy const rhs) noexcept
         {
             return get<index>(lhs) >= static_cast<alphabet_type>(rhs);
         }
 
-        //!\copydoc operator==(derived_type const lhs, component_proxy const rhs)
+        //!\copydoc seqan3::alphabet_tuple_base::component_proxy::operator==(derived_type const, component_proxy const)
         friend constexpr bool operator>=(component_proxy<alphabet_type, index> const lhs, derived_type const rhs) noexcept
         {
             return rhs <= lhs;

test/documentation/seqan3_doxygen_cfg.in

@@ -63,8 +63,6 @@ EXCLUDE_SYMBOLS        = seqan3::contrib
 FORMULA_FONTSIZE       = 14
 HTML_DYNAMIC_SECTIONS  = YES
 
-COLS_IN_ALPHA_INDEX    = 1
-
 ## detect headers without extensions (in std module)
 EXTENSION_MAPPING      = .no_extension=C++
 FILE_PATTERNS          = *