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[INFRA] Use doxygen 1.9.1 #2327

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merged 4 commits into from
Jan 12, 2021
Merged

[INFRA] Use doxygen 1.9.1 #2327

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4042736
[DOC] Remove deprecated doxygen config entry
eseiler Jan 11, 2021
93af0aa
[DOC] Use qualified names in copydoc
eseiler Jan 11, 2021
4cbe8f9
[INFRA] Use doxygen 1.9.1
eseiler Jan 11, 2021
74a8a3c
[MISC] Add changelog entry for new doxygen version
eseiler Jan 11, 2021
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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

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2 changes: 1 addition & 1 deletion .github/workflows/documentation.yaml
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Expand Up @@ -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:
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -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)).
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10 changes: 4 additions & 6 deletions include/seqan3/alignment/matrix/detail/alignment_matrix_column_major_range_base.hpp
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Expand Up @@ -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;
}
Expand All @@ -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;
}
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24 changes: 12 additions & 12 deletions include/seqan3/alphabet/composite/alphabet_tuple_base.hpp
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Expand Up @@ -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.
Expand Down Expand Up @@ -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;
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2 changes: 0 additions & 2 deletions test/documentation/seqan3_doxygen_cfg.in
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Expand Up @@ -63,8 +63,6 @@ EXCLUDE_SYMBOLS = seqan3::contrib
FORMULA_FONTSIZE = 14
HTML_DYNAMIC_SECTIONS = YES

COLS_IN_ALPHA_INDEX = 1

Comment on lines -66 to -67
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Why this change?

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the option was remvoed

## detect headers without extensions (in std module)
EXTENSION_MAPPING = .no_extension=C++
FILE_PATTERNS = *
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