Merge pull request #51 from eseiler/infra/namespace

[MISC] Rename hibf namespace to seqan::hibf

include/hibf/all.hpp

@@ -11,7 +11,7 @@
  */
 
 /*!\defgroup search_dream_index DREAM Index
- * \brief Provides hibf::interleaved_bloom_filter.
+ * \brief Provides seqan::hibf::interleaved_bloom_filter.
  * \ingroup search
  * \see search
  */

include/hibf/config.hpp

@@ -21,7 +21,7 @@
 #include <cereal/access.hpp> // for access
 #include <cereal/cereal.hpp> // for make_nvp, CEREAL_NVP
 
-namespace hibf
+namespace seqan::hibf
 {
 
 using insert_iterator = std::insert_iterator<robin_hood::unordered_flat_set<uint64_t>>;
@@ -111,4 +111,4 @@ struct config
     }
 };
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/contrib/aligned_allocator.hpp

@@ -22,7 +22,7 @@
 #    pragma GCC warning "Non-C++17 compliant compiler! Please open an issue with your compiler and platform!"
 #endif // __cpp_aligned_new < 201606
 
-namespace hibf::contrib
+namespace seqan::hibf::contrib
 {
 
 /*!\brief Allocates uninitialized storage whose memory-alignment is specified by *alignment*.
@@ -151,14 +151,14 @@ class aligned_allocator
     }
 
     /*!\brief Deallocates the storage referenced by the pointer p, which must be a pointer obtained by an earlier call
-     * to hibf::aligned_allocator::allocate.
+     * to seqan::hibf::aligned_allocator::allocate.
      *
      * \param[in] p The pointer to the memory to be deallocated.
      * \param[in] n The number of elements to be deallocated.
      *
      * \details
      *
-     * The argument `n` must be equal to the first argument of the call to hibf::aligned_allocator::allocate that
+     * The argument `n` must be equal to the first argument of the call to seqan::hibf::aligned_allocator::allocate that
      * originally produced `p`, otherwise the behavior is undefined. This function calls
      * [operator delete](https://en.cppreference.com/w/cpp/memory/new/operator_delete) to deallocate the memory of
      * specified size.
@@ -237,4 +237,4 @@ class aligned_allocator
     //!\}
 };
 
-} // namespace hibf::contrib
+} // namespace seqan::hibf::contrib

include/hibf/contrib/std/all_view.hpp

@@ -7,7 +7,7 @@
 
 /*!\file
  * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
- * \brief Provides seqan::std::views::{all, all_t}, and seqan::std::ranges::owning_view.
+ * \brief Provides seqan::stl::views::{all, all_t}, and seqan::stl::ranges::owning_view.
  */
 
 // File might be included from multiple libraries.
@@ -18,33 +18,33 @@
 
 #if __cpp_lib_ranges >= 202110L
 
-namespace seqan::std::ranges
+namespace seqan::stl::ranges
 {
 
 using ::std::ranges::owning_view;
 
-} // namespace seqan::std::ranges
+} // namespace seqan::stl::ranges
 
-namespace seqan::std::views
+namespace seqan::stl::views
 {
 
 using ::std::ranges::views::all;
 using ::std::ranges::views::all_t;
 
-} // namespace seqan::std::views
+} // namespace seqan::stl::views
 #else
 #    include "concepts.hpp"
 #    include "detail/adaptor_base.hpp"
 #    include "detail/exposition_only.hpp"
 
-namespace seqan::std::ranges
+namespace seqan::stl::ranges
 {
 
 /*!\brief A move-only view that takes unique ownership of a range.
  * \sa https://en.cppreference.com/w/cpp/ranges/owning_view
  */
 template <::std::ranges::range rng_t>
-    requires ::std::movable<rng_t> && (!seqan::std::detail::is_initializer_list<::std::remove_cvref_t<rng_t>>)
+    requires ::std::movable<rng_t> && (!seqan::stl::detail::is_initializer_list<::std::remove_cvref_t<rng_t>>)
 class owning_view : public ::std::ranges::view_interface<owning_view<rng_t>>
 {
 private:
@@ -158,13 +158,13 @@ class owning_view : public ::std::ranges::view_interface<owning_view<rng_t>>
     }
 };
 
-/*!\brief The functor for seqan::std::views::all.
+/*!\brief The functor for seqan::stl::views::all.
  */
-class all_fn : public seqan::std::detail::adaptor_base<all_fn>
+class all_fn : public seqan::stl::detail::adaptor_base<all_fn>
 {
 private:
     //!\brief Befriend the base class.
-    friend seqan::std::detail::adaptor_base<all_fn>;
+    friend seqan::stl::detail::adaptor_base<all_fn>;
 
     //!\brief Checks whether a type is a view.
     template <typename t>
@@ -179,7 +179,7 @@ class all_fn : public seqan::std::detail::adaptor_base<all_fn>
     static constexpr bool valid_for_owning_view = requires { owning_view(::std::declval<t>()); };
 
 public:
-    using seqan::std::detail::adaptor_base<all_fn>::adaptor_base;
+    using seqan::stl::detail::adaptor_base<all_fn>::adaptor_base;
 
     /*!\brief Returns a view that includes all elements of the range argument.
      * \sa https://en.cppreference.com/w/cpp/ranges/all_view
@@ -191,7 +191,7 @@ class all_fn : public seqan::std::detail::adaptor_base<all_fn>
      *   * A ::std::ranges::ref_view of `rng` if that expression is valid.
      *   * Otherwise, a seqan3::detail::owning_view of `rng`.
      */
-    template <seqan::std::ranges::viewable_range rng_t>
+    template <seqan::stl::ranges::viewable_range rng_t>
         requires decays_to_view<rng_t> || valid_for_ref_view<rng_t> || valid_for_owning_view<rng_t>
     static auto impl(rng_t && rng)
     {
@@ -204,21 +204,21 @@ class all_fn : public seqan::std::detail::adaptor_base<all_fn>
     }
 };
 
-} // namespace seqan::std::ranges
+} // namespace seqan::stl::ranges
 
-namespace seqan::std::views
+namespace seqan::stl::views
 {
 
 /*!\copydoc all_fn::impl
  */
-inline constexpr auto all = seqan::std::ranges::all_fn{};
+inline constexpr auto all = seqan::stl::ranges::all_fn{};
 
 /*!\brief Returns the type that results from appying seqan3::detail::all to a range.
  */
-template <seqan::std::ranges::viewable_range rng_t>
+template <seqan::stl::ranges::viewable_range rng_t>
 using all_t = decltype(all(::std::declval<rng_t>()));
 
-} // namespace seqan::std::views
+} // namespace seqan::stl::views
 
 #endif // __cpp_lib_ranges >= 202110L
 

include/hibf/contrib/std/chunk_view.hpp

@@ -7,7 +7,7 @@
 
 /*!\file
  * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
- * \brief Provides seqan::std::views::chunk.
+ * \brief Provides seqan::stl::views::chunk.
  */
 
 // File might be included from multiple libraries.
@@ -18,12 +18,12 @@
 
 #ifdef __cpp_lib_ranges_chunk
 
-namespace seqan::std::views
+namespace seqan::stl::views
 {
 
 using ::std::ranges::views::chunk;
 
-} // namespace seqan::std::views
+} // namespace seqan::stl::views
 
 #else
 
@@ -37,7 +37,7 @@ using ::std::ranges::views::chunk;
 #    include "detail/exposition_only.hpp"
 #    include "detail/non_propagating_cache.hpp"
 
-namespace seqan::std::detail::chunk
+namespace seqan::stl::detail::chunk
 {
 
 template <class I>
@@ -55,9 +55,9 @@ constexpr auto to_unsigned_like(T v) noexcept
     return static_cast<::std::make_unsigned_t<T>>(v);
 }
 
-} // namespace seqan::std::detail::chunk
+} // namespace seqan::stl::detail::chunk
 
-namespace seqan::std::ranges
+namespace seqan::stl::ranges
 {
 
 template <::std::ranges::view V>
@@ -74,7 +74,7 @@ SEQAN_STD_NESTED_VISIBILITY
     ::std::ranges::range_difference_t<V> n_;
     ::std::ranges::range_difference_t<V> remainder_ = 0;
 
-    seqan::std::detail::non_propagating_cache<::std::ranges::iterator_t<V>> current_;
+    seqan::stl::detail::non_propagating_cache<::std::ranges::iterator_t<V>> current_;
 
 private:
     class outer_iterator;
@@ -115,19 +115,19 @@ SEQAN_STD_NESTED_VISIBILITY
     constexpr auto size()
         requires ::std::ranges::sized_range<V>
     {
-        return seqan::std::detail::chunk::to_unsigned_like(
-            seqan::std::detail::chunk::div_ceil(::std::ranges::distance(base_), n_));
+        return seqan::stl::detail::chunk::to_unsigned_like(
+            seqan::stl::detail::chunk::div_ceil(::std::ranges::distance(base_), n_));
     }
     constexpr auto size() const
         requires ::std::ranges::sized_range<V const>
     {
-        return seqan::std::detail::chunk::to_unsigned_like(
-            seqan::std::detail::chunk::div_ceil(::std::ranges::distance(base_), n_));
+        return seqan::stl::detail::chunk::to_unsigned_like(
+            seqan::stl::detail::chunk::div_ceil(::std::ranges::distance(base_), n_));
     }
 };
 
 template <class R>
-chunk_view(R &&, ::std::ranges::range_difference_t<R>) -> chunk_view<seqan::std::views::all_t<R>>;
+chunk_view(R &&, ::std::ranges::range_difference_t<R>) -> chunk_view<seqan::stl::views::all_t<R>>;
 
 template <::std::ranges::view V>
     requires ::std::ranges::input_range<V>
@@ -180,7 +180,7 @@ class chunk_view<V>::outer_iterator
         {
             return dist == 0 ? 0 : 1;
         }
-        return seqan::std::detail::chunk::div_ceil(dist - x.parent_->remainder_, x.parent_->n_) + 1;
+        return seqan::stl::detail::chunk::div_ceil(dist - x.parent_->remainder_, x.parent_->n_) + 1;
     }
     friend constexpr difference_type operator-(outer_iterator const & x, ::std::default_sentinel_t y)
         requires ::std::sized_sentinel_for<::std::ranges::sentinel_t<V>, ::std::ranges::iterator_t<V>>
@@ -214,7 +214,7 @@ struct chunk_view<V>::outer_iterator::value_type : ::std::ranges::view_interface
     constexpr auto size() const
         requires ::std::sized_sentinel_for<::std::ranges::sentinel_t<V>, ::std::ranges::iterator_t<V>>
     {
-        return seqan::std::detail::chunk::to_unsigned_like(
+        return seqan::stl::detail::chunk::to_unsigned_like(
             ::std::ranges::min(parent_->remainder_, ::std::ranges::end(parent_->base_) - *parent_->current_));
     }
 };
@@ -326,7 +326,7 @@ class chunk_view<V> : public ::std::ranges::view_interface<chunk_view<V>>
     }
 
     constexpr auto begin()
-        requires (!seqan::std::detail::simple_view<V>)
+        requires (!seqan::stl::detail::simple_view<V>)
     {
         return iterator<false>{this, ::std::ranges::begin(base_)};
     }
@@ -338,7 +338,7 @@ class chunk_view<V> : public ::std::ranges::view_interface<chunk_view<V>>
     }
 
     constexpr auto end()
-        requires (!seqan::std::detail::simple_view<V>)
+        requires (!seqan::stl::detail::simple_view<V>)
     {
         if constexpr (::std::ranges::common_range<V> && ::std::ranges::sized_range<V>)
         {
@@ -376,14 +376,14 @@ class chunk_view<V> : public ::std::ranges::view_interface<chunk_view<V>>
     constexpr auto size()
         requires ::std::ranges::sized_range<V>
     {
-        return seqan::std::detail::chunk::to_unsigned_like(
-            seqan::std::detail::chunk::div_ceil(::std::ranges::distance(base_), n_));
+        return seqan::stl::detail::chunk::to_unsigned_like(
+            seqan::stl::detail::chunk::div_ceil(::std::ranges::distance(base_), n_));
     }
     constexpr auto size() const
         requires ::std::ranges::sized_range<V const>
     {
-        return seqan::std::detail::chunk::to_unsigned_like(
-            seqan::std::detail::chunk::div_ceil(::std::ranges::distance(base_), n_));
+        return seqan::stl::detail::chunk::to_unsigned_like(
+            seqan::stl::detail::chunk::div_ceil(::std::ranges::distance(base_), n_));
     }
 };
 
@@ -393,8 +393,8 @@ template <bool Const>
 class chunk_view<V>::iterator
 {
 private:
-    using Parent = seqan::std::detail::maybe_const<Const, chunk_view>;
-    using Base = seqan::std::detail::maybe_const<Const, V>;
+    using Parent = seqan::stl::detail::maybe_const<Const, chunk_view>;
+    using Base = seqan::stl::detail::maybe_const<Const, V>;
 
     ::std::ranges::iterator_t<Base> current_ = ::std::ranges::iterator_t<Base>{};
     ::std::ranges::sentinel_t<Base> end_ = ::std::ranges::sentinel_t<Base>{};
@@ -575,7 +575,7 @@ class chunk_view<V>::iterator
     friend constexpr difference_type operator-(::std::default_sentinel_t y, iterator const & x)
         requires ::std::sized_sentinel_for<::std::ranges::sentinel_t<Base>, ::std::ranges::iterator_t<Base>>
     {
-        return seqan::std::detail::chunk::div_ceil(x.end_ - x.current_, x.n_);
+        return seqan::stl::detail::chunk::div_ceil(x.end_ - x.current_, x.n_);
     }
 
     friend constexpr difference_type operator-(iterator const & x, ::std::default_sentinel_t y)
@@ -590,24 +590,24 @@ struct chunk_fn
     template <typename Difference>
     constexpr auto operator()(Difference n) const
     {
-        return seqan::std::detail::adaptor_from_functor{*this, n};
+        return seqan::stl::detail::adaptor_from_functor{*this, n};
     }
 
-    template <seqan::std::ranges::viewable_range Range, typename Difference = ::std::ranges::range_difference_t<Range>>
+    template <seqan::stl::ranges::viewable_range Range, typename Difference = ::std::ranges::range_difference_t<Range>>
     constexpr auto operator()(Range && range, ::std::type_identity_t<Difference> n) const
     {
         return chunk_view{::std::forward<Range>(range), n};
     }
 };
 
-} // namespace seqan::std::ranges
+} // namespace seqan::stl::ranges
 
-namespace seqan::std::views
+namespace seqan::stl::views
 {
 
-inline constexpr auto chunk = seqan::std::ranges::chunk_fn{};
+inline constexpr auto chunk = seqan::stl::ranges::chunk_fn{};
 
-} // namespace seqan::std::views
+} // namespace seqan::stl::views
 
 #endif // ifdef __cpp_lib_ranges_chunk
 

include/hibf/contrib/std/concepts.hpp

@@ -7,7 +7,7 @@
 
 /*!\file
  * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
- * \brief Provides seqan::std concepts.
+ * \brief Provides seqan::stl concepts.
  */
 
 // File might be included from multiple libraries.
@@ -17,15 +17,15 @@
 #include <ranges>
 
 #if __cpp_lib_ranges >= 202110L
-namespace seqan::std::ranges
+namespace seqan::stl::ranges
 {
 
 using ::std::ranges::viewable_range;
 
 }
 #else
 #    include "detail/exposition_only.hpp"
-namespace seqan::std::ranges
+namespace seqan::stl::ranges
 {
 
 template <class T>
@@ -35,9 +35,9 @@ concept viewable_range = ::std::ranges::range<T>
                           || (!::std::ranges::view<::std::remove_cvref_t<T>>
                               && (::std::is_lvalue_reference_v<T>
                                   || (::std::movable<::std::remove_reference_t<T>>
-                                      && !seqan::std::detail::is_initializer_list<::std::remove_cvref_t<T>>))));
+                                      && !seqan::stl::detail::is_initializer_list<::std::remove_cvref_t<T>>))));
 
-} // namespace seqan::std::ranges
+} // namespace seqan::stl::ranges
 
 #endif