[INFRA] Update contrib/std

include/seqan3/contrib/std/LICENSE → include/seqan3/contrib/std/LICENSE.md

@@ -1,5 +1,5 @@
-Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
-Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
+Copyright (c) 2006-2024, Knut Reinert & Freie Universität Berlin
+Copyright (c) 2016-2024, Knut Reinert & MPI für molekulare Genetik
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

include/seqan3/contrib/std/LICENSES/BSD-3-Clause.txt

@@ -0,0 +1,11 @@
+Copyright (c) <year> <owner>. 
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
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+
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include/seqan3/contrib/std/LICENSES/CC0-1.0.txt

@@ -0,0 +1,121 @@
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include/seqan3/contrib/std/README.md

@@ -1,6 +1,8 @@
-# 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
+<!--
+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
+-->
 
 # seqan-std
 Implementation of several C++23 views

include/seqan3/contrib/std/chunk_by_view.hpp

@@ -0,0 +1,232 @@
+// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+// SPDX-License-Identifier: BSD-3-Clause
+
+/*!\file
+ * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
+ * \brief Provides seqan::stl::views::chunk_by.
+ */
+
+// File might be included from multiple libraries.
+#ifndef SEQAN_STD_CHUNK_BY_VIEW
+#define SEQAN_STD_CHUNK_BY_VIEW
+
+#include <algorithm>
+#include <cassert>
+#include <ranges>
+
+#ifdef __cpp_lib_ranges_chunk_by
+
+namespace seqan::stl::views
+{
+
+using std::ranges::views::chunk_by;
+
+} // namespace seqan::stl::views
+
+#else
+
+#    include "all_view.hpp"
+#    include "concepts.hpp"
+#    include "detail/adaptor_from_functor.hpp"
+#    include "detail/compiler_definitions.hpp"
+#    include "detail/movable_box.hpp"
+#    include "detail/non_propagating_cache.hpp"
+
+namespace seqan::stl::ranges
+{
+
+template <std::ranges::forward_range V,
+          std::indirect_binary_predicate<std::ranges::iterator_t<V>, std::ranges::iterator_t<V>> Pred>
+    requires std::ranges::view<V> && std::is_object_v<Pred>
+class chunk_by_view : public std::ranges::view_interface<chunk_by_view<V, Pred>>
+{
+private:
+    V base_ = V();
+    seqan::stl::detail::movable_box<Pred> pred_;
+    class iterator;
+
+    seqan::stl::detail::non_propagating_cache<std::ranges::iterator_t<V>> current_;
+
+    constexpr std::ranges::iterator_t<V> find_next(std::ranges::iterator_t<V> current)
+    {
+        assert(pred_.has_value());
+        auto pred = [this]<typename lhs_t, typename rhs_t>(lhs_t && lhs, rhs_t && rhs)
+        {
+            // Call pred with two arguments, return logical not.
+            return !bool((*pred_)(std::forward<lhs_t>(lhs), std::forward<rhs_t>(rhs)));
+        };
+        auto it = std::ranges::adjacent_find(current, std::ranges::end(base_), pred);
+        return std::ranges::next(it, 1, std::ranges::end(base_));
+    }
+
+    constexpr std::ranges::iterator_t<V> find_prev(std::ranges::iterator_t<V> current)
+        requires std::ranges::bidirectional_range<V>
+    {
+        assert(pred_.has_value());
+        auto pred = [this]<typename lhs_t, typename rhs_t>(lhs_t && lhs, rhs_t && rhs)
+        {
+            // Call pred with two (reversed) arguments, return logical not.
+            return !bool((*pred_)(std::forward<rhs_t>(rhs), std::forward<lhs_t>(lhs)));
+        };
+        auto rbegin = std::make_reverse_iterator(current);
+        auto rend = std::make_reverse_iterator(std::ranges::begin(base_));
+        assert(rbegin != rend);
+        auto it = std::ranges::adjacent_find(rbegin, rend, pred).base();
+        return std::ranges::prev(it, 1, std::ranges::begin(base_));
+    }
+
+public:
+    chunk_by_view()
+        requires std::default_initializable<V> && std::default_initializable<Pred>
+    = default;
+
+    constexpr explicit chunk_by_view(V base, Pred pred) : base_{std::move(base)}, pred_{std::move(pred)}
+    {}
+
+    constexpr V base() const &
+        requires std::copy_constructible<V>
+    {
+        return base_;
+    }
+    constexpr V base() &&
+    {
+        return std::move(base_);
+    }
+
+    constexpr Pred const & pred() const
+    {
+        return *pred_;
+    }
+
+    constexpr iterator begin()
+    {
+        assert(pred_.has_value());
+        std::ranges::iterator_t<V> it;
+        if (current_.has_value())
+        {
+            it = current_.value();
+        }
+        else
+        {
+            it = find_next(std::ranges::begin(base_));
+            current_ = it;
+        }
+
+        return iterator{*this, std::ranges::begin(base_), it};
+    }
+    constexpr auto end()
+    {
+        if constexpr (std::ranges::common_range<V>)
+        {
+            return iterator{*this, std::ranges::end(base_), std::ranges::end(base_)};
+        }
+        else
+        {
+            return std::default_sentinel;
+        }
+    }
+};
+
+template <class R, class Pred>
+chunk_by_view(R &&, Pred) -> chunk_by_view<seqan::stl::views::all_t<R>, Pred>;
+
+template <std::ranges::forward_range V,
+          std::indirect_binary_predicate<std::ranges::iterator_t<V>, std::ranges::iterator_t<V>> Pred>
+    requires std::ranges::view<V> && std::is_object_v<Pred>
+class chunk_by_view<V, Pred>::iterator
+{
+private:
+    chunk_by_view * parent_ = nullptr;
+    std::ranges::iterator_t<V> current_ = std::ranges::iterator_t<V>{};
+    std::ranges::iterator_t<V> next_ = std::ranges::iterator_t<V>{};
+
+    constexpr iterator(chunk_by_view & parent, std::ranges::iterator_t<V> current, std::ranges::iterator_t<V> next) :
+        parent_{std::addressof(parent)},
+        current_{std::move(current)},
+        next_{std::move(next)}
+    {}
+
+    friend chunk_by_view;
+
+public:
+    using value_type = std::ranges::subrange<std::ranges::iterator_t<V>>;
+    using difference_type = std::ranges::range_difference_t<V>;
+    using iterator_category = std::input_iterator_tag;
+    using iterator_concept = std::conditional_t<std::ranges::bidirectional_range<V>, //
+                                                std::bidirectional_iterator_tag,
+                                                std::forward_iterator_tag>;
+
+    iterator() = default;
+
+    constexpr value_type operator*() const
+    {
+        assert(current_ != next_);
+        return std::ranges::subrange{current_, next_};
+    }
+    constexpr iterator & operator++()
+    {
+        assert(current_ != next_);
+        current_ = next_;
+        next_ = parent_->find_next(current_);
+        return *this;
+    }
+    constexpr iterator operator++(int)
+    {
+        auto tmp = *this;
+        ++*this;
+        return tmp;
+    }
+
+    constexpr iterator & operator--()
+        requires std::ranges::bidirectional_range<V>
+    {
+        next_ = current_;
+        current_ = parent_->find_prev(next_);
+        return *this;
+    }
+    constexpr iterator operator--(int)
+        requires std::ranges::bidirectional_range<V>
+    {
+        auto tmp = *this;
+        --*this;
+        return tmp;
+    }
+
+    friend constexpr bool operator==(iterator const & x, iterator const & y)
+    {
+        return x.current_ == y.current_;
+    }
+    friend constexpr bool operator==(iterator const & x, std::default_sentinel_t)
+    {
+        return x.current_ == x.next_;
+    }
+};
+
+struct chunk_by_fn
+{
+    template <typename Predicate>
+    constexpr auto operator()(Predicate && pred) const
+    {
+        return seqan::stl::detail::adaptor_from_functor{*this, std::forward<Predicate>(pred)};
+    }
+
+    template <seqan::stl::ranges::viewable_range Range, typename Predicate>
+    constexpr auto operator()(Range && range, Predicate && pred) const
+    {
+        return chunk_by_view{std::forward<Range>(range), std::forward<Predicate>(pred)};
+    }
+};
+
+} // namespace seqan::stl::ranges
+
+namespace seqan::stl::views
+{
+
+inline constexpr auto chunk_by = seqan::stl::ranges::chunk_by_fn{};
+
+} // namespace seqan::stl::views
+
+#endif // ifdef __cpp_lib_ranges_chunk_by
+
+#endif // SEQAN_STD_CHUNK_BY_VIEW