[FIX] API stability (#2559)

* [FIX] api stability since 3.0.2

* [MISC] interleaved_bloom_filter: make single argument  constructor explicit

* [MISC] add deprecated equality operator

include/seqan3/alphabet/nucleotide/dna16sam.hpp

@@ -217,3 +217,24 @@ constexpr std::array<dna16sam, dna16sam::alphabet_size> dna16sam::complement_tab
 };
 
 } // namespace seqan3
+
+namespace seqan3
+{
+//!\deprecated Please use seqan3::dna16sam instead.
+using sam_dna16 SEQAN3_DEPRECATED_310 = seqan3::dna16sam;
+
+//!\deprecated Please use seqan3::dna16sam_vector instead.
+using sam_dna16_vector SEQAN3_DEPRECATED_310 = dna16sam_vector;
+
+//!\deprecated Please use seqan3::operator""_dna16sam instead.
+SEQAN3_DEPRECATED_310 constexpr dna16sam operator""_sam_dna16(char const c) noexcept
+{
+    return seqan3::operator""_dna16sam(c);
+}
+
+//!\deprecated Please use seqan3::operator""_dna16sam instead.
+SEQAN3_DEPRECATED_310 inline dna16sam_vector operator""_sam_dna16(char const * s, size_t n)
+{
+    return seqan3::operator""_dna16sam(s, n);
+}
+} // namespace seqan3

include/seqan3/alphabet/nucleotide/sam_dna16.hpp

@@ -15,11 +15,5 @@
 
 #include <seqan3/alphabet/nucleotide/dna16sam.hpp>
 
-namespace seqan3
-{
-//!\deprecated Please use seqan3::dna16sam instead.
-using sam_dna16 SEQAN3_DEPRECATED_310 = seqan3::dna16sam;
-} // namespace seqan3
-
 SEQAN3_DEPRECATED_HEADER(
    "This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/alphabet/nucleotide/dna16sam.hpp> instead.")

include/seqan3/alphabet/quality/phred68legacy.hpp

@@ -16,11 +16,5 @@
 
 #include <seqan3/alphabet/quality/phred68solexa.hpp>
 
-namespace seqan3
-{
-//!\deprecated Please use seqan3::phred68solexa instead.
-using phred68legacy SEQAN3_DEPRECATED_310 = seqan3::phred68solexa;
-} // namespace seqan3
-
 SEQAN3_DEPRECATED_HEADER(
    "This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/alphabet/quality/phred68solexa.hpp> instead.")

include/seqan3/alphabet/quality/phred68solexa.hpp

@@ -125,3 +125,21 @@ inline std::vector<phred68solexa> operator""_phred68solexa(char const * s, std::
 //!\}
 
 } // namespace seqan3
+
+namespace seqan3
+{
+//!\deprecated Please use seqan3::phred68solexa instead.
+using phred68legacy SEQAN3_DEPRECATED_310 = seqan3::phred68solexa;
+
+//!\deprecated Please use seqan3::operator""_phred68solexa instead.
+SEQAN3_DEPRECATED_310 constexpr phred68solexa operator""_phred68legacy(char const c) noexcept
+{
+    return seqan3::operator""_phred68solexa(c);
+}
+
+//!\deprecated Please use seqan3::operator""_phred68solexa instead.
+SEQAN3_DEPRECATED_310 inline std::vector<phred68solexa> operator""_phred68legacy(char const * s, size_t n)
+{
+    return seqan3::operator""_phred68solexa(s, n);
+}
+} // namespace seqan3

include/seqan3/search/dream_index/interleaved_bloom_filter.hpp

@@ -592,7 +592,9 @@ class interleaved_bloom_filter<data_layout_mode>::membership_agent
      * \private
      * \param ibf The seqan3::interleaved_bloom_filter.
      */
-    membership_agent(ibf_t const & ibf) : ibf_ptr(std::addressof(ibf)), result_buffer(ibf.bin_count()) {}
+    explicit membership_agent(ibf_t const & ibf) :
+        ibf_ptr(std::addressof(ibf)), result_buffer(ibf.bin_count())
+    {}
     //!\}
 
     //!\brief Stores the result of bulk_contains().
@@ -679,7 +681,9 @@ class interleaved_bloom_filter<data_layout_mode>::membership_agent::binning_bitv
     ~binning_bitvector() = default; //!< Defaulted.
 
     //!\brief Construct with given size.
-    binning_bitvector(size_t const size) : data(size) {}
+    explicit binning_bitvector(size_t const size) :
+        data(size)
+    {}
     //!\}
 
     //!\brief Returns the number of elements.
@@ -730,6 +734,36 @@ class interleaved_bloom_filter<data_layout_mode>::membership_agent::binning_bitv
     {
         return !(lhs == rhs);
     }
+
+#ifdef SEQAN3_DEPRECATED_310
+    //!\brief Test for equality.
+    //!\deprecated Use binning_bitvector.raw_data() == rhs
+    SEQAN3_DEPRECATED_310 friend bool operator==(binning_bitvector const & lhs, sdsl::bit_vector const & rhs) noexcept
+    {
+        return lhs.data == rhs;
+    }
+
+    //!\brief Test for equality.
+    //!\deprecated Use lhs == binning_bitvector.raw_data()
+    SEQAN3_DEPRECATED_310 friend bool operator==(sdsl::bit_vector const & lhs, binning_bitvector const & rhs) noexcept
+    {
+        return lhs == rhs.data;
+    }
+
+    //!\brief Test for inequality.
+    //!\deprecated Use binning_bitvector.raw_data() != rhs
+    SEQAN3_DEPRECATED_310 friend bool operator!=(binning_bitvector const & lhs, sdsl::bit_vector const & rhs) noexcept
+    {
+        return !(lhs.data == rhs);
+    }
+
+    //!\brief Test for inequality.
+    //!\deprecated Use lhs != binning_bitvector.raw_data()
+    SEQAN3_DEPRECATED_310 friend bool operator!=(sdsl::bit_vector const & lhs, binning_bitvector const & rhs) noexcept
+    {
+        return !(lhs == rhs.data);
+    }
+#endif // SEQAN3_DEPRECATED_310
     //!\}
 
     /*!\name Access
@@ -916,7 +950,7 @@ class interleaved_bloom_filter<data_layout_mode>::counting_agent_type
      * \private
      * \param ibf The seqan3::interleaved_bloom_filter.
      */
-    counting_agent_type(ibf_t const & ibf) :
+    explicit counting_agent_type(ibf_t const & ibf) :
         ibf_ptr(std::addressof(ibf)), membership_agent(ibf), result_buffer(ibf.bin_count())
     {}
     //!\}

test/api_stability/3.0.2/0023-NOAPI-INCLUDE-add-missing-includes-seqan3-views-pers.patch

@@ -0,0 +1,38 @@
+From 12b7805b266a7477492657756fa77dda9b8f5fe5 Mon Sep 17 00:00:00 2001
+From: marehr <[email protected]>
+Date: Sun, 25 Apr 2021 18:12:55 +0200
+Subject: [PATCH 23/24] [NOAPI] [INCLUDE] add missing includes
+ seqan3::views::persist
+
+---
+ .../pairwise_alignment/pairwise_alignment_solution_6.cpp         | 1 +
+ .../fm_index_cursor/bi_fm_index_cursor_collection_test.cpp       | 1 +
+ 2 files changed, 2 insertions(+)
+
+diff --git a/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_6.cpp b/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_6.cpp
+index 1ed35c8cd..32b6077d2 100644
+--- a/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_6.cpp
++++ b/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_6.cpp
+@@ -6,6 +6,7 @@
+ #include <seqan3/alphabet/nucleotide/dna4.hpp>
+ #include <seqan3/core/debug_stream.hpp>
+ #include <seqan3/range/views/pairwise_combine.hpp>
++#include <seqan3/range/views/persist.hpp>
+ #include <seqan3/std/ranges>
+
+ using seqan3::operator""_dna4;
+diff --git a/test/unit/search/fm_index_cursor/bi_fm_index_cursor_collection_test.cpp b/test/unit/search/fm_index_cursor/bi_fm_index_cursor_collection_test.cpp
+index 48be041bc..5d055adb9 100644
+--- a/test/unit/search/fm_index_cursor/bi_fm_index_cursor_collection_test.cpp
++++ b/test/unit/search/fm_index_cursor/bi_fm_index_cursor_collection_test.cpp
+@@ -9,6 +9,7 @@
+
+ #include <seqan3/alphabet/nucleotide/dna4.hpp>
+ #include <seqan3/alphabet/nucleotide/dna5.hpp>
++#include <seqan3/range/views/persist.hpp>
+ #include <seqan3/range/views/slice.hpp>
+ #include <seqan3/range/views/char_to.hpp>
+ #include <seqan3/range/views/to.hpp>
+-- 
+2.31.1
+

test/api_stability/3.0.2/0024-NOAPI-INCLUDE-add-missing-includes-std-isnan.patch

@@ -0,0 +1,24 @@
+From ccf8a01d614f20c114d384003092a60366056be8 Mon Sep 17 00:00:00 2001
+From: marehr <[email protected]>
+Date: Sun, 25 Apr 2021 18:13:15 +0200
+Subject: [PATCH 24/24] [NOAPI] [INCLUDE] add missing includes std::isnan
+
+---
+ test/unit/std/charconv_float_test.cpp | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/test/unit/std/charconv_float_test.cpp b/test/unit/std/charconv_float_test.cpp
+index 123f2e3d8..654d2a8c2 100644
+--- a/test/unit/std/charconv_float_test.cpp
++++ b/test/unit/std/charconv_float_test.cpp
+@@ -7,6 +7,7 @@
+
+ #include <gtest/gtest.h>
+
++#include <cmath>
+ #include <iostream>
+ #include <limits>
+
+-- 
+2.31.1
+