[MISC] Deprecate seqan3::views::get

seqan · Apr 26, 2021 · 57a5098 · 57a5098
1 parent c25182c
commit 57a5098
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Showing 15 changed files with 42 additions and 34 deletions.
diff --git a/doc/tutorial/sam_file/sam_file_solution1.cpp b/doc/tutorial/sam_file/sam_file_solution1.cpp
@@ -30,7 +30,6 @@ write_file_dummy_struct go{};
 
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/io/sam_file/all.hpp>
-#include <seqan3/range/views/get.hpp>
 
 int main()
 {

diff --git a/doc/tutorial/sequence_file/sequence_file_solution3.cpp b/doc/tutorial/sequence_file/sequence_file_solution3.cpp
@@ -1,7 +1,7 @@
+#include <seqan3/std/filesystem>
 #include <fstream>
 
 #include <seqan3/core/debug_stream.hpp>
-#include <seqan3/std/filesystem>
 
 struct write_file_dummy_struct
 {
@@ -51,12 +51,12 @@ IIIIIHIIJJIIIII
 write_file_dummy_struct go{};
 
 //![solution]
+#include <seqan3/std/filesystem>
+#include <seqan3/std/ranges>
+
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/io/sequence_file/all.hpp>
-#include <seqan3/range/views/get.hpp>
 #include <seqan3/range/views/move.hpp>
-#include <seqan3/std/filesystem>
-#include <seqan3/std/ranges>
 
 int main()
 {
@@ -83,7 +83,7 @@ int main()
                                  | std::views::take(2)                              // take first two records
                                  | std::views::transform(&decltype(fin)::record_type::id) // select only ID from record
                                  // this is the same as writing:
-//                                 | std::views::transform([](auto && record)         
+//                                 | std::views::transform([](auto && record)
 //                                   {
 //                                       return record.id();
 //                                   })

diff --git a/include/seqan3/alignment/pairwise/alignment_algorithm.hpp b/include/seqan3/alignment/pairwise/alignment_algorithm.hpp
@@ -30,7 +30,6 @@
 #include <seqan3/core/detail/empty_type.hpp>
 #include <seqan3/range/container/aligned_allocator.hpp>
 #include <seqan3/range/views/drop.hpp>
-#include <seqan3/range/views/get.hpp>
 #include <seqan3/range/views/take.hpp>
 #include <seqan3/utility/simd/concept.hpp>
 #include <seqan3/utility/simd/simd.hpp>
@@ -204,8 +203,8 @@ class alignment_algorithm :
         static_assert(simd_concept<typename traits_t::trace_type>, "Expected simd trace type.");
 
         // Extract the batch of sequences for the first and the second sequence.
-        auto sequence1_range = indexed_sequence_pairs | views::get<0> | views::get<0>;
-        auto sequence2_range = indexed_sequence_pairs | views::get<0> | views::get<1>;
+        auto sequence1_range = indexed_sequence_pairs | std::views::elements<0> | std::views::elements<0>;
+        auto sequence2_range = indexed_sequence_pairs | std::views::elements<0> | std::views::elements<1>;
 
         // Initialise the find_optimum policy in the simd case.
         this->initialise_find_optimum_policy(sequence1_range,

diff --git a/include/seqan3/alignment/pairwise/detail/pairwise_alignment_algorithm.hpp b/include/seqan3/alignment/pairwise/detail/pairwise_alignment_algorithm.hpp
@@ -18,7 +18,6 @@
 #include <seqan3/alignment/pairwise/detail/type_traits.hpp>
 #include <seqan3/core/detail/empty_type.hpp>
 #include <seqan3/range/container/aligned_allocator.hpp>
-#include <seqan3/range/views/get.hpp>
 #include <seqan3/utility/detail/type_name_as_string.hpp>
 #include <seqan3/utility/simd/views/to_simd.hpp>
 
@@ -161,8 +160,8 @@ class pairwise_alignment_algorithm : protected policies_t...
         using original_score_t = typename traits_type::original_score_type;
 
         // Extract the batch of sequences for the first and the second sequence.
-        auto seq1_collection = indexed_sequence_pairs | views::get<0> | views::get<0>;
-        auto seq2_collection = indexed_sequence_pairs | views::get<0> | views::get<1>;
+        auto seq1_collection = indexed_sequence_pairs | std::views::elements<0> | std::views::elements<0>;
+        auto seq2_collection = indexed_sequence_pairs | std::views::elements<0> | std::views::elements<1>;
 
         this->initialise_tracker(seq1_collection, seq2_collection);
 

diff --git a/include/seqan3/alignment/pairwise/detail/pairwise_alignment_algorithm_banded.hpp b/include/seqan3/alignment/pairwise/detail/pairwise_alignment_algorithm_banded.hpp
@@ -123,8 +123,8 @@ class pairwise_alignment_algorithm_banded :
         using original_score_t = typename traits_type::original_score_type;
 
         // Extract the batch of sequences for the first and the second sequence.
-        auto seq1_collection = indexed_sequence_pairs | views::get<0> | views::get<0>;
-        auto seq2_collection = indexed_sequence_pairs | views::get<0> | views::get<1>;
+        auto seq1_collection = indexed_sequence_pairs | std::views::elements<0> | std::views::elements<0>;
+        auto seq2_collection = indexed_sequence_pairs | std::views::elements<0> | std::views::elements<1>;
 
         this->initialise_tracker(seq1_collection, seq2_collection);
 

diff --git a/include/seqan3/io/sequence_file/output.hpp b/include/seqan3/io/sequence_file/output.hpp
@@ -36,7 +36,6 @@
 #include <seqan3/io/sequence_file/output_format_concept.hpp>
 #include <seqan3/io/sequence_file/output_options.hpp>
 #include <seqan3/io/stream/concept.hpp>
-#include <seqan3/range/views/get.hpp>
 #include <seqan3/utility/tuple/concept.hpp>
 #include <seqan3/utility/type_list/traits.hpp>
 #include <seqan3/utility/views/convert.hpp>
@@ -603,9 +602,9 @@ class sequence_file_output
             {
                 f.write_sequence_record(*secondary_stream,
                                         options,
-                                        seq_qual | views::get<0>,
+                                        seq_qual | std::views::elements<0>,
                                         id,
-                                        seq_qual | views::get<1>);
+                                        seq_qual | std::views::elements<1>);
             }
             else
             {

diff --git a/include/seqan3/io/structure_file/output.hpp b/include/seqan3/io/structure_file/output.hpp
@@ -32,7 +32,6 @@
 #include <seqan3/io/structure_file/output_format_concept.hpp>
 #include <seqan3/io/structure_file/output_options.hpp>
 #include <seqan3/io/structure_file/format_vienna.hpp>
-#include <seqan3/range/views/get.hpp>
 #include <seqan3/utility/tuple/concept.hpp>
 #include <seqan3/utility/type_list/traits.hpp>
 #include <seqan3/utility/views/convert.hpp>
@@ -627,10 +626,10 @@ class structure_file_output
             {
                 f.write_structure_record(*secondary_stream,
                                          options,
-                                         structured_seq | views::get<0>,
+                                         structured_seq | std::views::elements<0>,
                                          id,
                                          bpp,
-                                         structured_seq | views::get<1>,
+                                         structured_seq | std::views::elements<1>,
                                          energy,
                                          react,
                                          react_error,

diff --git a/include/seqan3/range/views/all.hpp b/include/seqan3/range/views/all.hpp
@@ -19,7 +19,6 @@
 #include <seqan3/alphabet/views/trim_quality.hpp>
 #include <seqan3/range/views/complement.hpp>
 #include <seqan3/range/views/enforce_random_access.hpp>
-#include <seqan3/range/views/get.hpp>
 #include <seqan3/range/views/interleave.hpp>
 #include <seqan3/range/views/istreambuf.hpp>
 #include <seqan3/range/views/move.hpp>

diff --git a/include/seqan3/range/views/get.hpp b/include/seqan3/range/views/get.hpp
@@ -7,7 +7,7 @@
 
 /*!\file
  * \author Joshua Kim <joshua.kim AT fu-berlin.de>
- * \brief Provides seqan3::views::get.
+ * \brief [DEPRECATED] Provides seqan3::views::get.
  */
 
 #pragma once
@@ -59,11 +59,15 @@ namespace seqan3::views
  *
  * ### Example
  *
- * \include test/snippet/range/views/get.cpp
+ * \snippet test/snippet/range/views/get.cpp snippet
  * \hideinitializer
+ *
+ * \deprecated Use `std::views::elements<index>` if index is a size type, otherwise use
+ *             `std::views::transform([] (auto && tuple) { using std::get; return get<index>(tuple); });`.
  */
+#ifdef SEQAN3_DEPRECATED_310
 template <auto index>
-inline auto const get = std::views::transform([] (auto && in) -> decltype(auto)
+SEQAN3_DEPRECATED_310 inline constexpr auto get = std::views::transform([] (auto && in) -> decltype(auto)
 {
     using std::get;
     using seqan3::get;
@@ -76,6 +80,7 @@ inline auto const get = std::views::transform([] (auto && in) -> decltype(auto)
     using ret_type = remove_rvalue_reference_t<decltype(get<index>(std::forward<decltype(in)>(in)))>;
     return static_cast<ret_type>(get<index>(std::forward<decltype(in)>(in)));
 });
+#endif // SEQAN3_DEPRECATED_310
 
 //!\}
 

diff --git a/test/snippet/argument_parser/custom_enumeration.cpp b/test/snippet/argument_parser/custom_enumeration.cpp
@@ -1,6 +1,4 @@
 #include <seqan3/argument_parser/all.hpp>
-#include <seqan3/range/views/all.hpp>
-#include <seqan3/range/views/get.hpp>
 
 namespace foo
 {
@@ -29,7 +27,7 @@ int main(int argc, char const * argv[])
     // Because of the enumeration_names function
     // you can now add an option that takes a value of type bar:
     parser.add_option(value, 'f', "foo", "Give me a foo value.", seqan3::option_spec::standard,
-                      seqan3::value_list_validator{(seqan3::enumeration_names<foo::bar> | seqan3::views::get<1>)});
+                      seqan3::value_list_validator{(seqan3::enumeration_names<foo::bar> | std::views::values)});
 
     try
     {

diff --git a/test/snippet/io/sequence_file/sequence_file_input_custom_fields.cpp b/test/snippet/io/sequence_file/sequence_file_input_custom_fields.cpp
@@ -3,7 +3,6 @@
 
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/io/sequence_file/input.hpp>
-#include <seqan3/range/views/get.hpp>
 
 auto input = R"(> TEST1
 ACGT

diff --git a/test/snippet/io/sequence_file/sequence_file_output_fields_trait_1.cpp b/test/snippet/io/sequence_file/sequence_file_output_fields_trait_1.cpp
@@ -7,7 +7,6 @@
 #include <seqan3/alphabet/quality/phred42.hpp>
 #include <seqan3/alphabet/quality/qualified.hpp>
 #include <seqan3/io/sequence_file/output.hpp>
-#include <seqan3/range/views/get.hpp>
 
 int main()
 {
@@ -26,8 +25,8 @@ int main()
                                                                                {'A'_dna5, '1'_phred42},
                                                                                {'C'_dna5, '3'_phred42}};
 
-        auto view_on_seq  = seqan3::views::get<0>(seq_qual);
-        auto view_on_qual = seqan3::views::get<1>(seq_qual);
+        auto view_on_seq  = std::views::elements<0>(seq_qual);
+        auto view_on_qual = std::views::elements<1>(seq_qual);
 
         // ...
 

diff --git a/test/snippet/io/structure_file/structure_file_input_skip_fields.cpp b/test/snippet/io/structure_file/structure_file_input_skip_fields.cpp
@@ -3,7 +3,6 @@
 #include <seqan3/alphabet/views/to_char.hpp>
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/io/structure_file/input.hpp>
-#include <seqan3/range/views/get.hpp>
 
 auto input = R"(> S.cerevisiae_tRNA-PHE M10740/1-73
 GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA
@@ -26,7 +25,7 @@ int main()
         seqan3::debug_stream << "ID: "        << id                                                         << '\n';
         // sequence and structure are part of the same vector, of type std::vector<structured_rna<rna5, wuss51>>
         // sequence and structure strings are extracted and converted to char on-the-fly
-        seqan3::debug_stream << "SEQ: "       << (struc_seq | seqan3::views::get<0> | seqan3::views::to_char) << '\n';
-        seqan3::debug_stream << "STRUCTURE: " << (struc_seq | seqan3::views::get<1> | seqan3::views::to_char) << '\n';
+        seqan3::debug_stream << "SEQ: "       << (struc_seq | std::views::elements<0> | seqan3::views::to_char) << '\n';
+        seqan3::debug_stream << "STRUCTURE: " << (struc_seq | std::views::elements<1> | seqan3::views::to_char) << '\n';
     }
 }
diff --git a/test/snippet/range/views/get.cpp b/test/snippet/range/views/get.cpp
@@ -1,3 +1,7 @@
+#ifdef SEQAN3_DEPRECATED_310
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wdeprecated-declarations"
+//![snippet]
 #include <vector>
 
 #include <seqan3/alphabet/nucleotide/dna4.hpp>
@@ -21,3 +25,6 @@ int main()
     seqan3::debug_stream << (qv | seqan3::views::get<0> | seqan3::views::to_char) << '\n'; // Prints [A,C,G,T]
     seqan3::debug_stream << (qv | seqan3::views::get<1> | seqan3::views::to_char) << '\n'; // Prints [!,",#,$]
 }
+//![snippet]
+#pragma GCC diagnostic pop
+#endif // SEQAN3_DEPRECATED_310
diff --git a/test/unit/range/views/get_test.cpp b/test/unit/range/views/get_test.cpp
@@ -25,6 +25,10 @@
 using seqan3::operator""_dna4;
 using seqan3::operator""_phred42;
 
+#ifdef SEQAN3_DEPRECATED_310
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wdeprecated-declarations"
+
 TEST(view_get, basic)
 {
     // TODO remove const-ness from input vector once alphabet_proxy's complement doesnt cause ICE
@@ -142,3 +146,6 @@ TEST(view_get, nested_zip_view)
 
     EXPECT_EQ(vec1[0], -1);
 }
+
+#pragma GCC diagnostic pop
+#endif // SEQAN3_DEPRECATED_310