Merge pull request #2952 from eseiler/infra/drop_gcc9

[INFRA] Drop gcc9
seqan · Mar 31, 2022 · dc1ef8c · dc1ef8c · vercel · Mar 31, 2022
2 parents 576322c + d081e66
commit dc1ef8c
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Showing 302 changed files with 971 additions and 3,992 deletions.
diff --git a/.github/workflows/api.yml b/.github/workflows/api.yml
@@ -30,7 +30,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: [9, 10, 11]
+        compiler: [10, 11]
 
     steps:
       - name: Checkout SeqAn3

diff --git a/.github/workflows/avx2.yml b/.github/workflows/avx2.yml
@@ -30,7 +30,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: [9, 10, 11]
+        compiler: [10, 11]
         build: [unit, snippet, performance, header]
 
     steps:

diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
@@ -52,13 +52,6 @@ jobs:
             build: unit
             build_type: Release
 
-          - name: "Unit gcc9 (c++2a)"
-            cxx: "g++-9"
-            cc: "gcc-9"
-            build: unit
-            build_type: Release
-            cxx_flags: "-std=c++2a"
-
     steps:
       - name: Checkout SeqAn3
         uses: actions/checkout@v2

diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml
@@ -48,14 +48,6 @@ jobs:
             build: unit
             build_type: Release
 
-          - name: "Unit gcc9 (c++2a)"
-            os: macos-10.15
-            cxx: "g++-9"
-            cc: "gcc-9"
-            build: unit
-            build_type: Release
-            cxx_flags: "-std=c++2a"
-
     steps:
       - name: Checkout SeqAn3
         uses: actions/checkout@v2

diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml
@@ -33,9 +33,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - name: "Snippet gcc9"
-            cxx: "g++-9"
-            cc: "gcc-9"
+          - name: "Snippet gcc10"
+            cxx: "g++-10"
+            cc: "gcc-10"
             build: snippet
             build_type: Release
             build_threads: 2
@@ -48,9 +48,9 @@ jobs:
             skip_run_tests: false
             use_include_dependencies: "OFF"
 
-          - name: "Performance gcc9"
-            cxx: "g++-9"
-            cc: "gcc-9"
+          - name: "Performance gcc10"
+            cxx: "g++-10"
+            cc: "gcc-10"
             build: performance
             build_type: Release
             build_threads: 2
@@ -77,9 +77,9 @@ jobs:
             skip_run_tests: false
             use_include_dependencies: "OFF"
 
-          - name: "Header gcc9"
-            cxx: "g++-9"
-            cc: "gcc-9"
+          - name: "Header gcc10"
+            cxx: "g++-10"
+            cc: "gcc-10"
             build: header
             build_type: Release
             build_threads: 2
@@ -93,8 +93,8 @@ jobs:
             use_include_dependencies: "OFF"
 
           - name: "Non-cyclic tests"
-            cxx: "g++-9"
-            cc: "gcc-9"
+            cxx: "g++-10"
+            cc: "gcc-10"
             build: unit
             build_type: Debug
             build_threads: 2
@@ -108,8 +108,8 @@ jobs:
             use_include_dependencies: "ON"
 
           - name: "CMake external project"
-            cxx: "g++-9"
-            cc: "gcc-9"
+            cxx: "g++-10"
+            cc: "gcc-10"
             build: external_project
             build_type: Debug
             build_threads: 1 # output is important to be in sequential order

diff --git a/.github/workflows/latest_libraries.yml b/.github/workflows/latest_libraries.yml
@@ -30,7 +30,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: [9, 10, 11]
+        compiler: [10, 11]
         build: [unit, snippet, performance, header]
 
     steps:

diff --git a/README.md b/README.md
@@ -66,7 +66,7 @@ Please see the [online documentation](https://docs.seqan.de/seqan/3-master-user/
 
 |                   | requirement                                          | version  | comment                                     |
 |-------------------|------------------------------------------------------|----------|---------------------------------------------|
-|**compiler**       | [GCC](https://gcc.gnu.org)                           | ≥ 7      | no other compiler is currently supported!   |
+|**compiler**       | [GCC](https://gcc.gnu.org)                           | ≥ 10     | no other compiler is currently supported!   |
 |**build system**   | [CMake](https://cmake.org)                           | ≥ 3.4    | optional, but recommended                   |
 |**required libs**  | [SDSL](https://github.com/xxsds/sdsl-lite)           | ≥ 3      |                                             |
 |                   | [Range-V3](https://github.com/ericniebler/range-v3)  | ≥ 0.11.0 |                                             |
@@ -86,18 +86,18 @@ Quick-Setup without CMake:
   * Clone the repository with submodules: `git clone --recurse-submodules https://github.com/seqan/seqan3.git`
   * Add the following to your compiler invocation:
     * the include directories of SeqAn and its dependencies
-    * C++17 mode with concepts support
+    * C++20 mode
     * Macros indicating the presence of zlib and bzip2 (set only if actually available in your paths!)
   * The command could look like this:
 ```sh
-g++-7 -O3 -DNDEBUG -Wall -Wextra                                \
-    -std=c++17 -fconcepts                                       \
+g++-11 -O3 -DNDEBUG -Wall -Wextra                               \
+    -std=c++20                                                  \
     -I       /path/to/seqan3/include                            \
     -isystem /path/to/seqan3/submodules/range-v3/include        \
     -isystem /path/to/seqan3/submodules/sdsl-lite/include       \
     -isystem /path/to/seqan3/submodules/cereal/include          \
     -DSEQAN3_HAS_ZLIB=1 -DSEQAN3_HAS_BZIP2=1                    \
-    -lz -lbz2 -lstdc++fs -pthread                               \
+    -lz -lbz2 -pthread                                          \
   your_file.cpp
 ```
 

diff --git a/doc/tutorial/argument_parser/solution3.cpp b/doc/tutorial/argument_parser/solution3.cpp
@@ -15,7 +15,7 @@ number_type to_number(range_type && range)
 {
     std::string str;
     number_type num;
-    std::ranges::copy(range, std::cpp20::back_inserter(str));
+    std::ranges::copy(range, std::back_inserter(str));
     auto res = std::from_chars(&str[0], &str[0] + str.size(), num);
 
     if (res.ec != std::errc{})

diff --git a/doc/tutorial/argument_parser/solution4.cpp b/doc/tutorial/argument_parser/solution4.cpp
@@ -14,7 +14,7 @@ number_type to_number(range_type && range)
 {
     std::string str;
     number_type num;
-    std::ranges::copy(range, std::cpp20::back_inserter(str));
+    std::ranges::copy(range, std::back_inserter(str));
     auto res = std::from_chars(&str[0], &str[0] + str.size(), num);
 
     if (res.ec != std::errc{})

diff --git a/doc/tutorial/argument_parser/solution5.cpp b/doc/tutorial/argument_parser/solution5.cpp
@@ -14,7 +14,7 @@ number_type to_number(range_type && range)
 {
     std::string str;
     number_type num;
-    std::ranges::copy(range, std::cpp20::back_inserter(str));
+    std::ranges::copy(range, std::back_inserter(str));
     auto res = std::from_chars(&str[0], &str[0] + str.size(), num);
 
     if (res.ec != std::errc{})

diff --git a/doc/tutorial/argument_parser/solution6.cpp b/doc/tutorial/argument_parser/solution6.cpp
@@ -14,7 +14,7 @@ number_type to_number(range_type && range)
 {
     std::string str;
     number_type num;
-    std::ranges::copy(range, std::cpp20::back_inserter(str));
+    std::ranges::copy(range, std::back_inserter(str));
     auto res = std::from_chars(&str[0], &str[0] + str.size(), num);
 
     if (res.ec != std::errc{})

diff --git a/doc/tutorial/concepts/index.md b/doc/tutorial/concepts/index.md
@@ -118,8 +118,6 @@ auto add(std::integral auto const v1, std::integral auto const v2)  // one const
 }
 ```
 
-\attention The terse syntax in this form is not yet available in GCC7, GCC8 and GCC9.
-
 Different constraints can be applied to different template parameters and a single template parameter can be constrained
 by multiple concepts.
 Syntaxes can also be combined:

diff --git a/doc/tutorial/concepts/overloading1.cpp b/doc/tutorial/concepts/overloading1.cpp
@@ -1,7 +1,5 @@
-#include <iostream>                 // for std::cout
-
-#include <seqan3/std/concepts>      // GCC7 - GCC9 or
-//#include <concepts>               // compilers with full C++20 support
+#include <concepts>
+#include <iostream> // for std::cout
 
 template <std::integral t>
 void print(t const v)
@@ -14,6 +12,6 @@ int main()
     int i{4};
     unsigned u{3};
 
-    print(i);                       // prints "integral value: 4"
-    print(u);                       // prints "integral value: 3"
+    print(i); // prints "integral value: 4"
+    print(u); // prints "integral value: 3"
 }
diff --git a/doc/tutorial/concepts/overloading2.cpp b/doc/tutorial/concepts/overloading2.cpp
@@ -1,7 +1,5 @@
-#include <iostream>                 // for std::cout
-
-#include <seqan3/std/concepts>      // GCC7 - GCC9 or
-//#include <concepts>               // compilers with full C++20 support
+#include <concepts>
+#include <iostream> // for std::cout
 
 template <std::integral t>
 void print(t const v)
@@ -20,6 +18,6 @@ int main()
     int i{4};
     unsigned u{3};
 
-    print(i);                       // prints "integral value: 4"
-    print(u);                       // prints "Unsigned value: 3"
+    print(i); // prints "integral value: 4"
+    print(u); // prints "Unsigned value: 3"
 }
diff --git a/doc/tutorial/concepts/specialisation.cpp b/doc/tutorial/concepts/specialisation.cpp
@@ -1,5 +1,5 @@
-#include <utility>                          // for std::pair
-#include <seqan3/std/concepts>
+#include <concepts>
+#include <utility> // for std::pair
 
 template <typename t>
 struct square_root_type;

diff --git a/doc/tutorial/read_mapper/read_mapper_step3.cpp b/doc/tutorial/read_mapper/read_mapper_step3.cpp
@@ -12,7 +12,7 @@
 #include <seqan3/io/sequence_file/input.hpp>
 #include <seqan3/search/all.hpp>
 #include <seqan3/search/fm_index/bi_fm_index.hpp>
-#include <seqan3/std/span>
+#include <span>
 
 struct reference_storage_t
 {

diff --git a/doc/tutorial/read_mapper/read_mapper_step4.cpp b/doc/tutorial/read_mapper/read_mapper_step4.cpp
@@ -12,7 +12,7 @@
 #include <seqan3/io/sequence_file/input.hpp>
 #include <seqan3/search/all.hpp>
 #include <seqan3/search/fm_index/bi_fm_index.hpp>
-#include <seqan3/std/span>
+#include <span>
 
 struct reference_storage_t
 {

diff --git a/doc/tutorial/sam_file/sam_file_solution2.cpp b/doc/tutorial/sam_file/sam_file_solution2.cpp
@@ -25,7 +25,7 @@ r003	2064	chr2	18	10	5M	*	0	0	TAGGC	*
 }; // std::filesystem::current_path() / "mapping.sam" will be deleted after the execution
 
 //![solution]
-#include <seqan3/std/algorithm> // std::ranges::count
+#include <algorithm> // std::ranges::count
 #include <filesystem>
 #include <seqan3/std/ranges>
 #include <string>

diff --git a/doc/tutorial/search/search_solution3.cpp b/doc/tutorial/search/search_solution3.cpp
@@ -2,7 +2,7 @@
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/search/search.hpp>
 #include <seqan3/search/fm_index/fm_index.hpp>
-#include <seqan3/std/span>
+#include <span>
 
 int main()
 {

diff --git a/doc/tutorial/search/search_solution5.cpp b/doc/tutorial/search/search_solution5.cpp
@@ -4,7 +4,7 @@
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/search/search.hpp>
 #include <seqan3/search/fm_index/fm_index.hpp>
-#include <seqan3/std/span>
+#include <span>
 
 using namespace seqan3::literals;
 

diff --git a/doc/tutorial/search/search_span.cpp b/doc/tutorial/search/search_span.cpp
@@ -1,5 +1,5 @@
 #include <seqan3/core/debug_stream.hpp>
-#include <seqan3/std/span>
+#include <span>
 
 int main()
 {

diff --git a/doc/tutorial/sequence_file/sequence_file_piping_in_out.cpp b/doc/tutorial/sequence_file/sequence_file_piping_in_out.cpp
@@ -22,7 +22,7 @@ IIIIHHGIIIIHHGIIIH
 seqan3::test::create_temporary_snippet_file output_fastq{"output.fastq", ""};
 
 //![main]
-#include <seqan3/std/algorithm>
+#include <algorithm>
 #include <seqan3/std/ranges>
 
 #include <seqan3/io/sequence_file/all.hpp>

diff --git a/doc/tutorial/sequence_file/sequence_file_solution2.cpp b/doc/tutorial/sequence_file/sequence_file_solution2.cpp
@@ -33,7 +33,7 @@ int main()
     }
 
     // But you can also do this:
-    std::ranges::copy(fin, std::cpp20::back_inserter(records));
+    std::ranges::copy(fin, std::back_inserter(records));
 
     seqan3::debug_stream << records << '\n';
 }

diff --git a/doc/tutorial/sequence_file/sequence_file_solution5.cpp b/doc/tutorial/sequence_file/sequence_file_solution5.cpp
@@ -30,7 +30,7 @@ IIIIIHIIJJIIIII
 seqan3::test::create_temporary_snippet_file output{"output.fastq", ""};
 
 //![solution]
-#include <seqan3/std/algorithm>
+#include <algorithm>
 #include <filesystem>
 #include <seqan3/std/ranges>
 

diff --git a/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp b/include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp
@@ -13,7 +13,7 @@
 
 #pragma once
 
-#include <seqan3/std/algorithm>
+#include <algorithm>
 #include <seqan3/std/ranges>
 
 #include <seqan3/alignment/exception.hpp>
@@ -228,13 +228,11 @@ concept writable_aligned_sequence =
     requires (t v, detail::unaligned_seq_t<t> unaligned)
     {
         // global functions for generic usability
-        SEQAN3_RETURN_TYPE_CONSTRAINT(insert_gap(v, std::ranges::begin(v)), std::same_as, std::ranges::iterator_t<t>);
-        SEQAN3_RETURN_TYPE_CONSTRAINT(insert_gap(v, std::ranges::begin(v), 2),
-                                      std::same_as, std::ranges::iterator_t<t>);
-        SEQAN3_RETURN_TYPE_CONSTRAINT(erase_gap(v, std::ranges::begin(v)), std::same_as, std::ranges::iterator_t<t>);
-        SEQAN3_RETURN_TYPE_CONSTRAINT(erase_gap(v, std::ranges::begin(v), std::ranges::end(v)),
-                                      std::same_as, std::ranges::iterator_t<t>);
-        SEQAN3_RETURN_TYPE_CONSTRAINT(assign_unaligned(v, unaligned), std::same_as, void);
+        {insert_gap(v, std::ranges::begin(v))} -> std::same_as<std::ranges::iterator_t<t>>;
+        {insert_gap(v, std::ranges::begin(v), 2)} -> std::same_as<std::ranges::iterator_t<t>>;
+        {erase_gap(v, std::ranges::begin(v))} -> std::same_as<std::ranges::iterator_t<t>>;
+        {erase_gap(v, std::ranges::begin(v), std::ranges::end(v))} -> std::same_as<std::ranges::iterator_t<t>>;
+        {assign_unaligned(v, unaligned)} -> std::same_as<void>;
     };
 //!\endcond
 

diff --git a/include/seqan3/alignment/configuration/align_config_output.hpp b/include/seqan3/alignment/configuration/align_config_output.hpp
@@ -15,7 +15,7 @@
 #include <seqan3/alignment/configuration/detail.hpp>
 #include <seqan3/alignment/pairwise/alignment_result.hpp>
 #include <seqan3/core/configuration/pipeable_config_element.hpp>
-#include <seqan3/utility/concept/exposition_only/core_language.hpp>
+#include <seqan3/utility/concept.hpp>
 
 namespace seqan3::align_cfg
 {

diff --git a/include/seqan3/alignment/configuration/align_config_result_type.hpp b/include/seqan3/alignment/configuration/align_config_result_type.hpp
@@ -12,7 +12,7 @@
 
 #pragma once
 
-#include <seqan3/std/type_traits>
+#include <type_traits>
 
 #include <seqan3/alignment/configuration/detail.hpp>
 #include <seqan3/alignment/pairwise/alignment_result.hpp>

diff --git a/include/seqan3/alignment/configuration/align_config_score_type.hpp b/include/seqan3/alignment/configuration/align_config_score_type.hpp
@@ -14,7 +14,7 @@
 
 #include <seqan3/alignment/configuration/detail.hpp>
 #include <seqan3/core/configuration/pipeable_config_element.hpp>
-#include <seqan3/utility/concept/exposition_only/core_language.hpp>
+#include <seqan3/utility/concept.hpp>
 
 namespace seqan3::align_cfg
 {

diff --git a/include/seqan3/alignment/configuration/align_config_scoring_scheme.hpp b/include/seqan3/alignment/configuration/align_config_scoring_scheme.hpp
@@ -13,7 +13,7 @@
 
 #pragma once
 
-#include <seqan3/std/concepts>
+#include <concepts>
 
 #include <seqan3/alignment/configuration/detail.hpp>
 #include <seqan3/alignment/scoring/scoring_scheme_concept.hpp>

diff --git a/include/seqan3/alignment/decorator/gap_decorator.hpp b/include/seqan3/alignment/decorator/gap_decorator.hpp
@@ -13,7 +13,7 @@
 
 #pragma once
 
-#include <seqan3/std/algorithm>
+#include <algorithm>
 #include <limits>
 #include <seqan3/std/ranges>
 #include <set>