Rebuilt for https://fedoraproject.org/wiki/Fedora_45_Mass_Rebuild

- Remove unused dependency on coin-or-lemon
- Convert License field to SPDX
- Note that the devel package bundles zipstream and bzip2stream
- Note that the devel package needs zlib-devel and bzip2-devel

.gitignore

@@ -3,3 +3,15 @@
 /seqan3-3.0.3.tar.gz
 /seqan3-3.1.0-rc1.tar.gz
 /seqan3-3.1.0.tar.gz
+/seqan3-3.2.0-rc1.tar.gz
+/seqan3-3.2.0.tar.gz
+/seqan3-404affbf6ee31aeda30ed9cc321b3700a50e5eae.tar.gz
+/seqan3-174255eea53d4847e7ce8cb0dc29415f177dc54d.tar.gz
+/seqan3-8c604d98e0d291bc3909ecbad78ca778b3ad5a5c.tar.gz
+/seqan3-3.3.0-rc.1.tar.gz
+/seqan3-3.3.0-rc.2.tar.gz
+/seqan3-3.4.0-rc.1.tar.gz
+/seqan3-3.4.0-rc.2.tar.gz
+/seqan3-3.4.0-rc.3.tar.gz
+/seqan3-3.4.0.tar.gz
+/seqan3-3.4.2.tar.gz

README.md

@@ -12,7 +12,7 @@ for:
 
 By leveraging *Modern C++* it provides unprecedented ease-of-use without sacrificing performance.
 
-Please see the [online documentation](https://docs.seqan.de/seqan/3-master-user/) for more details.
+Please see the [online documentation](https://docs.seqan.de/seqan/3.2.0/) for more details.
 
 ## Quick facts
 

seqan3-3.4.0-disable_CPM.patch

@@ -0,0 +1,80 @@
+--- a/cmake/seqan3-config.orig.cmake	2024-12-13 18:42:15.000000000 +0100
++++ b/cmake/seqan3-config.cmake	2025-01-19 21:13:45.692446573 +0100
+@@ -113,11 +113,7 @@
+ # ----------------------------------------------------------------------------
+ 
+ # This will be true for git clones and source packages, but not for installed packages.
+-if (EXISTS "${CMAKE_CURRENT_LIST_DIR}/CPM.cmake")
+-    set (SEQAN3_HAS_CPM TRUE)
+-else ()
+-    set (SEQAN3_HAS_CPM FALSE)
+-endif ()
++set (SEQAN3_HAS_CPM FALSE)
+ 
+ if (SEQAN3_HAS_CPM)
+     set (CPM_INDENT "  CMake Package Manager CPM: ")
+--- a/test/seqan3-test.orig.cmake	2024-12-13 18:42:15.000000000 +0100
++++ b/test/seqan3-test.cmake	2025-01-19 21:18:08.209434385 +0100
+@@ -27,10 +27,6 @@
+      "${CMAKE_CURRENT_LIST_DIR}/../cmake/"
+      CACHE STRING "Path to directory containing CPM.cmake.")
+ 
+-set (CPM_INDENT "CMake Package Manager CPM: ")
+-include ("${SEQAN3_TEST_CPM_DIR}/CPM.cmake")
+-CPMUsePackageLock ("${SEQAN3_TEST_CPM_DIR}/package-lock.cmake")
+-
+ include (CheckCXXCompilerFlag)
+ include (CheckCXXSourceCompiles)
+ include (CMakeDependentOption)
+@@ -51,7 +47,6 @@
+ cmake_dependent_option (SEQAN3_WITH_SEQAN2_CI "Build tests with SeqAn2." ON "DEFINED ENV{CI}" OFF)
+ 
+ if (SEQAN3_WITH_SEQAN2 OR SEQAN3_WITH_SEQAN2_CI)
+-    CPMGetPackage (seqan)
+     find_path (SEQAN3_SEQAN2_INCLUDE_DIR
+                NAMES seqan/version.h
+                HINTS "${seqan_SOURCE_DIR}/include")
+--- a/test/cmake/seqan3_require_ccache.orig.cmake	2024-12-13 18:42:15.000000000 +0100
++++ b/test/cmake/seqan3_require_ccache.cmake	2025-01-19 21:19:53.256828886 +0100
+@@ -4,4 +4,4 @@
+ 
+ # This file's only purpose is to be replaced with the content of the use_ccache CMakeLists.txt file
+ # when creating the source package.
+-CPMGetPackage (use_ccache)
++# CPMGetPackage (use_ccache)
+--- a/test/unit/CMakeLists.orig.txt	2024-12-13 18:42:15.000000000 +0100
++++ b/test/unit/CMakeLists.txt	2025-01-19 21:27:10.229117104 +0100
+@@ -8,7 +8,7 @@
+ include (../seqan3-test.cmake)
+ include (GoogleTest OPTIONAL)
+ 
+-CPMGetPackage (googletest)
++find_package(GTest REQUIRED)
+ 
+ include (diagnostics/list_missing_unit_tests)
+ include (diagnostics/list_unused_unit_tests)
+ 
+--- a/test/header/CMakeLists.orig.txt	2024-12-13 18:42:15.000000000 +0100
++++ b/test/header/CMakeLists.txt	2025-01-19 22:08:37.815744299 +0100
+@@ -7,8 +7,8 @@
+ 
+ include (../seqan3-test.cmake)
+ 
+-CPMGetPackage (googletest)
+-CPMGetPackage (benchmark)
++find_package(GTest REQUIRED)
++find_package(benchmark REQUIRED)
+ 
+ # We compile each header twice in separate compilation units, where the second compilation omits the header guard (check
+ # for cyclic includes). Each alone is sufficient to test that the header is functional, but both are needed to check for
+--- a/test/performance/CMakeLists.orig.txt	2024-12-13 18:42:15.000000000 +0100
++++ b/test/performance/CMakeLists.txt	2025-01-19 22:10:44.305669084 +0100
+@@ -7,7 +7,7 @@
+ 
+ include (../seqan3-test.cmake)
+ 
+-CPMGetPackage (benchmark)
++find_package(benchmark REQUIRED)
+ 
+ set (SEQAN3_BENCHMARK_MIN_TIME
+      "1s"

seqan3-fix_GCC15.patch

@@ -0,0 +1,20 @@
+--- a/test/unit/io/detail/misc_output_test.orig.cpp	2024-12-13 18:42:15.000000000 +0100
++++ b/test/unit/io/detail/misc_output_test.cpp	2025-01-20 21:58:35.651617085 +0100
+@@ -6,6 +6,7 @@
+ 
+ #include <fstream>
+ #include <vector>
++#include <functional>
+ 
+ #include <seqan3/core/debug_stream.hpp>
+ #include <seqan3/io/detail/misc_input.hpp>
+--- a/include/seqan3/io/detail/misc_input.orig.hpp	2024-12-13 18:42:15.000000000 +0100
++++ b/include/seqan3/io/detail/misc_input.hpp	2025-01-20 22:01:28.812235658 +0100
+@@ -17,6 +17,7 @@
+ #include <span>
+ #include <string>
+ #include <tuple>
++#include <functional>
+ 
+ #include <seqan3/contrib/stream/bgzf.hpp>
+ #include <seqan3/contrib/stream/bgzf_istream.hpp>

seqan3-fix_bug2848.patch

@@ -1,93 +0,0 @@
-From a710725398952965a27f1942e6633814a0c6a30b Mon Sep 17 00:00:00 2001
-From: marehr <marehr-github@marehr.dialup.fu-berlin.de>
-Date: Wed, 29 Sep 2021 16:54:19 +0200
-Subject: [PATCH] =?UTF-8?q?[FIX]=20error:=20testing=20if=20a=20concept-id?=
- =?UTF-8?q?=20is=20a=20valid=20expression;=20add=20=E2=80=98requires?=
- =?UTF-8?q?=E2=80=99=20to=20check=20satisfaction=20[-Werror=3Dmissing-requ?=
- =?UTF-8?q?ires]?=
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-```
-/seqan3/include/seqan3/utility/concept/exposition_only/core_language.hpp:59:5: error: testing if a concept-id is a valid expression; add ‘requires’ to check satisfaction [-Werror=missing-requires]
-   59 |     std::convertible_to<decltype(v1 <  v2), bool>;
-      |     ^
-      |     requires
-```
----
- .../concept/exposition_only/core_language.hpp | 26 +++++++++----------
- include/seqan3/utility/range/concept.hpp      | 16 ++++++------
- 2 files changed, 21 insertions(+), 21 deletions(-)
-
-diff --git a/include/seqan3/utility/concept/exposition_only/core_language.hpp b/include/seqan3/utility/concept/exposition_only/core_language.hpp
-index d842db4736..513e6195b5 100644
---- a/include/seqan3/utility/concept/exposition_only/core_language.hpp
-+++ b/include/seqan3/utility/concept/exposition_only/core_language.hpp
-@@ -31,10 +31,10 @@ SEQAN3_CONCEPT weakly_equality_comparable_with =
-     requires(std::remove_reference_t<T> const & t,
-              std::remove_reference_t<U> const & u)
-     {
--        std::convertible_to<decltype(t == u), bool>;
--        std::convertible_to<decltype(t != u), bool>;
--        std::convertible_to<decltype(u == t), bool>;
--        std::convertible_to<decltype(u != t), bool>;
-+        requires std::convertible_to<decltype(t == u), bool>;
-+        requires std::convertible_to<decltype(t != u), bool>;
-+        requires std::convertible_to<decltype(u == t), bool>;
-+        requires std::convertible_to<decltype(u != t), bool>;
-     };
- //!\endcond
- 
-@@ -56,15 +56,15 @@ template <typename t1, typename t2>
- SEQAN3_CONCEPT weakly_ordered_with = requires (std::remove_reference_t<t1> const & v1,
-                                                std::remove_reference_t<t2> const & v2)
- {
--    std::convertible_to<decltype(v1 <  v2), bool>;
--    std::convertible_to<decltype(v1 <= v2), bool>;
--    std::convertible_to<decltype(v1 >  v2), bool>;
--    std::convertible_to<decltype(v1 >= v2), bool>;
--
--    std::convertible_to<decltype(v2 <  v1), bool>;
--    std::convertible_to<decltype(v2 <= v1), bool>;
--    std::convertible_to<decltype(v2 >  v1), bool>;
--    std::convertible_to<decltype(v2 >= v1), bool>;
-+    requires std::convertible_to<decltype(v1 <  v2), bool>;
-+    requires std::convertible_to<decltype(v1 <= v2), bool>;
-+    requires std::convertible_to<decltype(v1 >  v2), bool>;
-+    requires std::convertible_to<decltype(v1 >= v2), bool>;
-+
-+    requires std::convertible_to<decltype(v2 <  v1), bool>;
-+    requires std::convertible_to<decltype(v2 <= v1), bool>;
-+    requires std::convertible_to<decltype(v2 >  v1), bool>;
-+    requires std::convertible_to<decltype(v2 >= v1), bool>;
- };
- //!\endcond
- 
-diff --git a/include/seqan3/utility/range/concept.hpp b/include/seqan3/utility/range/concept.hpp
-index e047dcc8f8..b90e967230 100644
---- a/include/seqan3/utility/range/concept.hpp
-+++ b/include/seqan3/utility/range/concept.hpp
-@@ -91,14 +91,14 @@ SEQAN3_CONCEPT pseudo_random_access_iterator =
-     std::sized_sentinel_for<iterator_t, iterator_t> &&
-     requires (iterator_t i, iterator_t const j, std::iter_difference_t<iterator_t> const n)
- {
--    std::same_as<decltype( i += n ), iterator_t &>;
--    std::same_as<decltype( j +  n ), iterator_t>;
--    std::same_as<decltype( n +  j ), iterator_t>;
--    std::same_as<decltype(   --i  ), iterator_t &>;
--    std::same_as<decltype(   i--  ), iterator_t>;
--    std::same_as<decltype( i -= n ), iterator_t &>;
--    std::same_as<decltype( j -  n ), iterator_t>;
--    std::same_as<decltype(  j[n]  ), std::iter_reference_t<iterator_t>>;
-+    requires std::same_as<decltype( i += n ), iterator_t &>;
-+    requires std::same_as<decltype( j +  n ), iterator_t>;
-+    requires std::same_as<decltype( n +  j ), iterator_t>;
-+    requires std::same_as<decltype(   --i  ), iterator_t &>;
-+    requires std::same_as<decltype(   i--  ), iterator_t>;
-+    requires std::same_as<decltype( i -= n ), iterator_t &>;
-+    requires std::same_as<decltype( j -  n ), iterator_t>;
-+    requires std::same_as<decltype(  j[n]  ), std::iter_reference_t<iterator_t>>;
- };
- //!\endcond
- 

seqan3-fix_bug2918.patch

@@ -1,96 +0,0 @@
-From 7cf66224fa98e9c940fea6c326b62337aa0e7ce8 Mon Sep 17 00:00:00 2001
-From: Enrico Seiler <enrico.seiler@hotmail.de>
-Date: Tue, 14 Dec 2021 15:12:27 +0100
-Subject: [PATCH] [FIX] Remove invisible characters
-
----
- include/seqan3/core/all.hpp                    | 2 +-
- include/seqan3/core/detail/iterator_traits.hpp | 4 ++--
- include/seqan3/core/platform.hpp               | 2 +-
- include/seqan3/std/bit                         | 2 +-
- include/seqan3/std/concepts                    | 2 +-
- include/seqan3/std/iterator                    | 2 +-
- 6 files changed, 7 insertions(+), 7 deletions(-)
-
-diff --git a/include/seqan3/core/all.hpp b/include/seqan3/core/all.hpp
-index 6742adb05d..e7c31560dd 100644
---- a/include/seqan3/core/all.hpp
-+++ b/include/seqan3/core/all.hpp
-@@ -50,7 +50,7 @@
-   * state to express a general intend of the API without being explicit about it.
-   *
-   * For example, see https://eel.is/c++draft/iterator.concept.readable where `indirectly-readable-impl` describes the
--  * general intention of the concept, but does not name it since it is a helper-entity for the std::indirectly_­readable
-+  * general intention of the concept, but does not name it since it is a helper-entity for the std::indirectly_readable
-   * concept.
-   */
- 
-diff --git a/include/seqan3/core/detail/iterator_traits.hpp b/include/seqan3/core/detail/iterator_traits.hpp
-index 4d94748929..53bfe98287 100644
---- a/include/seqan3/core/detail/iterator_traits.hpp
-+++ b/include/seqan3/core/detail/iterator_traits.hpp
-@@ -44,10 +44,10 @@ struct maybe_iterator_category
-     /*!\brief The iterator category tag. (not always present!)
-      * \details
-      *
--     * This member is only defined if and only if std::iterator_­traits<underlying_iterator_t>::​iterator_­category is
-+     * This member is only defined if and only if std::iterator_traits<underlying_iterator_t>::iterator_category is
-      * valid and denotes a type.
-      */
--    using iterator_category = MAYBE_PRESENT(std::iterator_­traits<underlying_iterator_t>::​iterator_­category);
-+    using iterator_category = MAYBE_PRESENT(std::iterator_traits<underlying_iterator_t>::iterator_category);
- #endif // SEQAN3_DOXYGEN_ONLY(1)0
- };
- 
-diff --git a/include/seqan3/core/platform.hpp b/include/seqan3/core/platform.hpp
-index ac81437d3c..817604600b 100644
---- a/include/seqan3/core/platform.hpp
-+++ b/include/seqan3/core/platform.hpp
-@@ -309,7 +309,7 @@
- #   endif // SEQAN3_DISABLE_LEGACY_STD_DIAGNOSTIC
- #endif // _GLIBCXX_USE_CXX11_ABI == 0
- 
--/*!\brief https://eel.is/c++draft/range.take#view defines e.g. `constexpr auto size() requires sized_­range<V>` without
-+/*!\brief https://eel.is/c++draft/range.take#view defines e.g. `constexpr auto size() requires sized_range<V>` without
-  *        any template. This syntax works since gcc-10, before that a dummy `template <typename = ...>` must be used.
-  */
- #ifndef SEQAN3_WORKAROUND_GCC_NON_TEMPLATE_REQUIRES
-diff --git a/include/seqan3/std/bit b/include/seqan3/std/bit
-index d9e9df0558..d26e155bea 100644
---- a/include/seqan3/std/bit
-+++ b/include/seqan3/std/bit
-@@ -139,7 +139,7 @@ namespace std
- template<class T> constexpr int countl_zero(T x) noexcept;
- #endif // SEQAN3_CPP_LIB_BITOPS
- 
--// // bit_­cast
-+// // bit_cast
- // template<class To, class From> constexpr To bit_cast(const From& from) noexcept;
- //
- // // integral powers of 2
-diff --git a/include/seqan3/std/concepts b/include/seqan3/std/concepts
-index 80c4167e5f..09fd5d17e4 100644
---- a/include/seqan3/std/concepts
-+++ b/include/seqan3/std/concepts
-@@ -68,7 +68,7 @@ using ::concepts::derived_from;
- // [concept.convertible], concept convertible_to
- using ::concepts::convertible_to;
- 
--// [concept.commonref], concept common_­reference_­with
-+// [concept.commonref], concept common_reference_with
- using ::concepts::common_reference_with;
- 
- // [concept.common], concept common_with
-diff --git a/include/seqan3/std/iterator b/include/seqan3/std/iterator
-index 4a87127a7c..9c2aba8809 100644
---- a/include/seqan3/std/iterator
-+++ b/include/seqan3/std/iterator
-@@ -122,7 +122,7 @@ using ::ranges::cpp20::forward_iterator;
- // [iterator.concept.bidir], concept bidirectional_iterator
- using ::ranges::cpp20::bidirectional_iterator;
- 
--// [iterator.concept.random.access], concept random_­access_­iterator
-+// [iterator.concept.random.access], concept random_access_iterator
- using ::ranges::cpp20::random_access_iterator;
- 
- // [iterator.concept.contiguous], concept contiguous_iterator

seqan3-unbundle_benchmark.patch

@@ -1,92 +0,0 @@
-Author: Michael R. Crusoe <michael.crusoe@gmail.com>
-Description: Use the Debian package of libbenchmark
---- seqan3.orig/test/seqan3-test.cmake
-+++ seqan3/test/seqan3-test.cmake
-@@ -57,7 +57,7 @@
- # seqan3::test::performance specifies required flags, includes and libraries
- # needed for performance test cases in seqan3/test/performance
- add_library (seqan3_test_performance INTERFACE)
--target_link_libraries (seqan3_test_performance INTERFACE "seqan3::test" "gbenchmark")
-+target_link_libraries (seqan3_test_performance INTERFACE "seqan3::test" "benchmark")
- 
- if (SEQAN3_BENCHMARK_ALIGN_LOOPS)
-     target_compile_options (seqan3_test_performance INTERFACE "-falign-loops=32")
---- a/test/cmake/seqan3_require_benchmark.orig.cmake 2021-03-12 15:32:16.217895000 +0100
-+++ b/test/cmake/seqan3_require_benchmark.cmake      2021-03-12 15:33:34.694342382 +0100
-@@ -5,75 +5,8 @@
- # shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
- # -----------------------------------------------------------------------------------------------------
- 
--# Exposes the google-benchmark target `gbenchmark`.
--macro (seqan3_require_benchmark_old gbenchmark_git_tag)
--    set (gbenchmark_project_args ${SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS})
--    list (APPEND gbenchmark_project_args "-DBENCHMARK_ENABLE_TESTING=false")
--    # google-benchmarks suggest to use LTO (link-time optimisation), but we don't really need that because we are a
--    # header only library. This option might be still interesting for external libraries benchmarks.
--    # see https://github.com/google/benchmark#debug-vs-release
--    # list (APPEND gbenchmark_project_args "-DBENCHMARK_ENABLE_LTO=true")
--
--    # force that libraries are installed to `lib/`, because GNUInstallDirs might install it into `lib64/`
--    list (APPEND gbenchmark_project_args "-DCMAKE_INSTALL_LIBDIR=${PROJECT_BINARY_DIR}/lib/")
--
--    set (gbenchmark_path "${PROJECT_BINARY_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}benchmark${CMAKE_STATIC_LIBRARY_SUFFIX}")
--
--    include (ExternalProject)
--    ExternalProject_Add (
--        gbenchmark_project
--        PREFIX gbenchmark_project
--        GIT_REPOSITORY "https://github.com/google/benchmark.git"
--        GIT_TAG "${gbenchmark_git_tag}"
--        SOURCE_DIR "${SEQAN3_BENCHMARK_CLONE_DIR}"
--        CMAKE_ARGS "${gbenchmark_project_args}"
--        BUILD_BYPRODUCTS "${gbenchmark_path}"
--        UPDATE_DISCONNECTED ${SEQAN3_TEST_BUILD_OFFLINE}
--    )
--    unset (gbenchmark_project_args)
--
--    add_library (gbenchmark STATIC IMPORTED)
--    add_dependencies (gbenchmark gbenchmark_project)
--    set_target_properties (gbenchmark PROPERTIES IMPORTED_LOCATION "${gbenchmark_path}")
--    set_property (TARGET gbenchmark APPEND PROPERTY INTERFACE_LINK_LIBRARIES "pthread")
--
--    # NOTE: google benchmarks needs Shlwapi (Shell Lightweight Utility Functions) on windows
--    # see https://msdn.microsoft.com/en-us/library/windows/desktop/bb759844(v=vs.85).aspx
--    # see https://github.com/google/benchmark/blob/c614dfc0d4eadcd19b188ff9c7e226c138f894a1/README.md#platform-specific-libraries
--    if(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
--        target_link_libraries (gbenchmark INTERFACE "Shlwapi")
--    endif()
--
--    unset (gbenchmark_path)
--endmacro ()
--
- macro (seqan3_require_benchmark)
-     enable_testing ()
- 
--    set (gbenchmark_git_tag "v1.5.0")
--
--    if (NOT CMAKE_VERSION VERSION_LESS 3.14)
--        # NOTE: setting the standard prevents an ICE involving passing -fconcepts through CMAKE_CXX_FLAGS
--        set (CMAKE_CXX_STANDARD 17)
--        message (STATUS "Fetch google benchmark:")
--
--        include (FetchContent)
--        FetchContent_Declare (
--            gbenchmark_fetch_content
--            GIT_REPOSITORY "https://github.com/google/benchmark.git"
--            GIT_TAG "${gbenchmark_git_tag}"
--        )
--        option (BENCHMARK_ENABLE_TESTING "" OFF)
--        FetchContent_MakeAvailable(gbenchmark_fetch_content)
--
--        # NOTE: google benchmark's CMakeLists.txt already defines Shlwapi
--        add_library (gbenchmark ALIAS benchmark_main)
--        unset (CMAKE_CXX_STANDARD)
--    else ()
--        message (STATUS "Use google benchmark as external project:")
--
--        seqan3_require_benchmark_old ("${gbenchmark_git_tag}")
--    endif ()
--
--    add_custom_target (gbenchmark_build DEPENDS gbenchmark)
-+    find_package(benchmark REQUIRED)
- endmacro ()

seqan3-unbundle_gtest.patch

@@ -1,106 +0,0 @@
---- seqan3.orig/test/seqan3-test.cmake
-+++ seqan3/test/seqan3-test.cmake
-@@ -34,13 +34,13 @@
- find_path (SEQAN3_TEST_CMAKE_MODULE_DIR NAMES seqan3_test_component.cmake HINTS "${CMAKE_CURRENT_LIST_DIR}/cmake/")
- list(APPEND CMAKE_MODULE_PATH "${SEQAN3_TEST_CMAKE_MODULE_DIR}")
- 
--set (SEQAN3_BENCHMARK_CLONE_DIR "${PROJECT_BINARY_DIR}/vendor/benchmark")
--set (SEQAN3_TEST_CLONE_DIR "${PROJECT_BINARY_DIR}/vendor/googletest")
-+set (SEQAN3_BENCHMARK_CLONE_DIR "${CMAKE_INSTALL_PREFIX}")
-+set (SEQAN3_TEST_CLONE_DIR "${CMAKE_INSTALL_PREFIX}")
- 
- # needed for add_library (seqan3::test::* INTERFACE IMPORTED)
- # see cmake bug https://gitlab.kitware.com/cmake/cmake/issues/15052
--file(MAKE_DIRECTORY ${SEQAN3_BENCHMARK_CLONE_DIR}/include/)
--file(MAKE_DIRECTORY ${SEQAN3_TEST_CLONE_DIR}/googletest/include/)
-+file(MAKE_DIRECTORY ${SEQAN3_BENCHMARK_CLONE_DIR}/include/benchmark/)
-+file(MAKE_DIRECTORY ${SEQAN3_TEST_CLONE_DIR}/include/gtest/)
- 
- # ----------------------------------------------------------------------------
- # Interface targets for the different test modules in seqan3.
-@@ -70,8 +70,8 @@
- # needed for unit test cases in seqan3/test/unit
- add_library (seqan3_test_unit INTERFACE)
- target_link_libraries (seqan3_test_unit INTERFACE "seqan3::test" "gtest_main" "gtest")
--target_include_directories (seqan3_test_unit INTERFACE "${SEQAN3_TEST_CLONE_DIR}/googletest/include/")
-+target_include_directories (seqan3_test_unit INTERFACE "${SEQAN3_TEST_CLONE_DIR}/include/gtest/")
- add_library (seqan3::test::unit ALIAS seqan3_test_unit)
- 
- # seqan3::test::coverage specifies required flags, includes and libraries
- # needed for coverage test cases in seqan3/test/coverage
---- a/test/cmake/seqan3_require_test.orig.cmake	2020-08-06 14:00:23.000000000 +0200
-+++ b/test/cmake/seqan3_require_test.cmake	2020-08-06 14:35:10.167198023 +0200
-@@ -5,72 +5,9 @@
- # shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
- # -----------------------------------------------------------------------------------------------------
- 
--# Exposes the google-test targets `gtest` and `gtest_main`.
--macro (seqan3_require_test_old gtest_git_tag)
--    set (gtest_project_args ${SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS})
--    list (APPEND gtest_project_args "-DBUILD_GMOCK=0")
--
--    # force that libraries are installed to `lib/`, because GNUInstallDirs might install it into `lib64/`
--    list (APPEND gtest_project_args "-DCMAKE_INSTALL_LIBDIR=${PROJECT_BINARY_DIR}/lib/")
--
--    # google sets CMAKE_DEBUG_POSTFIX = "d"
--    set (gtest_main_path "${PROJECT_BINARY_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}gtest_main${CMAKE_STATIC_LIBRARY_SUFFIX}")
--    if (CMAKE_BUILD_TYPE STREQUAL "Debug")
--        set (gtest_main_path "${PROJECT_BINARY_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}gtest_maind${CMAKE_STATIC_LIBRARY_SUFFIX}")
--    endif ()
--
--    set (gtest_path "${PROJECT_BINARY_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}gtest${CMAKE_STATIC_LIBRARY_SUFFIX}")
--    if (CMAKE_BUILD_TYPE STREQUAL "Debug")
--        set (gtest_path "${PROJECT_BINARY_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}gtestd${CMAKE_STATIC_LIBRARY_SUFFIX}")
--    endif ()
--
--    include (ExternalProject)
--    ExternalProject_Add (
--        gtest_project
--        PREFIX gtest_project
--        GIT_REPOSITORY "https://github.com/google/googletest.git"
--        GIT_TAG "${gtest_git_tag}"
--        SOURCE_DIR "${SEQAN3_TEST_CLONE_DIR}"
--        CMAKE_ARGS "${gtest_project_args}"
--        BUILD_BYPRODUCTS "${gtest_main_path}" "${gtest_path}"
--        UPDATE_DISCONNECTED ${SEQAN3_TEST_BUILD_OFFLINE}
--    )
--    unset (gtest_project_args)
--
--    add_library (gtest_main STATIC IMPORTED)
--    add_dependencies (gtest_main gtest_project)
--    set_target_properties (gtest_main PROPERTIES IMPORTED_LOCATION "${gtest_main_path}")
--
--    add_library (gtest STATIC IMPORTED)
--    add_dependencies (gtest gtest_main)
--    set_target_properties (gtest PROPERTIES IMPORTED_LOCATION "${gtest_path}")
--    set_property (TARGET gtest APPEND PROPERTY INTERFACE_LINK_LIBRARIES "pthread")
--
--    unset(gtest_main_path)
--    unset(gtest_path)
--endmacro ()
- 
- macro (seqan3_require_test)
-     enable_testing ()
- 
--    set (gtest_git_tag "release-1.11.0")
--
--    if (NOT CMAKE_VERSION VERSION_LESS 3.14)
--        message (STATUS "Fetch googletest:")
--
--        include (FetchContent)
--        FetchContent_Declare (
--            gtest_fetch_content
--            GIT_REPOSITORY "https://github.com/google/googletest.git"
--            GIT_TAG "${gtest_git_tag}"
--        )
--        option (BUILD_GMOCK "" OFF)
--        FetchContent_MakeAvailable(gtest_fetch_content)
--    else ()
--        message (STATUS "Use googletest as external project:")
--
--        seqan3_require_test_old ("${gtest_git_tag}")
--    endif ()
--
--    add_custom_target (gtest_build DEPENDS gtest_main gtest)
-+    find_package(GTest REQUIRED)
- endmacro ()

seqan3.spec

@@ -1,21 +1,20 @@
 %global debug_package %{nil}
 %global middle_release 0
 
-# Not ready for GCC-12
-# See rhbz#2047005
-%bcond_with check
-%bcond_with test_api
-%bcond_with test_header
-%bcond_with benchmark
-%bcond_without doc
+%bcond_without check
+%bcond_without test_api
+%bcond_without test_header
+%bcond_without benchmark
+# Documentation needs external online `cppreference-doc/releases/download/v20220201/html-book-20220201.tar.xz`
+%bcond_with doc
 
 # SeqAn3 aims to support any 64-bit architecture running Linux/POSIX;
 # currently big-endian CPU architectures like s390x are less supported.
 ExclusiveArch: %{power64} x86_64 aarch64
 
 %if 0%{?middle_release}
-%global  commit      4604f1b2db7131ea10b9d9ff56bf5a93e8c66847
-%global  date        .20210809git
+%global  commit      8c604d98e0d291bc3909ecbad78ca778b3ad5a5c
+%global  date        .20230403git
 %global  shortcommit %(c=%{commit}; echo ${c:0:8})
 %else
 %global  commit      %{nil}
@@ -25,46 +24,43 @@ ExclusiveArch: %{power64} x86_64 aarch64
 
 Name:      seqan3
 Summary:   The modern C++ library for sequence analysis
-Version:   3.1.0
-Release:   3%{date}%{shortcommit}%{?dist}
-License:   BSD
-URL:       http://www.seqan.de/
-%if 0%{?middle_release}
-# git clone -b 3.1.0-rc.1 --depth 1 --single-branch --progress --recursive https://github.com/seqan/seqan3.git
-# find . -name '.git*' -exec  rm -rf {} ';'
+Version:   3.4.2
+Release:   %autorelease
+License:   BSD-3-Clause
+URL:       https://www.seqan.de/
+# Source code archive generated by:
+# git clone -b 3.3.0 --depth 1 --single-branch --progress --recursive https://github.com/seqan/seqan3.git
+# find seqan3 -name '.git*' -exec  rm -rf {} ';'
 # find seqan3 -name '.git*' -exec  rm -f {} ';'
 # tar -czvf seqan3-%%{version}.tar.gz seqan3
-Source0:   https://github.com/seqan/%{name}/archive/%{commit}/%{name}-%{version}-rc1.tar.gz
+%if 0%{?middle_release}
+Source0:   https://github.com/seqan/%{name}/archive/%{commit}/%{name}-%{commit}.tar.gz
 %else
 Source0:   https://github.com/seqan/%{name}/archive/%{version}/%{name}-%{version}.tar.gz
 %endif
 
-BuildRequires: gcc, gcc-c++, dos2unix
+BuildRequires: gcc
+BuildRequires: gcc-c++
 BuildRequires: ccache
 BuildRequires: cmake >= 3.4
-BuildRequires: cereal-devel >= 1.3.0
-BuildRequires: sdsl-lite-devel >= 3.0.0
+BuildRequires: cereal-devel >= 1.3.2
+BuildRequires: sdsl-lite-devel >= 3.0.1
 BuildRequires: make
 BuildRequires: zlib-devel >= 1.2
 BuildRequires: bzip2-devel >= 1.0
 BuildRequires: range-v3-devel >= 0.11.0
-BuildRequires: coin-or-lemon-devel
 %if %{with check}
 BuildRequires: google-benchmark-devel
 BuildRequires: gtest-devel >= 1.10.0
 %endif
 %if %{with doc}
 BuildRequires: texlive-newunicodechar
-BuildRequires: doxygen >= 1.9.1
+BuildRequires: doxygen >= 1.9.4
 %endif
-
-# Patches for unbundling libraries and fix some errors
-Patch0: %{name}-unbundle_benchmark.patch
-Patch1: %{name}-unbundle_gtest.patch
-
-Patch2: %{name}-fix_bug2848.patch
-Patch3: %{name}-fix_bug2918.patch
-
+# Use Fedora's CMake only
+Patch1: %{name}-3.4.0-disable_CPM.patch
+# Include missing header files
+Patch2: %{name}-fix_GCC15.patch
 %description
 SeqAn3 is the new version of the popular SeqAn template
 library for the analysis of biological sequences.
@@ -79,13 +75,16 @@ data structures for:
 
 %package devel
 Summary: SeqAn3 header only files
+# bzip2stream and zipstream libraries are distributed under zlib/libpng
+License:  BSD-3-Clause AND Zlib
 Requires: cmake%{?_isa} >= 3.4
-Requires: cereal-devel%{?_isa} >= 1.3.0
-Requires: sdsl-lite-devel%{?_isa} >= 3.0.0
+Requires: cereal-devel%{?_isa} >= 1.3.2
+Requires: sdsl-lite-devel%{?_isa} >= 3.0.1
 Requires: zlib-devel%{?_isa} >= 1.2
 Requires: bzip2-devel%{?_isa} >= 1.0
 Requires: range-v3-devel%{?_isa} >= 0.11.0
-
+Provides: bundled(bzip2stream)
+Provides: bundled(zipstream)
 %description devel
 C++ headers files of SeqAn3, including CMake configuration files.
 
@@ -98,15 +97,10 @@ SeqAn3 documentation.
 %prep
 %autosetup -n %{name}-%{version} -N
 
-dos2unix test/cmake/seqan3_require_benchmark.cmake
-%patch0 -p1 -b .backup
-%patch1 -p1 -b .backup
-%if 0%{?fedora} > 35
-%patch2 -p1 -b .backup
-%patch3 -p1 -b .backup
-%endif
+%patch 1 -p1 -b .backup
+%patch 2 -p1 -b .backup
 
-# Unbundle libraries already on Fedora
+# Unbundle libraries already available in Fedora
 rm -rf submodules/cereal
 rm -rf submodules/range-v3
 rm -rf submodules/sdsl-lite
@@ -118,50 +112,71 @@ find . -type f -name "*.hpp" -exec chmod 0644 '{}' \;
 %if %{with check}
 %if %{with test_api}
 mkdir -p build
+export CXXFLAGS="%{build_cxxflags} -std=c++23"
 %cmake -S test/unit -B build -DCMAKE_BUILD_TYPE=Release \
+ -DCPM_USE_LOCAL_PACKAGES:BOOL=OFF -DCPM_LOCAL_PACKAGES_ONLY:BOOL=OFF \
+ -DCPM_DONT_UPDATE_MODULE_PATH:BOOL=ON -DCPM_DONT_CREATE_PACKAGE_LOCK:BOOL=ON \
  -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
  -DSEQAN3_CEREAL:BOOL=ON \
- -DSEQAN3_LEMON:BOOL=ON \
- -DSEQAN3_TEST_BUILD_OFFLINE:BOOL=ON
+ -DSEQAN3_TEST_BUILD_OFFLINE:BOOL=ON -DFETCHCONTENT_FULLY_DISCONNECTED:BOOL=ON \
+ -DFETCHCONTENT_UPDATES_DISCONNECTED:BOOL=ON \
+ -DSEQAN3_NO_ZLIB=OFF
 
 %define _vpath_builddir build
 %cmake_build
 %endif
 %if %{with test_header}
 mkdir -p build-header
+export CXXFLAGS="%{build_cxxflags} -std=c++23"
 %cmake -S test/header -B build-header -DCMAKE_BUILD_TYPE=Release \
+ -DCPM_USE_LOCAL_PACKAGES:BOOL=OFF -DCPM_LOCAL_PACKAGES_ONLY:BOOL=OFF \
+ -DCPM_DONT_UPDATE_MODULE_PATH:BOOL=ON -DCPM_DONT_CREATE_PACKAGE_LOCK:BOOL=ON \
  -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
  -DSEQAN3_CEREAL:BOOL=ON \
- -DSEQAN3_LEMON:BOOL=ON \
- -DSEQAN3_TEST_BUILD_OFFLINE:BOOL=ON
+ -DSEQAN3_TEST_BUILD_OFFLINE:BOOL=ON -DFETCHCONTENT_FULLY_DISCONNECTED:BOOL=ON \
+ -DFETCHCONTENT_UPDATES_DISCONNECTED:BOOL=ON \
+ -DSEQAN3_NO_ZLIB=OFF
 
 %define _vpath_builddir build-header
 %cmake_build
 %endif
 %if %{with benchmark}
 mkdir -p build-performance
+export CXXFLAGS="%{build_cxxflags} -std=c++23"
 %cmake -S test/performance -B build-performance -DCMAKE_BUILD_TYPE=Release \
+ -DCPM_USE_LOCAL_PACKAGES:BOOL=OFF -DCPM_LOCAL_PACKAGES_ONLY:BOOL=OFF \
+ -DCPM_DONT_UPDATE_MODULE_PATH:BOOL=ON -DCPM_DONT_CREATE_PACKAGE_LOCK:BOOL=ON \
  -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
  -DSEQAN3_CEREAL:BOOL=ON \
- -DSEQAN3_LEMON:BOOL=ON \
- -DSEQAN3_TEST_BUILD_OFFLINE:BOOL=ON
+ -DSEQAN3_TEST_BUILD_OFFLINE:BOOL=ON -DFETCHCONTENT_FULLY_DISCONNECTED:BOOL=ON \
+ -DFETCHCONTENT_UPDATES_DISCONNECTED:BOOL=ON \
+ -DSEQAN3_NO_ZLIB=OFF
 
 %define _vpath_builddir build-performance
 %cmake_build
 %endif
 %endif
 %if %{with doc}
-# This command needs to download a 'cppreference-doxygen-web.tag.xml' file
-#mkdir -p build-doc
-#%%cmake -S test/documentation -B build-doc -DCMAKE_BUILD_TYPE=Release 
-#make -j1 -C build-doc
+mkdir -p build-doc
+%cmake -S test/documentation -B build-doc -DCMAKE_BUILD_TYPE=Release
+%define _vpath_builddir build-doc
+%cmake_build -- -j1
 %endif
 
 %install
 mkdir -p %{buildroot}%{_libdir}/cmake/%{name}
 cp -a include %{buildroot}%{_prefix}/
+rm %{buildroot}%{_includedir}/%{name}/contrib/std/.{clang-format,gitignore}
 
-install -pm 644 build_system/*.cmake %{buildroot}%{_libdir}/cmake/%{name}/
+install -pm 644 cmake/seqan3-config-version.cmake %{buildroot}%{_libdir}/cmake/%{name}/
+install -pm 644 cmake/seqan3-config.cmake %{buildroot}%{_libdir}/cmake/%{name}/
+
+%if %{with doc}
+mkdir -p build-doc
+%cmake -S test/documentation -B build-doc -DCMAKE_BUILD_TYPE=Release
+%define _vpath_builddir build-doc
+%cmake_install
+%endif
 
 %if %{with check}
 %check
@@ -197,62 +212,4 @@ install -pm 644 build_system/*.cmake %{buildroot}%{_libdir}/cmake/%{name}/
 %endif
 
 %changelog
-* Sat Feb 05 2022 Fedora Release Engineering <releng@fedoraproject.org> - 3.1.0-3
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
-- Patched for GCC-12
-
-* Mon Jan 17 2022 Kevin Fenzi <kevin@scrye.com> - 3.1.0-2
-- Rebuild for hiredis 1.0.2
-
-* Fri Nov 26 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.0-1
-- Release 3.1.0
-
-* Sun Sep 05 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.0-0.2.20210809git4604f1b2
-- Rebuild for gtest-1.11.0
-
-* Mon Aug 09 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.0-0.1.20210809git4604f1b2
-- Pre-release 3.1.0
-
-* Fri Jul 23 2021 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.3-2
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
-
-* Fri May 28 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.0.3-1
-- Release 3.0.3
-
-* Wed May 26 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.0.3-0.1.rc1
-- Pre-release 3.0.3-rc1
-
-* Sun Feb 14 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.0.2-7
-- Disable tests with GCC-11 (rhbz#1923593)
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
-
-* Fri Dec 11 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.2-6
-- Rebuild for GCC-11
-
-* Tue Nov 03 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.2-5
-- Bundle sdsl header files
-
-* Sat Oct 17 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.2-4
-- Remove old License file from bundled libraries
-- Redefine vpath builddir
-
-* Fri Oct 16 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.2-3
-- Fix Requires packages
-
-* Wed Oct 14 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.2-2
-- Use -std=c++2a flag
-- Patched for upstream bugs #2209 #2210
-
-* Tue Oct 13 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.2-1
-- Release 3.0.2
-
-* Fri Aug 07 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.2-0.2.20200806gitbf04354
-- Pre-release 3.0.2 with bundled range-v3
-
-* Thu Aug 06 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.2-0.1.20200806gitbf04354
-- Pre-release 3.0.2
-
-* Thu Mar 05 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.1-1
-- Execute header/performance tests
-- Build docs
-- First package
+%autochangelog

sources

@@ -1 +1 @@
-SHA512 (seqan3-3.1.0.tar.gz) = 7ffbb82dc678cb6836b8f6cc952f1d4e501dbb90ed5a420e3c983e79a7d797f6d29fbb413347f6493e1f9b8bfec49749654e415012ba8b34e03de1a10858048e
+SHA512 (seqan3-3.4.2.tar.gz) = 6337bb3d49406e89e277ab4b9e751f6b2a0524c32c7aecf2093b795863870c2337bb1df1c798791aee82325cb3f0b19ecb57e109d73db847e6fe6a2a033bbaae