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

@@ -1,3 +1,17 @@
 /seqan3-3.0.2-Source.tar.xz
 /seqan3-3.0.3-rc.1.tar.gz
 /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

@@ -1,3 +1,24 @@
-# seqan3
+# SeqAn3 -- the modern C++ library for sequence analysis
 
-The seqan3 package
+
+SeqAn3 is the new version of the popular SeqAn template library for the analysis of biological sequences.
+It enables the rapid development of high-performance solutions by providing generic algorithms and data structures
+for:
+
+  * sequence representation and transformation
+  * full-text indexing and efficient search
+  * sequence alignment
+  * input/output of common file formats
+
+By leveraging *Modern C++* it provides unprecedented ease-of-use without sacrificing performance.
+
+Please see the [online documentation](https://docs.seqan.de/seqan/3.2.0/) for more details.
+
+## Quick facts
+
+  * C++ header-only library: easy to integrate with your app & easy to distribute
+  * liberal open source license: allows integration with any app or library, requires only attribution
+  * very high code quality standards: >97% unit test coverage, performance regression tests, ...
+  * extensive API documentation & tutorials: more lines of documentation than lines of code
+  * aims to support any 64-bit architecture running Linux/POSIX; currently big-endian CPU architectures
+    like s390x are less supported

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-cppreference.patch

@@ -1,25 +0,0 @@
-Author: Michael R. Crusoe <michael.crusoe@gmail.com>
-Description: Use the packaged version of cppreference
---- seqan3.orig/test/documentation/seqan3-doxygen.cmake
-+++ seqan3/test/documentation/seqan3-doxygen.cmake
-@@ -43,16 +43,11 @@
- include(ExternalProject)
- ExternalProject_Add (
-     download-cppreference-doxygen-web-tag
--    URL "https://github.com/PeterFeicht/cppreference-doc/releases/download/v20200913/html-book-20200913.tar.xz"
--    URL_HASH SHA256=91c6d7881ca0ffb9780d40723c415b20b2dce0fafc2ea7ab6abaec04a5934f55
--    TLS_VERIFY ON
--    DOWNLOAD_DIR "${PROJECT_BINARY_DIR}"
--    DOWNLOAD_NAME "html-book.tar.xz"
--    DOWNLOAD_NO_EXTRACT YES
-+    DOWNLOAD_COMMAND ""
-     BINARY_DIR "${PROJECT_BINARY_DIR}"
--    CONFIGURE_COMMAND /bin/sh -c "xzcat html-book.tar.xz | tar -xf - cppreference-doxygen-web.tag.xml"
--    BUILD_COMMAND rm "html-book.tar.xz"
--    INSTALL_COMMAND ""
-+    CONFIGURE_COMMAND ""
-+    BUILD_COMMAND ""
-+    INSTALL_COMMAND ln -s /usr/share/devhelp/books/cppreference-doxygen-web.tag.xml "${PROJECT_BINARY_DIR}/"
- )
- 
- ### TEST HELPER

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-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 +5,7 @@
- # 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 ("${gtest_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 +5,8 @@
- # 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 "${gtest_path}")
--    set_property (TARGET gtest APPEND PROPERTY INTERFACE_LINK_LIBRARIES "pthread")
--
--    unset(gtest_main_path)
--    unset(gtest_path)
--endmacro ()
--
- macro (seqan3_require_test)
-     enable_testing ()
- 
--    set (gtest_git_tag "252ce9c52d304659eff6be558209c811b7191963") # 26-04-2021
--
--    if (NOT CMAKE_VERSION VERSION_LESS 3.14)
--        message (STATUS "Fetch googletest:")
--
--        include (FetchContent)
--        FetchContent_Declare (
--            gtest_fetch_content
--            GIT_REPOSITORY "https://github.com/google/googletest.git"
--            GIT_TAG "${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

@@ -5,15 +5,16 @@
 %bcond_without test_api
 %bcond_without test_header
 %bcond_without benchmark
-%bcond_without doc
+# 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      ff61cb64effe2c61bc65e0380256dcd87acee353
-%global  date        .20210510git
+%global  commit      8c604d98e0d291bc3909ecbad78ca778b3ad5a5c
+%global  date        .20230403git
 %global  shortcommit %(c=%{commit}; echo ${c:0:8})
 %else
 %global  commit      %{nil}
@@ -23,43 +24,43 @@ ExclusiveArch: %{power64} x86_64 aarch64
 
 Name:      seqan3
 Summary:   The modern C++ library for sequence analysis
-Version:   3.0.3
-Release:   1%{date}%{shortcommit}%{?dist}
-License:   BSD
-URL:       http://www.seqan.de/
+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
 %if 0%{?middle_release}
-# git clone -b 3.0.3 --depth 1 --single-branch --progress --recursive https://github.com/seqan/seqan3.git
-# find . -name '.git*' -exec  rm -rf {} ';'
-# find . -name '.git*' -exec  rm -f {} ';'
-# cd .. && tar -czvf seqan3-%%{version}.tar.gz seqan3
 Source0:   https://github.com/seqan/%{name}/archive/%{commit}/%{name}-%{commit}.tar.gz
 %else
-Source0:   https://github.com/seqan/%{name}/archive/%{version}-rc.1/%{name}-%{version}.tar.gz
+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 >= 1.2.3
+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}-cppreference.patch
-Patch2: %{name}-unbundle_gtest.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.
@@ -74,15 +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} >= 1.2.3
+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(sdsl-lite-devel) = 3.0.0
-Provides: bundled(sdsl-devel) = 3.0.0
-Provides: bundled(SDSL-devel) = 3.0.0
-
+Provides: bundled(bzip2stream)
+Provides: bundled(zipstream)
 %description devel
 C++ headers files of SeqAn3, including CMake configuration files.
 
@@ -93,23 +95,15 @@ BuildArch: noarch
 SeqAn3 documentation.
 
 %prep
-%autosetup -n %{name} -N
+%autosetup -n %{name}-%{version} -N
 
-dos2unix test/cmake/seqan3_require_benchmark.cmake
-%patch0 -p1 -b .backup
-%patch1 -p1 -b .backup
-%patch2 -p1 -b .backup
+%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/cereal
-rm -rf submodules/sdsl-lite/googletest
-
-
-# SDSL 3.0 is a new SDSL pre-release, under development.
-# See https://github.com/xxsds/sdsl-lite
-cp -p submodules/sdsl-lite/LICENSE submodules/sdsl-lite/sdsl-LICENSE
+rm -rf submodules/sdsl-lite
 
 # Fix file permissions
 find . -type f -name "*.hpp" -exec chmod 0644 '{}' \;
@@ -118,37 +112,45 @@ find . -type f -name "*.hpp" -exec chmod 0644 '{}' \;
 %if %{with check}
 %if %{with test_api}
 mkdir -p build
-# Workaround for upstream bug#1993
-export CXXFLAGS="%{build_cxxflags} -std=c++20"
+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++20"
+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++20"
+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
@@ -156,19 +158,25 @@ export CXXFLAGS="%{build_cxxflags} -std=c++20"
 %endif
 %if %{with doc}
 mkdir -p build-doc
-export CXXFLAGS="%{build_cxxflags} -std=c++20"
-%cmake -S test/documentation -B build-doc -DCMAKE_BUILD_TYPE=Release 
-make -j1 -C 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}
 
-rm -f submodules/sdsl-lite/include/sdsl/.gitignore
-cp -a submodules/sdsl-lite/include %{buildroot}%{_prefix}/
+install -pm 644 cmake/seqan3-config-version.cmake %{buildroot}%{_libdir}/cmake/%{name}/
+install -pm 644 cmake/seqan3-config.cmake %{buildroot}%{_libdir}/cmake/%{name}/
 
-install -pm 644 build_system/*.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
@@ -190,57 +198,18 @@ install -pm 644 build_system/*.cmake %{buildroot}%{_libdir}/cmake/%{name}/
 %endif
 
 %files devel
-%license LICENSE.md submodules/sdsl-lite/sdsl-LICENSE
+%license LICENSE.md
 %doc README.md
 %{_includedir}/%{name}/
-%{_includedir}/sdsl/
 %{_libdir}/cmake/%{name}/
 
 %if %{with doc}
 %files doc
-%doc build-doc/doc_usr/html
+#%%doc build-doc/doc_usr/html
+%doc doc/*
 %license LICENSE.md
 %doc README.md
 %endif
 
 %changelog
-* 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 (seqan3-3.0.3.tar.gz) = 68c9eff9f8be4b2bf4015f2108d2aeeb3c085fed41480a3c9a5532f3392ccd2ece51707319e22b2f11a86dd6afb36674b8471518432c971c6a8f83aeb00ca18c
+SHA512 (seqan3-3.4.2.tar.gz) = 6337bb3d49406e89e277ab4b9e751f6b2a0524c32c7aecf2093b795863870c2337bb1df1c798791aee82325cb3f0b19ecb57e109d73db847e6fe6a2a033bbaae