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

@@ -0,0 +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-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.spec

@@ -0,0 +1,215 @@
+%global debug_package %{nil}
+%global middle_release 0
+
+%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      8c604d98e0d291bc3909ecbad78ca778b3ad5a5c
+%global  date        .20230403git
+%global  shortcommit %(c=%{commit}; echo ${c:0:8})
+%else
+%global  commit      %{nil}
+%global  date        %{nil}
+%global  shortcommit %{nil}
+%endif
+
+Name:      seqan3
+Summary:   The modern C++ library for sequence analysis
+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}
+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
+BuildRequires: gcc-c++
+BuildRequires: ccache
+BuildRequires: cmake >= 3.4
+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
+%if %{with check}
+BuildRequires: google-benchmark-devel
+BuildRequires: gtest-devel >= 1.10.0
+%endif
+%if %{with doc}
+BuildRequires: texlive-newunicodechar
+BuildRequires: doxygen >= 1.9.4
+%endif
+# 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.
+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
+
+%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} >= 1.3.2
+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.
+
+%package doc
+Summary: SeqAn3 documentation
+BuildArch: noarch
+%description doc
+SeqAn3 documentation.
+
+%prep
+%autosetup -n %{name}-%{version} -N
+
+%patch 1 -p1 -b .backup
+%patch 2 -p1 -b .backup
+
+# Unbundle libraries already available in Fedora
+rm -rf submodules/cereal
+rm -rf submodules/range-v3
+rm -rf submodules/sdsl-lite
+
+# Fix file permissions
+find . -type f -name "*.hpp" -exec chmod 0644 '{}' \;
+
+%build
+%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_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_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_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}
+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 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
+# Tests the API of the library
+%if %{with test_api}
+%define _vpath_builddir build
+%ctest
+%endif
+# Tests that every header includes all required headers and detects linkage issues
+%if %{with test_header}
+%define _vpath_builddir build-header
+%ctest
+%endif
+# Microbenchmarks
+%if %{with benchmark}
+%define _vpath_builddir build-performance
+%ctest
+%endif
+%endif
+
+%files devel
+%license LICENSE.md
+%doc README.md
+%{_includedir}/%{name}/
+%{_libdir}/cmake/%{name}/
+
+%if %{with doc}
+%files doc
+#%%doc build-doc/doc_usr/html
+%doc doc/*
+%license LICENSE.md
+%doc README.md
+%endif
+
+%changelog
+%autochangelog

sources

@@ -0,0 +1 @@
+SHA512 (seqan3-3.4.2.tar.gz) = 6337bb3d49406e89e277ab4b9e751f6b2a0524c32c7aecf2093b795863870c2337bb1df1c798791aee82325cb3f0b19ecb57e109d73db847e6fe6a2a033bbaae