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No commits in common. "rawhide" and "f33" have entirely different histories.
6 changed files with 2 additions and 356 deletions
17
.gitignore
vendored
17
.gitignore
vendored
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@ -1,17 +0,0 @@
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/seqan3-3.0.2-Source.tar.xz
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/seqan3-3.0.3-rc.1.tar.gz
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/seqan3-3.0.3.tar.gz
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/seqan3-3.1.0-rc1.tar.gz
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/seqan3-3.1.0.tar.gz
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/seqan3-3.2.0-rc1.tar.gz
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/seqan3-3.2.0.tar.gz
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/seqan3-404affbf6ee31aeda30ed9cc321b3700a50e5eae.tar.gz
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/seqan3-174255eea53d4847e7ce8cb0dc29415f177dc54d.tar.gz
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/seqan3-8c604d98e0d291bc3909ecbad78ca778b3ad5a5c.tar.gz
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/seqan3-3.3.0-rc.1.tar.gz
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/seqan3-3.3.0-rc.2.tar.gz
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/seqan3-3.4.0-rc.1.tar.gz
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/seqan3-3.4.0-rc.2.tar.gz
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/seqan3-3.4.0-rc.3.tar.gz
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/seqan3-3.4.0.tar.gz
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/seqan3-3.4.2.tar.gz
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25
README.md
25
README.md
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@ -1,24 +1,3 @@
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# SeqAn3 -- the modern C++ library for sequence analysis
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# seqan3
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SeqAn3 is the new version of the popular SeqAn template library for the analysis of biological sequences.
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It enables the rapid development of high-performance solutions by providing generic algorithms and data structures
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for:
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* sequence representation and transformation
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* full-text indexing and efficient search
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* sequence alignment
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* input/output of common file formats
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By leveraging *Modern C++* it provides unprecedented ease-of-use without sacrificing performance.
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Please see the [online documentation](https://docs.seqan.de/seqan/3.2.0/) for more details.
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## Quick facts
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* C++ header-only library: easy to integrate with your app & easy to distribute
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* liberal open source license: allows integration with any app or library, requires only attribution
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* very high code quality standards: >97% unit test coverage, performance regression tests, ...
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* extensive API documentation & tutorials: more lines of documentation than lines of code
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* aims to support any 64-bit architecture running Linux/POSIX; currently big-endian CPU architectures
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like s390x are less supported
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The seqan3 package
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@ -1,80 +0,0 @@
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--- a/cmake/seqan3-config.orig.cmake 2024-12-13 18:42:15.000000000 +0100
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+++ b/cmake/seqan3-config.cmake 2025-01-19 21:13:45.692446573 +0100
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@@ -113,11 +113,7 @@
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# ----------------------------------------------------------------------------
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# This will be true for git clones and source packages, but not for installed packages.
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-if (EXISTS "${CMAKE_CURRENT_LIST_DIR}/CPM.cmake")
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- set (SEQAN3_HAS_CPM TRUE)
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-else ()
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- set (SEQAN3_HAS_CPM FALSE)
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-endif ()
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+set (SEQAN3_HAS_CPM FALSE)
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if (SEQAN3_HAS_CPM)
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set (CPM_INDENT " CMake Package Manager CPM: ")
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--- a/test/seqan3-test.orig.cmake 2024-12-13 18:42:15.000000000 +0100
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+++ b/test/seqan3-test.cmake 2025-01-19 21:18:08.209434385 +0100
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@@ -27,10 +27,6 @@
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"${CMAKE_CURRENT_LIST_DIR}/../cmake/"
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CACHE STRING "Path to directory containing CPM.cmake.")
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-set (CPM_INDENT "CMake Package Manager CPM: ")
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-include ("${SEQAN3_TEST_CPM_DIR}/CPM.cmake")
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-CPMUsePackageLock ("${SEQAN3_TEST_CPM_DIR}/package-lock.cmake")
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-
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include (CheckCXXCompilerFlag)
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include (CheckCXXSourceCompiles)
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include (CMakeDependentOption)
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@@ -51,7 +47,6 @@
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cmake_dependent_option (SEQAN3_WITH_SEQAN2_CI "Build tests with SeqAn2." ON "DEFINED ENV{CI}" OFF)
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if (SEQAN3_WITH_SEQAN2 OR SEQAN3_WITH_SEQAN2_CI)
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- CPMGetPackage (seqan)
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find_path (SEQAN3_SEQAN2_INCLUDE_DIR
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NAMES seqan/version.h
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HINTS "${seqan_SOURCE_DIR}/include")
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--- a/test/cmake/seqan3_require_ccache.orig.cmake 2024-12-13 18:42:15.000000000 +0100
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+++ b/test/cmake/seqan3_require_ccache.cmake 2025-01-19 21:19:53.256828886 +0100
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@@ -4,4 +4,4 @@
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# This file's only purpose is to be replaced with the content of the use_ccache CMakeLists.txt file
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# when creating the source package.
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-CPMGetPackage (use_ccache)
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+# CPMGetPackage (use_ccache)
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--- a/test/unit/CMakeLists.orig.txt 2024-12-13 18:42:15.000000000 +0100
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+++ b/test/unit/CMakeLists.txt 2025-01-19 21:27:10.229117104 +0100
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@@ -8,7 +8,7 @@
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include (../seqan3-test.cmake)
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include (GoogleTest OPTIONAL)
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-CPMGetPackage (googletest)
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+find_package(GTest REQUIRED)
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include (diagnostics/list_missing_unit_tests)
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include (diagnostics/list_unused_unit_tests)
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--- a/test/header/CMakeLists.orig.txt 2024-12-13 18:42:15.000000000 +0100
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+++ b/test/header/CMakeLists.txt 2025-01-19 22:08:37.815744299 +0100
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@@ -7,8 +7,8 @@
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include (../seqan3-test.cmake)
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-CPMGetPackage (googletest)
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-CPMGetPackage (benchmark)
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+find_package(GTest REQUIRED)
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+find_package(benchmark REQUIRED)
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# We compile each header twice in separate compilation units, where the second compilation omits the header guard (check
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# for cyclic includes). Each alone is sufficient to test that the header is functional, but both are needed to check for
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--- a/test/performance/CMakeLists.orig.txt 2024-12-13 18:42:15.000000000 +0100
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+++ b/test/performance/CMakeLists.txt 2025-01-19 22:10:44.305669084 +0100
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@@ -7,7 +7,7 @@
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include (../seqan3-test.cmake)
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-CPMGetPackage (benchmark)
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+find_package(benchmark REQUIRED)
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set (SEQAN3_BENCHMARK_MIN_TIME
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"1s"
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@ -1,20 +0,0 @@
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--- a/test/unit/io/detail/misc_output_test.orig.cpp 2024-12-13 18:42:15.000000000 +0100
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+++ b/test/unit/io/detail/misc_output_test.cpp 2025-01-20 21:58:35.651617085 +0100
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@@ -6,6 +6,7 @@
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#include <fstream>
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#include <vector>
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+#include <functional>
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#include <seqan3/core/debug_stream.hpp>
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#include <seqan3/io/detail/misc_input.hpp>
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--- a/include/seqan3/io/detail/misc_input.orig.hpp 2024-12-13 18:42:15.000000000 +0100
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+++ b/include/seqan3/io/detail/misc_input.hpp 2025-01-20 22:01:28.812235658 +0100
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@@ -17,6 +17,7 @@
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#include <span>
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#include <string>
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#include <tuple>
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+#include <functional>
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#include <seqan3/contrib/stream/bgzf.hpp>
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#include <seqan3/contrib/stream/bgzf_istream.hpp>
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215
seqan3.spec
215
seqan3.spec
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@ -1,215 +0,0 @@
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%global debug_package %{nil}
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%global middle_release 0
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%bcond_without check
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%bcond_without test_api
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%bcond_without test_header
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%bcond_without benchmark
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# Documentation needs external online `cppreference-doc/releases/download/v20220201/html-book-20220201.tar.xz`
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%bcond_with doc
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# SeqAn3 aims to support any 64-bit architecture running Linux/POSIX;
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# currently big-endian CPU architectures like s390x are less supported.
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ExclusiveArch: %{power64} x86_64 aarch64
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%if 0%{?middle_release}
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%global commit 8c604d98e0d291bc3909ecbad78ca778b3ad5a5c
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%global date .20230403git
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%global shortcommit %(c=%{commit}; echo ${c:0:8})
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%else
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%global commit %{nil}
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%global date %{nil}
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%global shortcommit %{nil}
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%endif
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Name: seqan3
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Summary: The modern C++ library for sequence analysis
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Version: 3.4.2
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Release: %autorelease
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License: BSD-3-Clause
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URL: https://www.seqan.de/
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# Source code archive generated by:
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# git clone -b 3.3.0 --depth 1 --single-branch --progress --recursive https://github.com/seqan/seqan3.git
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# find seqan3 -name '.git*' -exec rm -rf {} ';'
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# find seqan3 -name '.git*' -exec rm -f {} ';'
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# tar -czvf seqan3-%%{version}.tar.gz seqan3
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%if 0%{?middle_release}
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Source0: https://github.com/seqan/%{name}/archive/%{commit}/%{name}-%{commit}.tar.gz
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%else
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Source0: https://github.com/seqan/%{name}/archive/%{version}/%{name}-%{version}.tar.gz
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%endif
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BuildRequires: gcc
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BuildRequires: gcc-c++
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BuildRequires: ccache
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BuildRequires: cmake >= 3.4
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BuildRequires: cereal-devel >= 1.3.2
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BuildRequires: sdsl-lite-devel >= 3.0.1
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BuildRequires: make
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BuildRequires: zlib-devel >= 1.2
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BuildRequires: bzip2-devel >= 1.0
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BuildRequires: range-v3-devel >= 0.11.0
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%if %{with check}
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BuildRequires: google-benchmark-devel
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BuildRequires: gtest-devel >= 1.10.0
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%endif
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%if %{with doc}
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BuildRequires: texlive-newunicodechar
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BuildRequires: doxygen >= 1.9.4
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%endif
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# Use Fedora's CMake only
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Patch1: %{name}-3.4.0-disable_CPM.patch
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# Include missing header files
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Patch2: %{name}-fix_GCC15.patch
|
||||
%description
|
||||
SeqAn3 is the new version of the popular SeqAn template
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||||
library for the analysis of biological sequences.
|
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It enables the rapid development of high-performance
|
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solutions by providing generic algorithms and
|
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data structures for:
|
||||
|
||||
- sequence representation and transformation
|
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- full-text indexing and efficient search
|
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- sequence alignment
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- input/output of common file formats
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|
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%package devel
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Summary: SeqAn3 header only files
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# bzip2stream and zipstream libraries are distributed under zlib/libpng
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License: BSD-3-Clause AND Zlib
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Requires: cmake%{?_isa} >= 3.4
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Requires: cereal-devel%{?_isa} >= 1.3.2
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||||
Requires: sdsl-lite-devel%{?_isa} >= 3.0.1
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Requires: zlib-devel%{?_isa} >= 1.2
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||||
Requires: bzip2-devel%{?_isa} >= 1.0
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||||
Requires: range-v3-devel%{?_isa} >= 0.11.0
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Provides: bundled(bzip2stream)
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Provides: bundled(zipstream)
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%description devel
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C++ headers files of SeqAn3, including CMake configuration files.
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%package doc
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Summary: SeqAn3 documentation
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BuildArch: noarch
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%description doc
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SeqAn3 documentation.
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%prep
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%autosetup -n %{name}-%{version} -N
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%patch 1 -p1 -b .backup
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||||
%patch 2 -p1 -b .backup
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||||
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||||
# Unbundle libraries already available in Fedora
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rm -rf submodules/cereal
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rm -rf submodules/range-v3
|
||||
rm -rf submodules/sdsl-lite
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||||
# Fix file permissions
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||||
find . -type f -name "*.hpp" -exec chmod 0644 '{}' \;
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%build
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%if %{with check}
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%if %{with test_api}
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mkdir -p build
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export CXXFLAGS="%{build_cxxflags} -std=c++23"
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%cmake -S test/unit -B build -DCMAKE_BUILD_TYPE=Release \
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-DCPM_USE_LOCAL_PACKAGES:BOOL=OFF -DCPM_LOCAL_PACKAGES_ONLY:BOOL=OFF \
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-DCPM_DONT_UPDATE_MODULE_PATH:BOOL=ON -DCPM_DONT_CREATE_PACKAGE_LOCK:BOOL=ON \
|
||||
-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
|
||||
-DSEQAN3_CEREAL:BOOL=ON \
|
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-DSEQAN3_TEST_BUILD_OFFLINE:BOOL=ON -DFETCHCONTENT_FULLY_DISCONNECTED:BOOL=ON \
|
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-DFETCHCONTENT_UPDATES_DISCONNECTED:BOOL=ON \
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-DSEQAN3_NO_ZLIB=OFF
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|
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%define _vpath_builddir build
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%cmake_build
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%endif
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%if %{with test_header}
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mkdir -p build-header
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export CXXFLAGS="%{build_cxxflags} -std=c++23"
|
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%cmake -S test/header -B build-header -DCMAKE_BUILD_TYPE=Release \
|
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-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 \
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||||
-DSEQAN3_NO_ZLIB=OFF
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||||
|
||||
%define _vpath_builddir build-header
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||||
%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
|
||||
1
sources
1
sources
|
|
@ -1 +0,0 @@
|
|||
SHA512 (seqan3-3.4.2.tar.gz) = 6337bb3d49406e89e277ab4b9e751f6b2a0524c32c7aecf2093b795863870c2337bb1df1c798791aee82325cb3f0b19ecb57e109d73db847e6fe6a2a033bbaae
|
||||
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