[INFRA] Put SDSL into contrib

seqan · Feb 6, 2025 · a594be4 · a594be4
1 parent ee18011
commit a594be4
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diff --git a/.github/workflows/cron_latest_libraries.yml b/.github/workflows/cron_latest_libraries.yml
@@ -51,7 +51,7 @@ jobs:
           FILE="cmake/package-lock.cmake"
           sed -i -E 's@(set \(SEQAN3_\S+_VERSION )[^\)]+\)@\1main)@g' $FILE
           sed -i -E 's@VERSION( \$\{SEQAN3_\S+_VERSION\})@GIT_TAG\1@g' $FILE
-          sed -i -E 's@SEQAN3_(SDSL|CEREAL)_VERSION main@SEQAN3_\1_VERSION master@g' $FILE
+          sed -i -E 's@SEQAN3_CEREAL_VERSION main@SEQAN3_\1_VERSION master@g' $FILE
           cat $FILE
 
       - name: Configure tests

diff --git a/README.md b/README.md
@@ -76,7 +76,6 @@ Please see the [online documentation](https://docs.seqan.de/seqan3/main_user/) f
 |                   | [Clang](https://clang.llvm.org)                      | ≥ 17     | tested with `-stdlib=libc++`                |
 |                   | [IntelOneAPI]()                                      | ≥ 2024.0 |                                             |
 |**build system**   | [CMake](https://cmake.org)                           | ≥ 3.20   | optional, but recommended                   |
-|**required libs**  | [SDSL](https://github.com/xxsds/sdsl-lite)           | ≥ 3.0.3  |                                             |
 |**optional libs**  | [cereal](https://github.com/USCiLab/cereal)          | ≥ 1.3.1  | required for serialisation and CTD support  |
 |                   | [zlib](https://github.com/madler/zlib)               | ≥ 1.2    | required for `*.gz` and `.bam` file support |
 |                   | [bzip2](https://www.sourceware.org/bzip2)            | ≥ 1.0    | required for `*.bz2` file support           |

diff --git a/cmake/cpack_install.cmake.in b/cmake/cpack_install.cmake.in
@@ -5,7 +5,6 @@
 # Only if creating the source package (`make package_source`):
 # Copy dependency include directories into package's staging folder
 if (CPACK_SOURCE_INSTALLED_DIRECTORIES)
-    file (COPY "@SEQAN3_SDSL_INCLUDE_DIR@/" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/include/seqan3/vendor")
     file (COPY "@SEQAN3_CEREAL_INCLUDE_DIR@/" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/include/seqan3/vendor")
     configure_file ("@CPM_DOWNLOAD_LOCATION@" "${CMAKE_CURRENT_BINARY_DIR}/cmake/CPM.cmake" COPYONLY)
     if ("@use_ccache_ADDED@" STREQUAL "YES")

diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake
@@ -23,16 +23,6 @@ CPMDeclarePackage (cereal
                    GITHUB_REPOSITORY USCiLab/cereal
                    DOWNLOAD_ONLY TRUE
                    QUIET YES)
-# sdsl-lite
-# Use URL download of the commit archive such that we do not clone submodules
-# Package name is still sdsl (name as v2 at xxsds/sdsl), but sdsl-lite is not currently being packaged
-# To avoid accidentally using the older sdsl, NAME is set to sdsl-lite
-set (SEQAN3_SDSL_VERSION 14cd017027ea742353fc5b500d1cb1d95896b77e CACHE STRING "" FORCE)
-CPMDeclarePackage (sdsl-lite
-                   NAME sdsl-lite
-                   URL https://github.com/xxsds/sdsl-lite/archive/${SEQAN3_SDSL_VERSION}.tar.gz # master
-                   DOWNLOAD_ONLY YES
-                   QUIET YES)
 # benchmark
 set (SEQAN3_BENCHMARK_VERSION 1.9.1 CACHE STRING "" FORCE)
 CPMDeclarePackage (benchmark

diff --git a/cmake/seqan3-config.cmake b/cmake/seqan3-config.cmake
@@ -15,10 +15,6 @@
 #   C++20
 #   pthread
 #
-# SeqAn requires the following libraries:
-#
-#   SDSL      -- the succinct data structure library
-#
 # SeqAn has the following optional dependencies:
 #
 #   ZLIB      -- zlib compression library
@@ -137,36 +133,6 @@ else ()
     seqan3_config_error ("SeqAn3 include directory could not be found (SEQAN3_INCLUDE_DIR: '${SEQAN3_INCLUDE_DIR}')")
 endif ()
 
-# ----------------------------------------------------------------------------
-# Require SDSL
-# ----------------------------------------------------------------------------
-
-find_path (SEQAN3_SDSL_INCLUDE_DIR
-           NAMES sdsl/version.hpp
-           HINTS "${SEQAN3_INCLUDE_DIR}/seqan3/vendor")
-
-# 1) Check the vendor directory of SeqAn3. This directory exists for source packages and installed packages.
-if (SEQAN3_SDSL_INCLUDE_DIR)
-    seqan3_config_print ("Required dependency:        SDSL found.")
-    set (SEQAN3_DEPENDENCY_INCLUDE_DIRS ${SEQAN3_SDSL_INCLUDE_DIR} ${SEQAN3_DEPENDENCY_INCLUDE_DIRS})
-    # 2) Get package via CPM.
-elseif (SEQAN3_HAS_CPM)
-    CPMGetPackage (sdsl-lite)
-
-    find_path (SEQAN3_SDSL_INCLUDE_DIR
-               NAMES sdsl/version.hpp
-               HINTS "${sdsl-lite_SOURCE_DIR}/include")
-
-    if (SEQAN3_SDSL_INCLUDE_DIR)
-        seqan3_config_print ("Required dependency:        SDSL found.")
-        set (SEQAN3_DEPENDENCY_INCLUDE_DIRS ${SEQAN3_SDSL_INCLUDE_DIR} ${SEQAN3_DEPENDENCY_INCLUDE_DIRS})
-    else ()
-        seqan3_config_error ("The SDSL library is required, but wasn't found.")
-    endif ()
-else ()
-    seqan3_config_error ("The SDSL library is required, but wasn't found.")
-endif ()
-
 # ----------------------------------------------------------------------------
 # Force-deactivate optional dependencies
 # ----------------------------------------------------------------------------

diff --git a/cmake/seqan3-install.cmake b/cmake/seqan3-install.cmake
@@ -21,5 +21,4 @@ install (FILES "${SEQAN3_CLONE_DIR}/cmake/seqan3-config.cmake" "${SEQAN3_CLONE_D
 # install seqan3 header files in /include/seqan3
 install (DIRECTORY "${SEQAN3_INCLUDE_DIR}/seqan3" TYPE INCLUDE)
 
-install (DIRECTORY "${SEQAN3_SDSL_INCLUDE_DIR}/sdsl" DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/seqan3/vendor")
 install (DIRECTORY "${SEQAN3_CEREAL_INCLUDE_DIR}/cereal" DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/seqan3/vendor")
diff --git a/include/seqan3/alphabet/container/bitpacked_sequence.hpp b/include/seqan3/alphabet/container/bitpacked_sequence.hpp
@@ -14,11 +14,10 @@
 #include <ranges>
 #include <type_traits>
 
-#include <sdsl/int_vector.hpp>
-
 #include <seqan3/alphabet/detail/alphabet_proxy.hpp>
 #include <seqan3/alphabet/views/to_char.hpp>
 #include <seqan3/alphabet/views/to_rank.hpp>
+#include <seqan3/contrib/sdsl-lite.hpp>
 #include <seqan3/core/concept/cereal.hpp>
 #include <seqan3/core/range/detail/random_access_iterator.hpp>
 #include <seqan3/utility/math.hpp>