Fix/update seqan3

.github/workflows/ci_linux.yml

@@ -12,7 +12,7 @@ concurrency:
  cancel-in-progress: true
 
 env:
- CMAKE_VERSION: 3.10.3
+ CMAKE_VERSION: 3.16.9
  SEQAN3_NO_VERSION_CHECK: 1
  TZ: Europe/Berlin
 
@@ -32,22 +32,30 @@ jobs:
  - name: "Coverage gcc12"
  cxx: "g++-12"
  cc: "gcc-12"
+ cxx_flags: "-std=c++20"
+ pkg: "g++-12"
  build: coverage
  build_type: Coverage
 
+ - name: "gcc13"
+ cxx: "g++"
+ cc: "gcc"
+ cxx_flags: "-std=c++20"
+ pkg: "g++-13"
+ build_type: Release
+
  - name: "gcc12"
  cxx: "g++-12"
  cc: "gcc-12"
+ cxx_flags: "-std=c++20"
+ pkg: "g++-12"
  build_type: Release
 
  - name: "gcc11"
  cxx: "g++-11"
  cc: "gcc-11"
- build_type: Release
-
- - name: "gcc10"
- cxx: "g++-10"
- cc: "gcc-10"
+ cxx_flags: "-std=c++20"
+ pkg: "g++-11"
  build_type: Release
 
  steps:
@@ -68,7 +76,7 @@ jobs:
  run: sudo apt-get install --yes ccache
 
  - name: Install compiler ${{ matrix.cxx }}
- run: sudo apt-get install --yes ${{ matrix.cxx }}
+ run: sudo apt-get install --yes ${{ matrix.pkg }}
 
  - name: Install lcov
  if: matrix.build == 'coverage'

.github/workflows/ci_macos.yml

@@ -12,7 +12,7 @@ concurrency:
  cancel-in-progress: true
 
 env:
- CMAKE_VERSION: 3.10.3
+ CMAKE_VERSION: 3.16.9
  SEQAN3_NO_VERSION_CHECK: 1
  TZ: Europe/Berlin
 
@@ -29,19 +29,22 @@ jobs:
  fail-fast: true
  matrix:
  include:
+ - name: "gcc13"
+ cxx: "g++-13"
+ cc: "gcc-13"
+ cxx_flags: "-std=c++20"
+ build_type: Release
+
  - name: "gcc12"
  cxx: "g++-12"
  cc: "gcc-12"
+ cxx_flags: "-std=c++20"
  build_type: Release
 
  - name: "gcc11"
  cxx: "g++-11"
  cc: "gcc-11"
- build_type: Release
-
- - name: "gcc10"
- cxx: "g++-10"
- cc: "gcc-10"
+ cxx_flags: "-std=c++20"
  build_type: Release
 
  steps:

.github/workflows/ci_misc.yml

@@ -30,9 +30,10 @@ jobs:
  include:
  - name: "Documentation"
  build: documentation
+ cxx_flags: "-std=c++20"
  build_threads: 2
  test_threads: 2
- cmake: 3.10.3
+ cmake: 3.16.9
  doxygen: 1.9.4
  requires_toolchain: false
  requires_ccache: false

.gitmodules

@@ -5,3 +5,6 @@
 [submodule "lib/robin-hood-hashing"]
  path = lib/robin-hood-hashing
  url = https://github.com/martinus/robin-hood-hashing
+[submodule "lib/sharg-parser"]
+ path = lib/sharg-parser
+ url = https://github.com/seqan/sharg-parser.git

CMakeLists.txt

@@ -27,6 +27,9 @@ set (FontReset "${Esc}[m")
 # Dependency: SeqAn3.
 find_package (SeqAn3 QUIET REQUIRED HINTS lib/seqan3/build_system)
 
+# Dependency: sharg
+find_package (sharg QUIET REQUIRED HINTS lib/sharg-parser/build_system)
+
 # Use ccache.
 include ("${SEQAN3_CLONE_DIR}/test/cmake/seqan3_require_ccache.cmake")
 seqan3_require_ccache ()

include/shared.h

@@ -124,5 +124,5 @@ void store_ibf(IBFType const & ibf,
 {
  std::ofstream os{opath, std::ios::binary};
  cereal::BinaryOutputArchive oarchive{os};
- oarchive(seqan3::interleaved_bloom_filter(ibf));
+ oarchive(ibf);
 }

src/CMakeLists.txt

@@ -2,9 +2,12 @@ cmake_minimum_required (VERSION 3.9)
 
 find_package(OpenMP REQUIRED)
 add_library ("${PROJECT_NAME}_lib" STATIC ibf.cpp estimate.cpp)
-target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC seqan3::seqan3)
-target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC robin_hood)
-target_link_libraries("${PROJECT_NAME}_lib" PUBLIC OpenMP::OpenMP_CXX)
+target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC
+ seqan3::seqan3
+ robin_hood
+ OpenMP::OpenMP_CXX
+ sharg::sharg
+)
 
 target_include_directories ("${PROJECT_NAME}_lib" PUBLIC ../include)