diff --git a/.codecov.yml b/.codecov.yml
index ffa259b..2733b79 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -9,9 +9,8 @@ coverage:
     project:  # project is the overall code coverage of the whole codebase
       default:
         if_ci_failed: success # per default, codecov would fail if any CI fails
-        target: auto          # the target coverage, usually the code coverage of the base-branch
-        threshold: 0.02%      # codecov/project fails if there is a drop of more than 0.02%
-    patch:  # patch is the code-coverage of the changed lines in the PR
+        informational: true   # the codecov/patch status is never "fail"
+    patch:  # patch is the code-coverage of the changed lines in the PR and often reports false positives
       default:
         if_ci_failed: success # per default, codecov would fail if any CI fails
         informational: true   # the codecov/patch status is never "fail"
diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml
index 466dbed..dd53966 100644
--- a/.github/workflows/ci_coverage.yml
+++ b/.github/workflows/ci_coverage.yml
@@ -1,25 +1,21 @@
-name: CI on Linux
+name: Coverage
 
 on:
   push:
-    branches:
-      - 'main'
   pull_request:
   workflow_dispatch:
 
 concurrency:
   group: coverage-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: ${{ github.event_name != 'push' }}
+  cancel-in-progress: false
 
 env:
-  CMAKE_VERSION: 3.16.9
-  SEQAN3_NO_VERSION_CHECK: 1
   SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 
 defaults:
   run:
-    shell: bash -ex {0}
+    shell: bash -Eexuo pipefail {0}
 
 jobs:
   build:
@@ -30,127 +26,73 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - name: "Coverage gcc12"
-            cxx: "g++-12"
-            cc: "gcc-12"
+          - name: "gcc13"
+            compiler: "gcc-13"
+            build: coverage
             build_type: Coverage
-            cxx_flags: "-std=c++23"
 
     steps:
-      - name: Set repository name
-        run: echo "REPOSITORY_NAME=$(echo '${{ github.repository }}' | awk -F '/' '{print $2}')" >> $GITHUB_ENV
-
       # How many commits do we need to fetch to also fetch the branch point?
       - name: Get fetch depth
         id: fetch_depth
         run: echo "depth=$(( ${{ github.event.pull_request.commits }} + 2 ))" >> $GITHUB_OUTPUT
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
-          path: ${{ env.REPOSITORY_NAME }}
           fetch-depth: ${{ steps.fetch_depth.outputs.depth }}
-          submodules: recursive
+          submodules: false
 
-      - name: Add package source
-        run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/configure_apt.sh
+      - name: Setup toolchain
+        uses: seqan/actions/setup-toolchain@main
+        with:
+          compiler: ${{ matrix.compiler }}
+          ccache_size: 125M
 
       - name: Install CMake
-        run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/install_cmake.sh
-
-      - name: Install ccache
-        run: |
-          conda install --yes --override-channels --channel conda-forge ccache
-          sudo ln -s $CONDA/bin/ccache /usr/bin/ccache
-
-      - name: Install compiler ${{ matrix.cxx }}
-        run: sudo apt-get install --yes ${{ matrix.cxx }}
+        uses: seqan/actions/setup-cmake@main
+        with:
+          cmake: 3.21.7
 
       - name: Install gcovr
-        env:
-          CC: ${{ matrix.cc }}
         run: |
           sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/${CC/gcc/gcov} 100
-          pip install gcovr==5.0
-
-      - name: Load ccache
-        uses: actions/cache@v3
-        with:
-          path: .ccache
-          key: ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }}-${{ github.run_number }}
-          # Restoring: From current branch, otherwise from base branch, otherwise from any branch.
-          restore-keys: |
-            ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }}
-            ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.base_ref }}
-            ${{ runner.os }}-${{ matrix.name }}-ccache-
-
-      - name: Tool versions
-        run: |
-          env cmake --version
-          env ${{ matrix.cxx }} --version
+          pip install gcovr==6.0
 
       - name: Configure tests
-        env:
-          CXX: ${{ matrix.cxx }}
-          CC: ${{ matrix.cc }}
         run: |
           mkdir build
           cd build
-          cmake ../${{ env.REPOSITORY_NAME }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                              -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size"
-          make -j2 gtest_build
-
-      - name: Build application
-        env:
-          CCACHE_BASEDIR: ${{ github.workspace }}
-          CCACHE_DIR: ${{ github.workspace }}/.ccache
-          CCACHE_COMPRESS: true
-          CCACHE_COMPRESSLEVEL: 12
-          CCACHE_MAXSIZE: 525M
-          CCACHE_IGNOREOPTIONS: "-fprofile-abs-path"
-        run: |
-          ccache -z
-          cd build
-          make -k -j2
-          ccache -sv
+          cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
+          make -j2 gtest_main benchmark_main yaml-cpp
 
       - name: Build tests
         env:
-          CCACHE_BASEDIR: ${{ github.workspace }}
-          CCACHE_DIR: ${{ github.workspace }}/.ccache
-          CCACHE_COMPRESS: true
-          CCACHE_COMPRESSLEVEL: 12
-          CCACHE_MAXSIZE: 525M
           CCACHE_IGNOREOPTIONS: "-fprofile-abs-path"
         run: |
           ccache -z
           cd build
-          make -k -j2 api_test cli_test
+          CMAKE_BUILD_PARALLEL_LEVEL=2 cmake --build . -- -k test
           ccache -sv
 
-      - name: Run tests
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
-
       - name: Generate coverage report
         run: |
-          gcovr --gcov-executable ${{ github.workspace }}/${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/gcov.sh \
-                --root ${{ github.workspace }}/${{ env.REPOSITORY_NAME }}/test/coverage \
+          gcovr --gcov-executable ${{ github.workspace }}/.github/workflows/scripts/gcov.sh \
+                --root ${{ github.workspace }}/test/coverage \
                 ${{ github.workspace }}/build \
-                --filter ${{ github.workspace }}/${{ env.REPOSITORY_NAME }}/include \
-                --filter ${{ github.workspace }}/${{ env.REPOSITORY_NAME }}/src \
+                --filter ${{ github.workspace }}/include \
+                --filter ${{ github.workspace }}/src \
                 --exclude-lines-by-pattern '^\s*$' \
                 --exclude-lines-by-pattern '^\s*};$' \
-                --exclude-lines-by-pattern '^.*GCOVR_EXCL_LINE.*$' \
                 --exclude-unreachable-branches \
                 --exclude-throw-branches \
+                --exclude-noncode-lines \
                 -j 2 \
                 --xml \
                 --output ${{ github.workspace }}/build/coverage_report.xml
 
-      - name: Submit coverage report
+      - name: Submit coverage build
         uses: codecov/codecov-action@v3
         with:
           files: ${{ github.workspace }}/build/coverage_report.xml
-          root_dir: ${{ github.workspace }}/${{ env.REPOSITORY_NAME }}
+          fail_ci_if_error: false
diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml
new file mode 100644
index 0000000..e010715
--- /dev/null
+++ b/.github/workflows/ci_documentation.yml
@@ -0,0 +1,63 @@
+name: Documentation
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: documentation-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: ${{ github.event_name != 'push' }}
+
+env:
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eexuo pipefail {0}
+
+jobs:
+  build:
+    name: Documentation
+    runs-on: ubuntu-22.04
+    timeout-minutes: 120
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+          submodules: false
+
+      - name: Install CMake
+        uses: seqan/actions/setup-cmake@main
+        with:
+          cmake: 3.21.7
+
+      - name: Install Doxygen
+        uses: seqan/actions/setup-doxygen@main
+        with:
+          doxygen: 1.9.8
+
+      - name: Configure
+        run: |
+          mkdir build
+          cd build
+          cmake ..
+
+      - name: Build documentation
+        run: |
+          cd build
+          make -k -j${{ matrix.test_threads }} doc 2>doxygen_warnings.txt
+          cat doxygen_warnings.txt
+          test ! -s doxygen_warnings.txt
+
+      - name: Package documentation
+        continue-on-error: true
+        run: tar -zcf documentation.tar.gz doc/html
+
+      - name: Upload documentation
+        continue-on-error: true
+        uses: actions/upload-artifact@v3
+        with:
+          name: documentation
+          path: documentation.tar.gz
diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
index ff9001f..30a9739 100644
--- a/.github/workflows/ci_linux.yml
+++ b/.github/workflows/ci_linux.yml
@@ -1,25 +1,21 @@
-name: CI on Linux
+name: Linux
 
 on:
   push:
-    branches:
-      - 'main'
   pull_request:
   workflow_dispatch:
 
 concurrency:
   group: linux-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: ${{ github.event_name != 'push' }}
 
 env:
-  CMAKE_VERSION: 3.16.9
-  SEQAN3_NO_VERSION_CHECK: 1
   SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 
 defaults:
   run:
-    shell: bash -ex {0}
+    shell: bash -Eeuxo pipefail {0}
 
 jobs:
   build:
@@ -27,105 +23,62 @@ jobs:
     runs-on: ubuntu-22.04
     timeout-minutes: 120
     strategy:
-      fail-fast: true
+      fail-fast: false
       matrix:
         include:
-          - name: "Unit gcc12"
-            cxx: "g++-12"
-            cc: "gcc-12"
+          - name: "clang17"
+            compiler: "clang-17"
+            build: unit
             build_type: Release
-            cxx_flags: "-std=c++23"
+            cxx_flags: "-stdlib=libc++"
 
-          - name: "Unit gcc11"
-            cxx: "g++-11"
-            cc: "gcc-11"
+          - name: "gcc13"
+            compiler: "gcc-13"
+            build: unit
             build_type: Release
-            cxx_flags: "-std=c++23"
 
-          - name: "Unit gcc10"
-            cxx: "g++-10"
-            cc: "gcc-10"
+          - name: "gcc12"
+            compiler: "gcc-12"
+            build: unit
             build_type: Release
 
-    steps:
-      - name: Set repository name
-        run: echo "REPOSITORY_NAME=$(echo '${{ github.repository }}' | awk -F '/' '{print $2}')" >> $GITHUB_ENV
+          - name: "gcc11"
+            compiler: "gcc-11"
+            build: unit
+            build_type: Release
 
+    steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
-          path: ${{ env.REPOSITORY_NAME }}
-          fetch-depth: 2
-          submodules: recursive
+          fetch-depth: 1
+          submodules: false
 
-      - name: Add package source
-        run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/configure_apt.sh
+      - name: Setup toolchain
+        uses: seqan/actions/setup-toolchain@main
+        with:
+          compiler: ${{ matrix.compiler }}
+          ccache_size: 75M
 
       - name: Install CMake
-        run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/install_cmake.sh
-
-      - name: Install ccache
-        run: |
-          conda install --yes --override-channels --channel conda-forge ccache
-          sudo ln -s $CONDA/bin/ccache /usr/bin/ccache
-
-      - name: Install compiler ${{ matrix.cxx }}
-        run: sudo apt-get install --yes ${{ matrix.cxx }}
-
-      - name: Load ccache
-        uses: actions/cache@v3
+        uses: seqan/actions/setup-cmake@main
         with:
-          path: .ccache
-          key: ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }}-${{ github.run_number }}
-          # Restoring: From current branch, otherwise from base branch, otherwise from any branch.
-          restore-keys: |
-            ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }}
-            ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.base_ref }}
-            ${{ runner.os }}-${{ matrix.name }}-ccache-
-
-      - name: Tool versions
-        run: |
-          env cmake --version
-          env ${{ matrix.cxx }} --version
+          cmake: 3.21.7
 
-      - name: Configure tests
-        env:
-          CXX: ${{ matrix.cxx }}
-          CC: ${{ matrix.cc }}
+      - name: Configure
         run: |
           mkdir build
           cd build
-          cmake ../${{ env.REPOSITORY_NAME }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                              -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
-          make -j2 gtest_build
+          cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+          make -j2 gtest_main benchmark_main yaml-cpp
 
       - name: Build application
-        env:
-          CCACHE_BASEDIR: ${{ github.workspace }}
-          CCACHE_DIR: ${{ github.workspace }}/.ccache
-          CCACHE_COMPRESS: true
-          CCACHE_COMPRESSLEVEL: 12
-          CCACHE_MAXSIZE: 75M
-        run: |
-          ccache -z
-          cd build
-          make -k -j2
-          ccache -sv
-
-      - name: Build tests
-        env:
-          CCACHE_BASEDIR: ${{ github.workspace }}
-          CCACHE_DIR: ${{ github.workspace }}/.ccache
-          CCACHE_COMPRESS: true
-          CCACHE_COMPRESSLEVEL: 12
-          CCACHE_MAXSIZE: 75M
         run: |
-          ccache -z
           cd build
-          make -k -j2 api_test cli_test
-          ccache -sv
+          CMAKE_BUILD_PARALLEL_LEVEL=2 cmake --build . -- -k
 
-      - name: Run tests
+      - name: Build and run tests
         run: |
           cd build
-          ctest . -j2 --output-on-failure
+          CMAKE_BUILD_PARALLEL_LEVEL=2 cmake --build . -- -k test
diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml
index 83baac0..d2be181 100644
--- a/.github/workflows/ci_macos.yml
+++ b/.github/workflows/ci_macos.yml
@@ -1,25 +1,21 @@
-name: CI on macOS
+name: macOS
 
 on:
   push:
-    branches:
-      - 'main'
   pull_request:
   workflow_dispatch:
 
 concurrency:
   group: macos-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: ${{ github.event_name != 'push' }}
 
 env:
-  CMAKE_VERSION: 3.16.9
-  SEQAN3_NO_VERSION_CHECK: 1
   SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 
 defaults:
   run:
-    shell: bash -ex {0}
+    shell: bash -Eeuxo pipefail {0}
 
 jobs:
   build:
@@ -27,106 +23,62 @@ jobs:
     runs-on: macos-12
     timeout-minutes: 120
     strategy:
-      fail-fast: true
+      fail-fast: false
       matrix:
         include:
-          - name: "Unit gcc12"
-            cxx: "g++-12"
-            cc: "gcc-12"
+          - name: "clang17"
+            compiler: "clang-17"
+            build: unit
             build_type: Release
-            cxx_flags: "-std=c++23"
+            cxx_flags: "-stdlib=libc++" # For verbosity. This is already the default.
 
-          - name: "Unit gcc11"
-            cxx: "g++-11"
-            cc: "gcc-11"
+          - name: "gcc13"
+            compiler: "gcc-13"
+            build: unit
             build_type: Release
-            cxx_flags: "-std=c++23"
 
-          - name: "Unit gcc10"
-            cxx: "g++-10"
-            cc: "gcc-10"
+          - name: "gcc12"
+            compiler: "gcc-12"
+            build: unit
             build_type: Release
 
-    steps:
-      - name: Set repository name
-        run: echo "REPOSITORY_NAME=$(echo '${{ github.repository }}' | awk -F '/' '{print $2}')" >> $GITHUB_ENV
+          - name: "gcc11"
+            compiler: "gcc-11"
+            build: unit
+            build_type: Release
 
+    steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
-          path: ${{ env.REPOSITORY_NAME }}
-          fetch-depth: 2
-          submodules: recursive
+          fetch-depth: 1
+          submodules: false
 
-      - name: Configure Homebrew
-        uses: Homebrew/actions/setup-homebrew@master
+      - name: Setup toolchain
+        uses: seqan/actions/setup-toolchain@main
+        with:
+          compiler: ${{ matrix.compiler }}
+          ccache_size: 75M
 
       - name: Install CMake
-        run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/install_cmake.sh
-
-      - name: Install ccache
-        run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/install_via_brew.sh ccache
-
-      - name: Install compiler ${{ matrix.cxx }}
-        env:
-          CC: ${{ matrix.cc }}
-        run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/install_via_brew.sh $(echo ${CC/clang/llvm} | awk -F '-' '{print $1, $2}')
-
-      - name: Load ccache
-        uses: actions/cache@v3
+        uses: seqan/actions/setup-cmake@main
         with:
-          path: .ccache
-          key: ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }}-${{ github.run_number }}
-          # Restoring: From current branch, otherwise from base branch, otherwise from any branch.
-          restore-keys: |
-            ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }}
-            ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.base_ref }}
-            ${{ runner.os }}-${{ matrix.name }}-ccache-
-
-      - name: Tool versions
-        run: |
-          env cmake --version
-          env ${{ matrix.cxx }} --version
-          sudo xcode-select -s '/Applications/Xcode_13.4.1.app/Contents/Developer' # https://github.com/actions/runner-images/issues/6350
+          cmake: 3.21.7
 
-      - name: Configure tests
-        env:
-          CXX: ${{ matrix.cxx }}
-          CC: ${{ matrix.cc }}
+      - name: Configure
         run: |
           mkdir build
           cd build
-          cmake ../${{ env.REPOSITORY_NAME }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                              -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
-          make -j3 gtest_build
+          cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+          make -j3 gtest_main benchmark_main yaml-cpp
 
       - name: Build application
-        env:
-          CCACHE_BASEDIR: ${{ github.workspace }}
-          CCACHE_DIR: ${{ github.workspace }}/.ccache
-          CCACHE_COMPRESS: true
-          CCACHE_COMPRESSLEVEL: 12
-          CCACHE_MAXSIZE: 75M
-        run: |
-          ccache -z
-          cd build
-          make -k -j3
-          ccache -sv
-
-      - name: Build tests
-        env:
-          CCACHE_BASEDIR: ${{ github.workspace }}
-          CCACHE_DIR: ${{ github.workspace }}/.ccache
-          CCACHE_COMPRESS: true
-          CCACHE_COMPRESSLEVEL: 12
-          CCACHE_MAXSIZE: 75M
         run: |
-          ccache -z
           cd build
-          make -k -j3 api_test cli_test
-          ccache -sv
+          CMAKE_BUILD_PARALLEL_LEVEL=3 cmake --build . -- -k
 
-      - name: Run tests
+      - name: Build and run tests
         run: |
           cd build
-          ctest . -j3 --output-on-failure
+          CMAKE_BUILD_PARALLEL_LEVEL=3 cmake --build . -- -k test
diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml
deleted file mode 100644
index 049767d..0000000
--- a/.github/workflows/ci_misc.yml
+++ /dev/null
@@ -1,175 +0,0 @@
-name: CI misc
-
-on:
-  push:
-    branches:
-      - 'main'
-  pull_request:
-  workflow_dispatch:
-
-concurrency:
-  group: misc-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-env:
-  CMAKE_VERSION: 3.16.9
-  SEQAN3_NO_VERSION_CHECK: 1
-  SHARG_NO_VERSION_CHECK: 1
-  TZ: Europe/Berlin
-
-defaults:
-  run:
-    shell: bash -ex {0}
-
-jobs:
-  build:
-    name: ${{ matrix.name }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
-    strategy:
-      fail-fast: false
-      matrix:
-        include:
-          - name: "Documentation"
-            build: documentation
-            build_threads: 2
-            test_threads: 2
-            cmake: 3.16.9
-            doxygen: 1.9.4
-            requires_toolchain: false
-            requires_ccache: false
-            skip_build_tests: true
-            skip_run_tests: false
-          - name: "Header gcc12"
-            cxx: "g++-12"
-            cc: "gcc-12"
-            build_type: Release
-            build: header
-            build_threads: 2
-            test_threads: 2
-            cmake: 3.16.9
-            requires_toolchain: true
-            requires_ccache: true
-            skip_build_tests: false
-            skip_run_tests: true
-          - name: "Header gcc10"
-            cxx: "g++-10"
-            cc: "gcc-10"
-            build_type: Release
-            build: header
-            build_threads: 2
-            test_threads: 2
-            cmake: 3.16.9
-            requires_toolchain: true
-            requires_ccache: true
-            skip_build_tests: false
-            skip_run_tests: true
-
-    steps:
-      - name: Set repository name
-        run: echo "REPOSITORY_NAME=$(echo '${{ github.repository }}' | awk -F '/' '{print $2}')" >> $GITHUB_ENV
-
-      - name: Checkout
-        uses: actions/checkout@v3
-        with:
-          path: ${{ env.REPOSITORY_NAME }}
-          fetch-depth: 2
-          submodules: recursive
-
-      - name: Add package source
-        run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/configure_apt.sh
-
-      - name: Install CMake
-        env:
-          BUILD: ${{ matrix.build }}
-          CMAKE_VERSION: ${{ matrix.cmake }}
-        run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/install_cmake.sh
-
-      - name: Install Doxygen
-        if: matrix.build == 'documentation'
-        env:
-          DOXYGEN_VERSION: ${{ matrix.doxygen }}
-        run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/install_doxygen.sh
-
-      - name: Install ccache
-        if: matrix.requires_ccache
-        run: |
-          conda install --yes --override-channels --channel conda-forge ccache
-          sudo ln -s $CONDA/bin/ccache /usr/bin/ccache
-
-      - name: Install compiler ${{ matrix.cxx }}
-        if: matrix.requires_toolchain
-        run: sudo apt-get install --yes ${{ matrix.cxx }}
-
-      - name: Load ccache
-        if: matrix.requires_ccache
-        uses: actions/cache@v3
-        with:
-          path: .ccache
-          key: ${{ matrix.name }}-ccache-${{ github.ref }}-${{ github.run_number }}
-          # Restoring: From current branch, otherwise from base branch, otherwise from any branch.
-          restore-keys: |
-            ${{ matrix.name }}-ccache-${{ github.ref }}
-            ${{ matrix.name }}-ccache-${{ github.base_ref }}
-            ${{ matrix.name }}-ccache-
-
-      - name: Tool versions
-        run: |
-          env cmake --version
-          env doxygen --version || true
-          env ${{ matrix.cxx }} --version || true
-
-      - name: Configure tests
-        env:
-          CXX: ${{ matrix.cxx }}
-          CC: ${{ matrix.cc }}
-        run: |
-          mkdir build
-          cd build
-          header_test_flag=$(echo "${{ env.REPOSITORY_NAME }}_HEADER_TEST_ONLY" | tr '[:lower:]' '[:upper:]')
-          cmake ../${{ env.REPOSITORY_NAME }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                              -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
-                                              -D${header_test_flag}=${{ matrix.build == 'header' && 'ON' || 'OFF'}}
-          if [[ "${{ matrix.build }}" =~ ^(header)$ ]]; then
-            make -j${{ matrix.build_threads }} gtest_build
-          fi
-
-      - name: Build tests
-        if: ${{!matrix.skip_build_tests}}
-        env:
-          CCACHE_BASEDIR: ${{ github.workspace }}
-          CCACHE_DIR: ${{ github.workspace }}/.ccache
-          CCACHE_COMPRESS: true
-          CCACHE_COMPRESSLEVEL: 12
-          CCACHE_MAXSIZE: 75M
-          CMAKE_BUILD_PARALLEL_LEVEL: ${{ matrix.build_threads }}
-        run: |
-          ccache -p || true
-          cd build
-          make -k test
-          ccache -s || true
-
-      - name: Run tests
-        if: ${{!matrix.skip_run_tests}}
-        run: |
-          cd build
-          if [[ "${{ matrix.build }}" =~ ^(documentation)$ ]]; then
-            make -k -j${{ matrix.test_threads }} doc 2>doxygen_warnings.txt
-            cat doxygen_warnings.txt
-            test ! -s doxygen_warnings.txt
-          else
-            ctest . -j${{ matrix.test_threads }} --output-on-failure
-          fi
-
-      - name: Package documentation
-        if: matrix.build == 'documentation'
-        continue-on-error: true
-        run: tar -zcf documentation.tar.gz build
-
-      - name: Upload documentation
-        if: matrix.build == 'documentation'
-        continue-on-error: true
-        uses: actions/upload-artifact@v3
-        with:
-          name: documentation
-          path: documentation.tar.gz
diff --git a/.github/workflows/scripts/gcov.sh b/.github/workflows/scripts/gcov.sh
new file mode 100755
index 0000000..258340d
--- /dev/null
+++ b/.github/workflows/scripts/gcov.sh
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+
+# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+set -Eeuo pipefail
+
+args=${@/--branch-counts/""}
+args=${args/--branch-probabilities/""}
+
+exec gcov $args
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 24b589e..639a5b8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -26,6 +26,11 @@ set (FontBold "${Esc}[1m")
 set (FontReset "${Esc}[m")
 
 list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
+
+# Use ccache.
+include (ccache)
+require_ccache ()
+
 set (CPM_INDENT "  CMake Package Manager CPM: ")
 include (CPM)
 include (CPMGetSystemPackage)
@@ -40,10 +45,6 @@ list (APPEND CMAKE_MODULE_PATH "${seqan3_SOURCE_DIR}/test/cmake/")
 # Allow to include CMake scripts from the app-template.
 list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/test/cmake/")
 
-# Use ccache.
-include (ccache)
-require_ccache ()
-
 # Add the application.
 add_subdirectory (src)
 message (STATUS "${FontBold}You can run `make` to build the application.${FontReset}")
diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake
index 7058b42..9774342 100644
--- a/cmake/package-lock.cmake
+++ b/cmake/package-lock.cmake
@@ -36,7 +36,7 @@ CPMDeclarePackage (seqan3
                    OPTIONS "INSTALL_SEQAN3 OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 # benchmark
-set (BENCHMARK_VERSION 1.8.2)
+set (BENCHMARK_VERSION 1.8.3)
 CPMDeclarePackage (benchmark
                    NAME benchmark
                    VERSION ${BENCHMARK_VERSION}
diff --git a/doc/doxygen_cfg b/doc/doxygen_cfg
index 20672f2..07cc4e6 100644
--- a/doc/doxygen_cfg
+++ b/doc/doxygen_cfg
@@ -1,4 +1,4 @@
-# Doxyfile 1.9.1
+# Doxyfile 1.9.8
 
 #---------------------------------------------------------------------------
 # Project related configuration options
@@ -10,6 +10,7 @@ PROJECT_BRIEF          = "A template for creation of SeqAn3 apps, with a FASTQ t
 PROJECT_LOGO           =
 OUTPUT_DIRECTORY       = ${APP_TEMPLATE_DOXYGEN_OUTPUT_DIR}
 CREATE_SUBDIRS         = NO
+CREATE_SUBDIRS_LEVEL   = 8
 ALLOW_UNICODE_NAMES    = NO
 OUTPUT_LANGUAGE        = English
 BRIEF_MEMBER_DESC      = YES
@@ -48,6 +49,7 @@ OPTIMIZE_OUTPUT_SLICE  = NO
 EXTENSION_MAPPING      =
 MARKDOWN_SUPPORT       = YES
 TOC_INCLUDE_HEADINGS   = 5
+MARKDOWN_ID_STYLE      = DOXYGEN
 AUTOLINK_SUPPORT       = YES
 BUILTIN_STL_SUPPORT    = NO
 CPP_CLI_SUPPORT        = NO
@@ -61,6 +63,7 @@ INLINE_SIMPLE_STRUCTS  = NO
 TYPEDEF_HIDES_STRUCT   = NO
 LOOKUP_CACHE_SIZE      = 0
 NUM_PROC_THREADS       = 1
+TIMESTAMP              = NO
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
@@ -81,6 +84,7 @@ INTERNAL_DOCS          = NO
 CASE_SENSE_NAMES       = NO
 HIDE_SCOPE_NAMES       = NO
 HIDE_COMPOUND_REFERENCE= NO
+SHOW_HEADERFILE        = YES
 SHOW_INCLUDE_FILES     = YES
 SHOW_GROUPED_MEMB_INC  = NO
 FORCE_LOCAL_INCLUDES   = NO
@@ -110,9 +114,12 @@ QUIET                  = NO
 WARNINGS               = YES
 WARN_IF_UNDOCUMENTED   = YES
 WARN_IF_DOC_ERROR      = YES
+WARN_IF_INCOMPLETE_DOC = YES
 WARN_NO_PARAMDOC       = NO
+WARN_IF_UNDOC_ENUM_VAL = NO
 WARN_AS_ERROR          = NO
 WARN_FORMAT            = "$file:$line: $text"
+WARN_LINE_FORMAT       = "at line $line of file $file"
 WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 # Configuration options related to the input files
@@ -121,6 +128,7 @@ INPUT                  = ${CMAKE_SOURCE_DIR}/include \
                          ${CMAKE_SOURCE_DIR}/src \
                          ${CMAKE_SOURCE_DIR}/LICENSE.md
 INPUT_ENCODING         = UTF-8
+INPUT_FILE_ENCODING    =
 FILE_PATTERNS          = *.c \
                          *.cc \
                          *.cxx \
@@ -182,6 +190,7 @@ FILTER_PATTERNS        =
 FILTER_SOURCE_FILES    = NO
 FILTER_SOURCE_PATTERNS =
 USE_MDFILE_AS_MAINPAGE =
+FORTRAN_COMMENT_AFTER  = 72
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
 #---------------------------------------------------------------------------
@@ -210,15 +219,17 @@ HTML_FOOTER            =
 HTML_STYLESHEET        =
 HTML_EXTRA_STYLESHEET  =
 HTML_EXTRA_FILES       =
+HTML_COLORSTYLE        = AUTO_LIGHT
 HTML_COLORSTYLE_HUE    = 220
 HTML_COLORSTYLE_SAT    = 100
 HTML_COLORSTYLE_GAMMA  = 80
-HTML_TIMESTAMP         = NO
 HTML_DYNAMIC_MENUS     = YES
 HTML_DYNAMIC_SECTIONS  = NO
+HTML_CODE_FOLDING      = YES
 HTML_INDEX_NUM_ENTRIES = 100
 GENERATE_DOCSET        = NO
 DOCSET_FEEDNAME        = "Doxygen generated docs"
+DOCSET_FEEDURL         =
 DOCSET_BUNDLE_ID       = org.doxygen.Project
 DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
 DOCSET_PUBLISHER_NAME  = Publisher
@@ -229,6 +240,7 @@ GENERATE_CHI           = NO
 CHM_INDEX_ENCODING     =
 BINARY_TOC             = NO
 TOC_EXPAND             = NO
+SITEMAP_URL            =
 GENERATE_QHP           = NO
 QCH_FILE               =
 QHP_NAMESPACE          = org.doxygen.Project
@@ -241,16 +253,18 @@ GENERATE_ECLIPSEHELP   = NO
 ECLIPSE_DOC_ID         = org.doxygen.Project
 DISABLE_INDEX          = NO
 GENERATE_TREEVIEW      = NO
+FULL_SIDEBAR           = NO
 ENUM_VALUES_PER_LINE   = 4
 TREEVIEW_WIDTH         = 250
 EXT_LINKS_IN_WINDOW    = NO
+OBFUSCATE_EMAILS       = YES
 HTML_FORMULA_FORMAT    = png
 FORMULA_FONTSIZE       = 10
-FORMULA_TRANSPARENT    = YES
 FORMULA_MACROFILE      =
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
+MATHJAX_VERSION        = MathJax_3
 MATHJAX_FORMAT         = HTML-CSS
-MATHJAX_RELPATH        = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/
+MATHJAX_RELPATH        = https://cdnjs.cloudflare.com/ajax/libs/mathjax/3.2.2/
 MATHJAX_EXTENSIONS     =
 MATHJAX_CODEFILE       =
 SEARCHENGINE           = YES
@@ -263,7 +277,7 @@ EXTRA_SEARCH_MAPPINGS  =
 #---------------------------------------------------------------------------
 # Configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
-GENERATE_LATEX         = YES
+GENERATE_LATEX         = NO
 LATEX_OUTPUT           = latex
 LATEX_CMD_NAME         =
 MAKEINDEX_CMD_NAME     = makeindex
@@ -280,7 +294,6 @@ USE_PDFLATEX           = YES
 LATEX_BATCHMODE        = NO
 LATEX_HIDE_INDICES     = NO
 LATEX_BIB_STYLE        = plain
-LATEX_TIMESTAMP        = NO
 LATEX_EMOJI_DIRECTORY  =
 #---------------------------------------------------------------------------
 # Configuration options related to the RTF output
@@ -316,6 +329,12 @@ DOCBOOK_OUTPUT         = docbook
 #---------------------------------------------------------------------------
 GENERATE_AUTOGEN_DEF   = NO
 #---------------------------------------------------------------------------
+# Configuration options related to Sqlite3 output
+#---------------------------------------------------------------------------
+GENERATE_SQLITE3       = NO
+SQLITE3_OUTPUT         = sqlite3
+SQLITE3_RECREATE_DB    = YES
+#---------------------------------------------------------------------------
 # Configuration options related to the Perl module output
 #---------------------------------------------------------------------------
 GENERATE_PERLMOD       = NO
@@ -343,14 +362,14 @@ ALLEXTERNALS           = NO
 EXTERNAL_GROUPS        = YES
 EXTERNAL_PAGES         = YES
 #---------------------------------------------------------------------------
-# Configuration options related to the dot tool
+# Configuration options related to diagram generator tools
 #---------------------------------------------------------------------------
-DIA_PATH               =
 HIDE_UNDOC_RELATIONS   = YES
 HAVE_DOT               = NO
 DOT_NUM_THREADS        = 0
-DOT_FONTNAME           = Helvetica
-DOT_FONTSIZE           = 10
+DOT_COMMON_ATTR        = "fontname=Helvetica,fontsize=10"
+DOT_EDGE_ATTR          = "labelfontname=Helvetica,labelfontsize=10"
+DOT_NODE_ATTR          = "shape=box,height=0.2,width=0.4"
 DOT_FONTPATH           =
 CLASS_GRAPH            = YES
 COLLABORATION_GRAPH    = YES
@@ -366,18 +385,20 @@ CALL_GRAPH             = NO
 CALLER_GRAPH           = NO
 GRAPHICAL_HIERARCHY    = YES
 DIRECTORY_GRAPH        = YES
+DIR_GRAPH_MAX_DEPTH    = 1
 DOT_IMAGE_FORMAT       = png
 INTERACTIVE_SVG        = NO
 DOT_PATH               =
 DOTFILE_DIRS           =
-MSCFILE_DIRS           =
+DIA_PATH               =
 DIAFILE_DIRS           =
 PLANTUML_JAR_PATH      =
 PLANTUML_CFG_FILE      =
 PLANTUML_INCLUDE_PATH  =
 DOT_GRAPH_MAX_NODES    = 50
 MAX_DOT_GRAPH_DEPTH    = 0
-DOT_TRANSPARENT        = NO
 DOT_MULTI_TARGETS      = NO
 GENERATE_LEGEND        = YES
 DOT_CLEANUP            = YES
+MSCGEN_TOOL            =
+MSCFILE_DIRS           =
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 1b763cf..c15d490 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -1,7 +1,17 @@
 cmake_minimum_required (VERSION 3.16)
 
+# CMake sometimes has trouble detecting pthreads on macOS, so we just assume a built-in pthreads.
+if (APPLE)
+    set (CMAKE_THREAD_LIBS_INIT "-lpthread")
+    set (CMAKE_HAVE_THREADS_LIBRARY 1)
+    set (CMAKE_USE_WIN32_THREADS_INIT 0)
+    set (CMAKE_USE_PTHREADS_INIT 1)
+    set (THREADS_PREFER_PTHREAD_FLAG ON)
+endif ()
+
 CPMGetSystemPackage (benchmark)
 CPMGetSystemPackage (googletest)
+include (GoogleTest OPTIONAL)
 
 # Set directories for test output files, input data and binaries.
 file (MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/output)