From ab593b143b4cb993803afff170003b54ff4bb12c Mon Sep 17 00:00:00 2001
From: Enrico Seiler <enrico.seiler@hotmail.de>
Date: Mon, 10 Jul 2023 12:44:45 +0200
Subject: [PATCH] [INFRA] Update CI

---
 .github/workflows/api.yml                     |  28 +--
 .github/workflows/ci_coverage.yml             |  72 ++------
 .github/workflows/ci_documentation.yml        |  61 ++++++
 .github/workflows/ci_linux.yml                |  80 +++-----
 .github/workflows/ci_macos.yml                |  75 ++------
 .github/workflows/ci_misc.yml                 | 129 ++-----------
 .github/workflows/clang_format.yml            | 173 ------------------
 .../{documentation.yaml => documentation.yml} |  14 +-
 .github/workflows/lint.yml                    |  75 ++++++++
 .github/workflows/scripts/gcov.sh             |   6 +
 test/coverage/CMakeLists.txt                  |  39 ++--
 11 files changed, 254 insertions(+), 498 deletions(-)
 create mode 100644 .github/workflows/ci_documentation.yml
 delete mode 100644 .github/workflows/clang_format.yml
 rename .github/workflows/{documentation.yaml => documentation.yml} (88%)
 create mode 100644 .github/workflows/lint.yml
 create mode 100755 .github/workflows/scripts/gcov.sh

diff --git a/.github/workflows/api.yml b/.github/workflows/api.yml
index c0fb448a..f3e60814 100644
--- a/.github/workflows/api.yml
+++ b/.github/workflows/api.yml
@@ -30,7 +30,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: [10, 11, 12]
+        compiler: [11, 12, 13]
 
     steps:
       - name: Checkout Sharg
@@ -40,30 +40,18 @@ jobs:
           fetch-depth: 1
           submodules: true
 
-      # To reuse scripts
-      - name: Checkout SeqAn3
-        uses: actions/checkout@v3
+      - name: Setup toolchain
+        uses: seqan/actions/setup-toolchain@main
         with:
-          repository: seqan/seqan3
-          ref: aa3df18a6df59679e07e9fe2de4e0998a94af7e7
-          path: seqan3
-          fetch-depth: 1
-          submodules: false
-
-      - name: Configure APT
-        continue-on-error: true
-        run: bash ./seqan3/.github/workflows/scripts/configure_apt.sh
+          compiler: gcc-${{ matrix.compiler }}
+          ccache_size: 75M
 
       - name: Install CMake
-        run: bash ./seqan3/.github/workflows/scripts/install_cmake.sh
-
-      - name: Install compiler g++-${{ matrix.compiler }}
-        run: sudo apt-get install --yes g++-${{ matrix.compiler }}
+        uses: seqan/actions/setup-cmake@main
+        with:
+          cmake: 3.16.9
 
       - name: Configure tests
-        env:
-          CXX: g++-${{ matrix.compiler }}
-          CC: gcc-${{ matrix.compiler }}
         run: |
           mkdir sharg-build
           cd sharg-build
diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml
index d49a6d8d..6d80f271 100644
--- a/.github/workflows/ci_coverage.yml
+++ b/.github/workflows/ci_coverage.yml
@@ -1,4 +1,4 @@
-name: CI on Linux
+name: Coverage
 
 on:
   push:
@@ -20,29 +20,27 @@ concurrency:
   cancel-in-progress: false # PRs will be canceled by the clang-format CI
 
 env:
-  CMAKE_VERSION: 3.16.9
   SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 
 defaults:
   run:
-    shell: bash -ex {0}
+    shell: bash -Eexuo pipefail {0}
 
 jobs:
   build:
     name: ${{ matrix.name }}
     runs-on: ubuntu-22.04
     timeout-minutes: 120
-    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'clang-format'
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: true
       matrix:
         include:
-          - name: "Coverage gcc12"
-            cxx: "g++-12"
-            cc: "gcc-12"
+          - name: "gcc13"
+            compiler: "gcc-13"
             build: coverage
-            build_type: Debug
+            build_type: Coverage
 
     steps:
       # How many commits do we need to fetch to also fetch the branch point?
@@ -57,58 +55,23 @@ jobs:
           fetch-depth: ${{ steps.fetch_depth.outputs.depth }}
           submodules: true
 
-      # To reuse scripts
-      - name: Checkout SeqAn3
-        uses: actions/checkout@v3
+      - name: Setup toolchain
+        uses: seqan/actions/setup-toolchain@main
         with:
-          repository: seqan/seqan3
-          ref: aa3df18a6df59679e07e9fe2de4e0998a94af7e7
-          path: seqan3
-          fetch-depth: 1
-          submodules: false
-
-      - name: Configure APT
-        continue-on-error: true
-        run: bash ./seqan3/.github/workflows/scripts/configure_apt.sh
+          compiler: ${{ matrix.compiler }}
+          ccache_size: 125M
 
       - name: Install CMake
-        run: bash ./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: 3.16.9
 
       - 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 sharg-build
           cd sharg-build
@@ -120,13 +83,8 @@ jobs:
 
       - name: Build tests
         env:
-          CCACHE_BASEDIR: ${{ github.workspace }}
-          CCACHE_DIR: ${{ github.workspace }}/.ccache
-          CCACHE_COMPRESS: true
-          CCACHE_COMPRESSLEVEL: 12
-          CCACHE_MAXSIZE: 125M
           CCACHE_IGNOREOPTIONS: "-fprofile-abs-path"
-          GCOV: ${{ github.workspace }}/seqan3/.github/workflows/scripts/gcov.sh
+          GCOV: ${{ github.workspace }}/sharg/.github/workflows/scripts/gcov.sh
         run: |
           ccache -z
           cd sharg-build
diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml
new file mode 100644
index 00000000..c03399d9
--- /dev/null
+++ b/.github/workflows/ci_documentation.yml
@@ -0,0 +1,61 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      # Push events to branches matching refs/heads/main
+      - 'main'
+      # Push events to branches matching refs/heads/release*
+      - 'release*'
+  # Trigger after PR was unlabeled
+  pull_request:
+    types:
+      - unlabeled
+  # Enables a manual trigger, may run on any branch
+  workflow_dispatch:
+
+concurrency:
+  group: documentation-${{ 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
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1
+          submodules: true
+
+      - name: Install CMake
+        uses: seqan/actions/setup-cmake@main
+        with:
+          cmake: 3.16.9
+
+      - name: Install Doxygen
+        uses: seqan/actions/setup-doxygen@main
+        with:
+          doxygen: 1.9.5
+
+      - name: Configure tests
+        run: |
+          mkdir build
+          cd build
+          cmake ../test/documentation
+          make -j2 download-cppreference-doxygen-web-tag
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest . -j2 --output-on-failure
diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
index 222e1016..2780f1b2 100644
--- a/.github/workflows/ci_linux.yml
+++ b/.github/workflows/ci_linux.yml
@@ -1,4 +1,4 @@
-name: CI on Linux
+name: Unit Linux
 
 on:
   push:
@@ -16,42 +16,43 @@ on:
 
 concurrency:
   group: linux-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: ${{ github.event_name == 'push' }}
+  cancel-in-progress: ${{ github.event_name != 'push' }}
 
 env:
-  CMAKE_VERSION: 3.16.9
   SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 
 defaults:
   run:
-    shell: bash -ex {0}
+    shell: bash -Eexuo pipefail {0}
 
 jobs:
   build:
     name: ${{ matrix.name }}
     runs-on: ubuntu-22.04
     timeout-minutes: 120
-    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'clang-format'
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: true
       matrix:
         include:
-          - name: "Unit gcc12"
-            cxx: "g++-12"
-            cc: "gcc-12"
+          - name: "clang17"
+            compiler: "clang-17"
             build: unit
             build_type: Release
 
-          - name: "Unit gcc11"
-            cxx: "g++-11"
-            cc: "gcc-11"
+          - name: "gcc13"
+            compiler: "gcc-13"
             build: unit
             build_type: Release
 
-          - name: "Unit gcc10"
-            cxx: "g++-10"
-            cc: "gcc-10"
+          - name: "gcc12"
+            compiler: "gcc-12"
+            build: unit
+            build_type: Release
+
+          - name: "gcc11"
+            compiler: "gcc-11"
             build: unit
             build_type: Release
 
@@ -63,51 +64,18 @@ jobs:
           fetch-depth: 1
           submodules: true
 
-      # To reuse scripts
-      - name: Checkout SeqAn3
-        uses: actions/checkout@v3
+      - name: Setup toolchain
+        uses: seqan/actions/setup-toolchain@main
         with:
-          repository: seqan/seqan3
-          ref: aa3df18a6df59679e07e9fe2de4e0998a94af7e7
-          path: seqan3
-          fetch-depth: 1
-          submodules: false
-
-      - name: Configure APT
-        continue-on-error: true
-        run: bash ./seqan3/.github/workflows/scripts/configure_apt.sh
+          compiler: ${{ matrix.compiler }}
+          ccache_size: 75M
 
       - name: Install CMake
-        run: bash ./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: 3.16.9
 
       - name: Configure tests
-        env:
-          CXX: ${{ matrix.cxx }}
-          CC: ${{ matrix.cc }}
         run: |
           mkdir sharg-build
           cd sharg-build
@@ -117,12 +85,6 @@ jobs:
           make -j2 gtest_build yaml-cpp
 
       - name: Build tests
-        env:
-          CCACHE_BASEDIR: ${{ github.workspace }}
-          CCACHE_DIR: ${{ github.workspace }}/.ccache
-          CCACHE_COMPRESS: true
-          CCACHE_COMPRESSLEVEL: 12
-          CCACHE_MAXSIZE: 50M
         run: |
           ccache -z
           cd sharg-build
diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml
index cd3d186b..b2111446 100644
--- a/.github/workflows/ci_macos.yml
+++ b/.github/workflows/ci_macos.yml
@@ -1,4 +1,4 @@
-name: CI on macOS
+name: Unit macOS
 
 on:
   push:
@@ -16,42 +16,38 @@ on:
 
 concurrency:
   group: macos-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: ${{ github.event_name == 'push' }}
+  cancel-in-progress: ${{ github.event_name != 'push' }}
 
 env:
-  CMAKE_VERSION: 3.16.9
   SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 
 defaults:
   run:
-    shell: bash -ex {0}
+    shell: bash -Eexuo pipefail {0}
 
 jobs:
   build:
     name: ${{ matrix.name }}
     runs-on: macos-12
     timeout-minutes: 120
-    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'clang-format'
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: true
       matrix:
         include:
-          - name: "Unit gcc12"
-            cxx: "g++-12"
-            cc: "gcc-12"
+          - name: "gcc13"
+            compiler: "gcc-13"
             build: unit
             build_type: Release
 
-          - name: "Unit gcc11"
-            cxx: "g++-11"
-            cc: "gcc-11"
+          - name: "gcc12"
+            compiler: "gcc-12"
             build: unit
             build_type: Release
 
-          - name: "Unit gcc10"
-            cxx: "g++-10"
-            cc: "gcc-10"
+          - name: "gcc11"
+            compiler: "gcc-11"
             build: unit
             build_type: Release
 
@@ -63,51 +59,18 @@ jobs:
           fetch-depth: 1
           submodules: true
 
-      # To reuse scripts
-      - name: Checkout SeqAn3
-        uses: actions/checkout@v3
+      - name: Setup toolchain
+        uses: seqan/actions/setup-toolchain@main
         with:
-          repository: seqan/seqan3
-          ref: aa3df18a6df59679e07e9fe2de4e0998a94af7e7
-          path: seqan3
-          fetch-depth: 1
-          submodules: false
-
-      - name: Configure Homebrew
-        uses: Homebrew/actions/setup-homebrew@master
+          compiler: ${{ matrix.compiler }}
+          ccache_size: 75M
 
       - name: Install CMake
-        run: bash ./seqan3/.github/workflows/scripts/install_cmake.sh
-
-      - name: Install ccache
-        run: bash ./seqan3/.github/workflows/scripts/install_via_brew.sh ccache
-
-      - name: Install compiler ${{ matrix.cxx }}
-        env:
-          CC: ${{ matrix.cc }}
-        run: bash ./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: 3.16.9
 
       - name: Configure tests
-        env:
-          CXX: ${{ matrix.cxx }}
-          CC: ${{ matrix.cc }}
         run: |
           mkdir sharg-build
           cd sharg-build
@@ -117,12 +80,6 @@ jobs:
           make -j3 gtest_build yaml-cpp
 
       - 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 sharg-build
diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml
index 0afbc306..b7eac2e2 100644
--- a/.github/workflows/ci_misc.yml
+++ b/.github/workflows/ci_misc.yml
@@ -1,4 +1,4 @@
-name: CI misc
+name: Linux
 
 on:
   push:
@@ -16,7 +16,7 @@ on:
 
 concurrency:
   group: misc-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: ${{ github.event_name == 'push' }}
+  cancel-in-progress: ${{ github.event_name != 'push' }}
 
 env:
   SHARG_NO_VERSION_CHECK: 1
@@ -24,68 +24,35 @@ env:
 
 defaults:
   run:
-    shell: bash -ex {0}
+    shell: bash -Eexuo pipefail {0}
 
 jobs:
   build:
     name: ${{ matrix.name }}
     runs-on: ubuntu-22.04
     timeout-minutes: 120
-    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'clang-format'
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: false
       matrix:
         include:
           - name: "Snippet gcc11"
-            cxx: "g++-11"
-            cc: "gcc-11"
+            compiler: "gcc-11"
             build: snippet
             build_type: Release
-            build_threads: 2
             test_threads: 1 # snippets create and delete files and some separate tests create/delete the same files
-            cxx_flags: "-std=c++20"
-            cmake: 3.16.9
-            requires_toolchain: true
-            requires_ccache: true
-            skip_build_tests: false
-            skip_run_tests: false
 
-          - name: "Header gcc12"
-            cxx: "g++-12"
-            cc: "gcc-12"
+          - name: "Header gcc13"
+            compiler: "gcc-13"
             build: header
             build_type: Debug
-            build_threads: 2
             test_threads: 2
-            cmake: 3.16.9
-            requires_toolchain: true
-            requires_ccache: true
-            skip_build_tests: false
-            skip_run_tests: false
 
-          - name: "Header gcc10"
-            cxx: "g++-10"
-            cc: "gcc-10"
+          - name: "Header gcc11"
+            compiler: "gcc-11"
             build: header
             build_type: Debug
-            build_threads: 2
             test_threads: 2
-            cmake: 3.16.9
-            requires_toolchain: true
-            requires_ccache: true
-            skip_build_tests: false
-            skip_run_tests: false
-
-          - name: "Documentation"
-            build: documentation
-            build_threads: 2
-            test_threads: 2
-            cmake: 3.16.9
-            doxygen: 1.9.5
-            requires_toolchain: false
-            requires_ccache: false
-            skip_build_tests: true
-            skip_run_tests: false
 
     steps:
       - name: Checkout
@@ -95,92 +62,36 @@ jobs:
           fetch-depth: 1
           submodules: true
 
-      # To reuse scripts
-      - name: Checkout SeqAn3
-        uses: actions/checkout@v3
+      - name: Setup toolchain
+        uses: seqan/actions/setup-toolchain@main
         with:
-          repository: seqan/seqan3
-          ref: aa3df18a6df59679e07e9fe2de4e0998a94af7e7
-          path: seqan3
-          fetch-depth: 1
-          submodules: false
-
-      - name: Configure APT
-        continue-on-error: true
-        run: bash ./seqan3/.github/workflows/scripts/configure_apt.sh
+          compiler: ${{ matrix.compiler }}
+          ccache_size: 75M
 
       - name: Install CMake
-        env:
-          BUILD: ${{ matrix.build }}
-          CMAKE_VERSION: ${{ matrix.cmake }}
-        run: bash ./seqan3/.github/workflows/scripts/install_cmake.sh
-
-      - name: Install Doxygen
-        if: matrix.build == 'documentation'
-        env:
-          DOXYGEN_VERSION: ${{ matrix.doxygen }}
-        run: bash ./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
+        uses: seqan/actions/setup-cmake@main
         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
+          cmake: 3.16.9
 
       - name: Configure tests
-        env:
-          CXX: ${{ matrix.cxx }}
-          CC: ${{ matrix.cc }}
         run: |
           mkdir sharg-build
           cd sharg-build
           cmake ../sharg/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                                  -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
                                                   -DSHARG_VERBOSE_TESTS=OFF
           case "${{ matrix.build }}" in
-            snippet) make -j${{ matrix.build_threads }} gtest_build yaml-cpp;;
-            header) make -j${{ matrix.build_threads }} gtest_build gbenchmark_build yaml-cpp;;
-            documentation) make -j${{ matrix.build_threads }} download-cppreference-doxygen-web-tag;;
+            snippet) make -j2 gtest_build yaml-cpp;;
+            header) make -j2 gtest_build gbenchmark_build yaml-cpp;;
           esac
 
       - name: Build tests
-        if: ${{ !matrix.skip_build_tests }}
-        env:
-          CCACHE_BASEDIR: ${{ github.workspace }}
-          CCACHE_DIR: ${{ github.workspace }}/.ccache
-          CCACHE_COMPRESS: true
-          CCACHE_COMPRESSLEVEL: 12
-          CCACHE_MAXSIZE: 75M
         run: |
-          ccache -z || true
+          ccache -z
           cd sharg-build
-          make -k -j${{ matrix.build_threads }}
-          ccache -sv || true
+          make -k -j2
+          ccache -sv
 
       - name: Run tests
-        if: ${{ !matrix.skip_run_tests }}
         run: |
           cd sharg-build
           ctest . -j${{ matrix.test_threads }} --output-on-failure
diff --git a/.github/workflows/clang_format.yml b/.github/workflows/clang_format.yml
deleted file mode 100644
index 35b1d242..00000000
--- a/.github/workflows/clang_format.yml
+++ /dev/null
@@ -1,173 +0,0 @@
-name: Sharg lint
-
-on:
-  pull_request_target:
-
-env:
-  TZ: Europe/Berlin
-
-defaults:
-  run:
-    shell: bash -exo pipefail {0}
-
-jobs:
-  # Cancel other workflows that are dependent on this workflow by adding jobs that have the same concurrency group.
-  cancel_linux:
-    name: Cancel Linux
-    concurrency:
-      group: linux-${{ github.event.pull_request.number }}
-      cancel-in-progress: true
-    runs-on: ubuntu-22.04
-    steps:
-      - name: "Cancel Linux"
-        run: echo "Cancelling Linux"
-  cancel_macos:
-    name: Cancel macOS
-    concurrency:
-      group: macos-${{ github.event.pull_request.number }}
-      cancel-in-progress: true
-    runs-on: ubuntu-22.04
-    steps:
-      - name: "Cancel macOS"
-        run: echo "Cancelling macOS"
-  cancel_misc:
-    name: Cancel Misc
-    concurrency:
-      group: misc-${{ github.event.pull_request.number }}
-      cancel-in-progress: true
-    runs-on: ubuntu-22.04
-    steps:
-      - name: "Cancel Misc"
-        run: echo "Cancelling Misc"
-  cancel_coverage:
-    name: Cancel Coverage
-    concurrency:
-      group: coverage-${{ github.event.pull_request.number }}
-      cancel-in-progress: true
-    runs-on: ubuntu-22.04
-    steps:
-      - name: "Cancel Coverage"
-        run: echo "Cancelling Coverage"
-  lint:
-    name: clang-format
-    concurrency:
-      group: clang-format-${{ github.event.pull_request.number }}
-      cancel-in-progress: true
-    needs: [cancel_linux, cancel_macos, cancel_misc, cancel_coverage]
-    runs-on: ubuntu-22.04
-    timeout-minutes: 15
-    steps:
-      - name: Add label
-        env:
-            GITHUB_TOKEN: ${{ secrets.SEQAN_ACTIONS_PAT }}
-            PR_URL: ${{ github.event.pull_request.html_url }}
-        run: gh pr edit $PR_URL --add-label "clang-format"
-
-      # How many commits need to be fetched such that the branch point of the PR branch is visible when fetching the
-      # upstream?
-      - name: Get fetch depth
-        id: fetch_depth
-        env:
-          GITHUB_TOKEN: ${{ secrets.SEQAN_ACTIONS_PAT }}
-          COMMIT_RANGE: ${{ github.event.pull_request.base.sha }}...${{ github.event.pull_request.head.sha }}
-        run: |
-          QUERY="/repos/${{ github.repository }}/compare/${COMMIT_RANGE}"
-          ANSWER=$(gh api -H "Accept: application/vnd.github.v3+json" ${QUERY})
-          NBEHIND=$(jq '.behind_by' <<< "${ANSWER}")
-          echo "depth=$(( ${NBEHIND} + 1 ))" >> $GITHUB_OUTPUT
-          echo "pr_depth=$(( ${{ github.event.pull_request.commits }} + 1 ))" >> $GITHUB_OUTPUT
-
-      - name: Checkout Sharg
-        uses: actions/checkout@v3
-        with:
-          repository: ${{ github.event.pull_request.head.repo.full_name }}
-          ref: ${{ github.event.pull_request.head.ref }}
-          path: sharg
-          fetch-depth: ${{ steps.fetch_depth.outputs.pr_depth }}
-          submodules: false
-
-      # Comments on each git line:
-      # Checkout new branch that will be rebased. Actual PR branch remains untouched.
-      # Add the upstream repository.
-      # Disallow (accidental) pushes to upstream.
-      # Fetch the upstream. Fetch as many commits such that the branch point of the PR branch is visible.
-      # For rebasing, use last commit's user name.
-      # For rebasing, use last commit's user email.
-      # Rebase on upstream.
-      - name: Rebase on upstream
-        run: |
-          cd sharg
-          git checkout -b seqan_clang_format_rebase_${{ github.event.pull_request.head.ref }}
-          git remote add upstream ${{ github.event.pull_request.base.repo.html_url }}
-          git remote set-url --push upstream nopush
-          git fetch --depth ${{ steps.fetch_depth.outputs.depth }} upstream ${{ github.event.pull_request.base.ref }}
-          git config user.name "$(git log -1 --format='%cn' ${{ github.event.pull_request.head.sha }})"
-          git config user.email "$(git log -1 --format='%ce' ${{ github.event.pull_request.head.sha }})"
-          git rebase upstream/${{ github.event.pull_request.base.ref }}
-
-      - name: Copy upstream .clang-format
-        run: |
-          cd sharg
-          git show upstream/${{ github.event.pull_request.base.ref }}:.clang-format | \
-          tee ${{ github.workspace }}/.clang-format
-
-      # Get filenames (--name-only) of added, copied, modified, renamed, changed (ACMRT) files relative to the base
-      # branch (github.event.pull_request.base.sha).
-      # Exclude contrib include folder, exclude submodules folder.
-      # Include only hpp and cpp files as well as files in the std include folder.
-      # { grep ... || test $? = 1; } ensures that grep exits with code 0 on empty output.
-      - name: Get changed files
-        id: changed_files
-        run: |
-          cd sharg
-          LIST=$(git diff --name-only --diff-filter=ACMRT ${{ github.event.pull_request.base.sha }} | \
-          { grep -E "(.cpp|.hpp|include/sharg/std/)" || test $? = 1; } | xargs)
-          echo "list=$LIST" >> $GITHUB_OUTPUT
-
-      - name: Install clang-format
-        if: ${{ steps.changed_files.outputs.list }}
-        run: |
-          echo 'APT::Acquire::Retries "5";' | sudo tee -a /etc/apt/apt.conf.d/80-retries > /dev/null
-          wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
-          sudo apt-add-repository --no-update --yes "deb http://apt.llvm.org/jammy/ llvm-toolchain-jammy-15 main"
-          sudo apt-add-repository --no-update --yes "deb http://apt.llvm.org/jammy/ llvm-toolchain-jammy main"
-          sudo apt-get update
-          sudo apt-get install --yes clang-format-15
-
-      - name: Run clang-format
-        if: ${{ steps.changed_files.outputs.list }}
-        run: |
-          cd sharg
-          git checkout ${{ github.event.pull_request.head.ref }}
-          echo "${{ steps.changed_files.outputs.list }}" | \
-          xargs clang-format-15 --style=file:${{ github.workspace }}/.clang-format -i
-
-      - name: Import GPG key
-        if: ${{ steps.changed_files.outputs.list }}
-        uses: crazy-max/ghaction-import-gpg@v5
-        with:
-          workdir: sharg
-          gpg_private_key: ${{ secrets.SEQAN_ACTIONS_GPG_KEY }}
-          passphrase: ${{ secrets.SEQAN_ACTIONS_GPG_PASSPHRASE }}
-          git_user_signingkey: true
-          git_commit_gpgsign: true
-
-      - name: Commit changes
-        if: ${{ steps.changed_files.outputs.list }}
-        uses: EndBug/add-and-commit@v9
-        with:
-          author_name: seqan-actions[bot]
-          author_email: seqan-actions@users.noreply.github.com
-          message: '[MISC] clang-format'
-          cwd: './sharg'
-
-      # Wait for 5 seconds such that workflows triggered by adding the label run on the newest commit.
-      - name: Defer workflow
-        if: ${{ steps.changed_files.outputs.list }}
-        run: sleep 5
-
-      - name: Remove label
-        env:
-            GITHUB_TOKEN: ${{ secrets.SEQAN_ACTIONS_PAT }}
-            PR_URL: ${{ github.event.pull_request.html_url }}
-        run: gh pr edit $PR_URL --remove-label "clang-format"
diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yml
similarity index 88%
rename from .github/workflows/documentation.yaml
rename to .github/workflows/documentation.yml
index 91143211..c928e699 100644
--- a/.github/workflows/documentation.yaml
+++ b/.github/workflows/documentation.yml
@@ -12,8 +12,6 @@ concurrency:
   cancel-in-progress: false
 
 env:
-  CMAKE_VERSION: 3.16.9
-  DOXYGEN_VERSION: 1.9.5
   TZ: Europe/Berlin
 
 defaults:
@@ -42,15 +40,15 @@ jobs:
           fetch-depth: 1
           submodules: false
 
-      - name: Configure APT
-        continue-on-error: true
-        run: bash ./seqan3/.github/workflows/scripts/configure_apt.sh
-
       - name: Install CMake
-        run: bash ./seqan3/.github/workflows/scripts/install_cmake.sh
+        uses: seqan/actions/setup-cmake@main
+        with:
+          cmake: 3.16.9
 
       - name: Install Doxygen
-        run: bash ./seqan3/.github/workflows/scripts/install_doxygen.sh
+        uses: seqan/actions/setup-doxygen@main
+        with:
+          doxygen: 1.9.5
 
       - name: Load cached documentation
         uses: actions/cache@v3
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 00000000..0befbe73
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,75 @@
+name: Lint
+
+on:
+  pull_request_target:
+
+env:
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eeuxo pipefail {0}
+
+jobs:
+  # Cancel other workflows that are dependent on this workflow by adding jobs that have the same concurrency group.
+  cancel_linux:
+    name: Cancel running Workflows
+    concurrency:
+      group: linux-${{ github.event.pull_request.number }}
+      cancel-in-progress: true
+    runs-on: ubuntu-22.04
+    steps:
+      - name: "Cancel Linux"
+        run: echo "Cancelling Linux"
+  cancel_macos:
+    name: Cancel running Workflows
+    concurrency:
+      group: macos-${{ github.event.pull_request.number }}
+      cancel-in-progress: true
+    runs-on: ubuntu-22.04
+    steps:
+      - name: "Cancel macOS"
+        run: echo "Cancelling macOS"
+  cancel_misc:
+    name: Cancel running Workflows
+    concurrency:
+      group: misc-${{ github.event.pull_request.number }}
+      cancel-in-progress: true
+    runs-on: ubuntu-22.04
+    steps:
+      - name: "Cancel Misc"
+        run: echo "Cancelling Misc"
+  cancel_coverage:
+    name: Cancel running Workflows
+    concurrency:
+      group: coverage-${{ github.event.pull_request.number }}
+      cancel-in-progress: true
+    runs-on: ubuntu-22.04
+    steps:
+      - name: "Cancel Coverage"
+        run: echo "Cancelling Coverage"
+  cancel_documentation:
+    name: Cancel running Workflows
+    concurrency:
+      group: documentation-${{ github.event.pull_request.number }}
+      cancel-in-progress: true
+    runs-on: ubuntu-22.04
+    steps:
+      - name: "Cancel Coverage"
+        run: echo "Cancelling Coverage"
+  lint:
+    name: Lint
+    concurrency:
+      group: lint-${{ github.event.pull_request.number }}
+      cancel-in-progress: true
+    needs: [cancel_linux, cancel_macos, cancel_misc, cancel_coverage, cancel_documentation]
+    runs-on: ubuntu-22.04
+    timeout-minutes: 15
+    steps:
+      - name: Run lint
+        uses: seqan/actions/lint@main
+        with:
+          clang_format: 15
+          token: ${{ secrets.SEQAN_ACTIONS_PAT }}
+          gpg_key: ${{ secrets.SEQAN_ACTIONS_GPG_KEY }}
+          gpg_passphrase: ${{ secrets.SEQAN_ACTIONS_GPG_PASSPHRASE }}
diff --git a/.github/workflows/scripts/gcov.sh b/.github/workflows/scripts/gcov.sh
new file mode 100755
index 00000000..9e38db66
--- /dev/null
+++ b/.github/workflows/scripts/gcov.sh
@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+args=${@/--branch-counts/""}
+args=${args/--branch-probabilities/""}
+
+exec gcov $args
diff --git a/test/coverage/CMakeLists.txt b/test/coverage/CMakeLists.txt
index 1676ae0c..a34e701e 100644
--- a/test/coverage/CMakeLists.txt
+++ b/test/coverage/CMakeLists.txt
@@ -27,37 +27,50 @@ set (SHARG_COVERAGE_PARALLEL_LEVEL
      "1"
      CACHE STRING "Number of threads to use for coverage report generation.")
 
+set (SHARG_GCOVR_ARGUMENTS "")
+
+macro (sharg_append_gcovr_args)
+    set (key ${ARGV0})
+    if (${ARGC} EQUAL 1)
+        list (APPEND SHARG_GCOVR_ARGUMENTS ${key})
+    else ()
+        string (REPLACE "'^" "\\''^" value "${ARGV1}")
+        string (REPLACE "$'" "$$'\\'" value "${value}")
+        string (REPLACE ";" "\\\\\\;" value "${value}")
+        list (APPEND SHARG_GCOVR_ARGUMENTS ${key} ${value})
+    endif ()
+endmacro ()
+
 # Arguments for gcovr.
 # Each line is an argument, ';' will end up being a whitespace due to expansion by CMake.
 # Special characters like '"', '\', ')' need to be escaped by a number of '\', depending how often they are evaluated.
 # gcovr uses python regex expressions.
 # See https://gcovr.com/en/5.0/guide.html#the-gcovr-command for an overview of parameters.
 # See https://gcovr.com/en/5.0/faq.html#why-does-c-code-have-so-many-uncovered-branches for an explanation on branches.
-set (SHARG_GCOVR_ARGUMENTS "")
+
 # The directory of the CMakeLists.txt used for invoking cmake.
-list (APPEND SHARG_GCOVR_ARGUMENTS "--root;${CMAKE_CURRENT_LIST_DIR}")
+sharg_append_gcovr_args ("--root" "${CMAKE_CURRENT_LIST_DIR}")
 # The build directory.
-list (APPEND SHARG_GCOVR_ARGUMENTS "${PROJECT_BINARY_DIR}")
+sharg_append_gcovr_args ("${PROJECT_BINARY_DIR}")
 # Include all files whose path match '${SHARG_CLONE_DIR}/include/sharg/.*'.
-list (APPEND SHARG_GCOVR_ARGUMENTS "--filter;\'${SHARG_CLONE_DIR}/include/sharg/.*\'")
+sharg_append_gcovr_args ("--filter" "${SHARG_CLONE_DIR}/include/sharg")
 # Include all files whose path match '${SHARG_CLONE_DIR}/test/include/sharg/test/.*'.
-list (APPEND SHARG_GCOVR_ARGUMENTS "--filter;\'${SHARG_CLONE_DIR}/test/include/sharg/test/.*\'")
+sharg_append_gcovr_args ("--filter" "${SHARG_CLONE_DIR}/test/include/sharg/test")
 # Remove all files whose path match '${SHARG_CLONE_DIR}/include/sharg/contrib/.*'.
-list (APPEND SHARG_GCOVR_ARGUMENTS "--exclude;\'${SHARG_CLONE_DIR}/include/sharg/contrib/.*\'")
+sharg_append_gcovr_args ("--exclude" "${SHARG_CLONE_DIR}/include/sharg/contrib")
 # Remove all files whose path match '${SHARG_CLONE_DIR}/include/sharg/std/.*'.
-list (APPEND SHARG_GCOVR_ARGUMENTS "--exclude;\'${SHARG_CLONE_DIR}/include/sharg/std/.*\'")
+sharg_append_gcovr_args ("--exclude" "${SHARG_CLONE_DIR}/include/sharg/std")
 # Remove line coverage for all lines that match '^\s*$', i.e. empty lines.
-list (APPEND SHARG_GCOVR_ARGUMENTS "--exclude-lines-by-pattern;\\\'^\\\\s*$$\\\'")
+sharg_append_gcovr_args ("--exclude-lines-by-pattern" [['^\\s*$']])
 # Remove line coverage for all lines that match "^\s*[\{\}]\s*\;*\s*(//.*)?$", i.e. lines with a single '{' or '}' which
 # might be followed by a semicolon or a comment '//'.
-list (APPEND SHARG_GCOVR_ARGUMENTS
-      "--exclude-lines-by-pattern;\\\'^\\\\s*[\\{\\}]\\\\s*\\\\\\;*\\\\s*\\(//.*\\)?$$\\\'")
+sharg_append_gcovr_args ("--exclude-lines-by-pattern" [['^\\s*[{}]{0,2}\\s*;*\\s*(//.*)?$']])
 # Will exclude branches that are unreachable.
-list (APPEND SHARG_GCOVR_ARGUMENTS "--exclude-unreachable-branches")
+sharg_append_gcovr_args ("--exclude-unreachable-branches")
 # Will exclude branches that are only generated for exception handling.
-list (APPEND SHARG_GCOVR_ARGUMENTS "--exclude-throw-branches")
+sharg_append_gcovr_args ("--exclude-throw-branches")
 # Run up to this many gcov instances in parallel.
-list (APPEND SHARG_GCOVR_ARGUMENTS "-j;${SHARG_COVERAGE_PARALLEL_LEVEL}")
+sharg_append_gcovr_args ("-j" "${SHARG_COVERAGE_PARALLEL_LEVEL}")
 
 add_custom_command (OUTPUT ${PROJECT_BINARY_DIR}/sharg_coverage.xml
                     # Run tests.