[INFRA] Update CI

.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"

.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

.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 build/doc/html
+
+      - name: Upload documentation
+        continue-on-error: true
+        uses: actions/upload-artifact@v3
+        with:
+          name: documentation
+          path: documentation.tar.gz