[INFRA] Use containers for CI

.codecov.yml

@@ -20,3 +20,7 @@ coverage:
         if_ci_failed: success # per default, codecov would fail if any CI fails
         informational: true   # the codecov/patch status is never "fail"
         only_pulls: true      # only post codecov/patch status on PRs
+
+parsers:
+  cobertura:
+    partials_as_hits: true

.github/workflows/ci_coverage.yml

@@ -26,90 +26,69 @@ defaults:
 
 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 == 'lint'
+    runs-on: ubuntu-latest
+    name: ${{ matrix.compiler }}
+    # if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
-      fail-fast: true
+      fail-fast: false
       matrix:
-        include:
-          - name: "gcc13"
-            compiler: "gcc-13"
-            build: coverage
-            build_type: Coverage
-
+        compiler: ["gcc-14"]
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
-      # 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@v4
         with:
-          fetch-depth: ${{ steps.fetch_depth.outputs.depth }}
-          submodules: false
-
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 525M
+          fetch-depth: 0
 
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
+      - name: Load ccache
+        uses: actions/cache@v4
         with:
-          cmake: 3.18.6
-
-      - name: Install gcovr
-        run: |
-          sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/${CC/gcc/gcov} 100
-          pip install gcovr==6.0
+          path: /home/runner/.ccache
+          save-always: true
+          key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}
 
       - name: Configure tests
         run: |
           mkdir build
           cd build
-          cmake ../test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                            -DHIBF_VERBOSE_TESTS=OFF
-          make -j2 gtest_main
+          cmake ../test/coverage -DCMAKE_BUILD_TYPE=Coverage
+          make -j gtest_main
 
       - name: Build tests
-        env:
-          CCACHE_IGNOREOPTIONS: "-fprofile-abs-path"
+        working-directory: build
         run: |
           ccache -z
-          cd build
-          make -k -j2
+          make -k -j
           ccache -sv
 
       - name: Run tests
+        working-directory: build
         run: |
-          cd build
-          ctest . -j2 --output-on-failure
+          ctest . -j --output-on-failure
 
       - name: Generate coverage report
         run: |
-          gcovr --gcov-executable ${{ github.workspace }}/.github/workflows/scripts/gcov.sh \
-                --root ${{ github.workspace }}/test/coverage \
-                ${{ github.workspace }}/build \
-                --filter ${{ github.workspace }}/include \
-                --filter ${{ github.workspace }}/test/include \
-                --filter ${{ github.workspace }}/src \
-                --exclude ${{ github.workspace }}/include/hibf/contrib \
-                --exclude ${{ github.workspace }}/test/include/hibf/test/iterator_test_template.hpp \
+          gcovr --root ${GITHUB_WORKSPACE}/test/coverage \
+                ${GITHUB_WORKSPACE}/build \
+                --filter ${GITHUB_WORKSPACE}/include \
+                --filter ${GITHUB_WORKSPACE}/test/include \
+                --filter ${GITHUB_WORKSPACE}/src \
+                --exclude ${GITHUB_WORKSPACE}/include/hibf/contrib \
+                --exclude ${GITHUB_WORKSPACE}/test/include/hibf/test/iterator_test_template.hpp \
                 --exclude-lines-by-pattern '^\s*$' \
                 --exclude-lines-by-pattern '^\s*};$' \
                 --exclude-unreachable-branches \
                 --exclude-throw-branches \
                 --exclude-noncode-lines \
-                -j 2 \
-                --xml \
-                --output ${{ github.workspace }}/build/coverage_report.xml
+                -j \
+                --cobertura \
+                --output ${GITHUB_WORKSPACE}/build/coverage_report.xml
 
       - name: Submit coverage build
         uses: codecov/[email protected]
         with:
-          files: ${{ github.workspace }}/build/coverage_report.xml
+          files: build/coverage_report.xml
           fail_ci_if_error: false

.github/workflows/ci_documentation.yml

@@ -33,14 +33,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 1
-          submodules: false
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.18.6
 
       - name: Install Doxygen
         uses: seqan/actions/setup-doxygen@main
@@ -55,6 +47,5 @@ jobs:
           make -j2 download-cppreference-doxygen-web-tag
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
+        working-directory: build
+        run: ctest . -j2 --output-on-failure

.github/workflows/ci_iwyu.yml

@@ -62,8 +62,7 @@ jobs:
           mkdir build
           cd build
           cmake ../hibf/test/iwyu -DCMAKE_BUILD_TYPE=Release \
-                                  -DCMAKE_CXX_FLAGS="-stdlib=libc++" \
-                                  -DHIBF_VERBOSE_TESTS=OFF
+                                  -DCMAKE_CXX_FLAGS="-stdlib=libc++"
 
       - name: Run Test
         run: |

.github/workflows/ci_linux.yml

@@ -26,77 +26,42 @@ defaults:
 
 jobs:
   build:
-    name: ${{ matrix.name }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
+    name: ${{ matrix.compiler }}
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
-      fail-fast: true
+      fail-fast: false
       matrix:
-        include:
-          - name: "clang17"
-            compiler: "clang-17"
-            build: unit
-            build_type: Release
-            cxx_flags: "-stdlib=libc++"
-
-          - name: "gcc13"
-            compiler: "gcc-13"
-            build: unit
-            build_type: Release
-
-          - name: "gcc12"
-            compiler: "gcc-12"
-            build: unit
-            build_type: Release
-
-          - name: "gcc11"
-            compiler: "gcc-11"
-            build: unit
-            build_type: Release
-
-          - name: "IntelLLVM"
-            compiler: "intel"
-            build: unit
-            build_type: Release
-
+        compiler: ["clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "gcc-11", "intel"]
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 1
-          submodules: false
-
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 75M
 
-      - name: Install CMake
-        if: contains(matrix.compiler, 'intel') == false
-        uses: seqan/actions/setup-cmake@main
+      - name: Load ccache
+        uses: actions/cache@v4
         with:
-          cmake: 3.18.6
+          path: /home/runner/.ccache
+          save-always: true
+          key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}
 
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
-          cmake ../test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                            -DHIBF_VERBOSE_TESTS=OFF \
-                                            -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
-          make -j2 gtest_main
+          mkdir build && cd build
+          cmake ../test/unit -DCMAKE_BUILD_TYPE=Release
+          make -j gtest_main
 
       - name: Build tests
+        working-directory: build
         run: |
           ccache -z
-          cd build
-          make -k -j2
+          make -k -j
           ccache -sv
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
+        working-directory: build
+        run: ctest . -j --output-on-failure
 

.github/workflows/ci_macos.yml

@@ -34,6 +34,11 @@ jobs:
       fail-fast: true
       matrix:
         include:
+          - name: "clang18"
+            compiler: "clang-18"
+            build: unit
+            build_type: Release
+
           - name: "clang17"
             compiler: "clang-17"
             build: unit
@@ -76,18 +81,16 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake ../test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                            -DHIBF_VERBOSE_TESTS=OFF
+          cmake ../test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
           make -j3 gtest_main
 
       - name: Build tests
+        working-directory: build
         run: |
           ccache -z
-          cd build
           make -k -j3
           ccache -sv
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j3 --output-on-failure
+        working-directory: build
+        run: ctest . -j3 --output-on-failure

.github/workflows/ci_misc.yml

@@ -27,7 +27,7 @@ defaults:
 jobs:
   build:
     name: ${{ matrix.name }}
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     timeout-minutes: 120
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
@@ -90,32 +90,27 @@ jobs:
             build: tutorial
             build_type: Debug
             use_include_dependencies: "OFF"
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
 
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 1
-          submodules: false
-
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 75M
 
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
+      - name: Load ccache
+        uses: actions/cache@v4
         with:
-          cmake: ${{ contains(matrix.build, 'tutorial') && '3.21.7' || '3.18.6' }}
+          path: /home/runner/.ccache
+          save-always: true
+          key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}
 
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
+          mkdir build && cd build
           cmake ../test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                            -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
-                                            -DHIBF_VERBOSE_TESTS=OFF \
+                                            -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
                                             -DHIBF_USE_INCLUDE_DEPENDENCIES="${{ matrix.use_include_dependencies }}"
           case "${{ matrix.build }}" in
             unit) make -j2 gtest_main;;
@@ -126,21 +121,20 @@ jobs:
 
       - name: Check cyclic includes
         if: matrix.use_include_dependencies == 'ON'
+        working-directory: build
         run: |
-          cd build
           make -k -j2 all_dependencies
           cmake .
 
       - name: Build tests
         if: matrix.use_include_dependencies == 'OFF'
+        working-directory: build
         run: |
           ccache -z
-          cd build
           make -k -j2
           ccache -sv
 
       - name: Run tests
         if: matrix.use_include_dependencies == 'OFF'
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
+        working-directory: build
+        run: ctest . -j2 --output-on-failure