Merge pull request #95 from eseiler/infra/ci

[INFRA] Update CI

Author: eseiler

.github/workflows/ci_coverage.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["gcc-14"]
+        compiler: ["gcc-latest"]
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
       volumes:
@@ -40,8 +40,8 @@ jobs:
         run: |
           mkdir build && cd build
           cmake .. -DCMAKE_BUILD_TYPE=Debug \
-                   -DCMAKE_CXX_FLAGS="--coverage -fprofile-arcs -ftest-coverage -Werror" \
-                   -DCMAKE_C_FLAGS="--coverage -fprofile-arcs -ftest-coverage -Werror" \
+                   -DCMAKE_CXX_FLAGS="--coverage -fprofile-arcs -ftest-coverage -fprofile-abs-path -Werror" \
+                   -DCMAKE_C_FLAGS="--coverage -fprofile-arcs -ftest-coverage -fprofile-abs-path -Werror" \
                    -DCMAKE_EXE_LINKER_FLAGS="-Wl,-lgcov" \
                    -DCMAKE_SHARED_LINKER_FLAGS="-Wl,-lgcov"
 
@@ -55,9 +55,11 @@ jobs:
                 ${GITHUB_WORKSPACE}/build \
                 --filter ${GITHUB_WORKSPACE}/include \
                 --filter ${GITHUB_WORKSPACE}/src \
-                --exclude-unreachable-branches \
-                --exclude-throw-branches \
+                --exclude-lines-by-pattern '^\s*}|^\s*};' \
                 --exclude-noncode-lines \
+                --exclude-throw-branches \
+                --exclude-unreachable-branches \
+                --merge-mode-functions separate \
                 -j \
                 --cobertura \
                 --output ${GITHUB_WORKSPACE}/build/coverage_report.xml

.github/workflows/ci_linux.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "intel"]
+        compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest", "intel"]
         include:
           - compiler: "intel"
             cxx_flags: "-fp-model=strict -Wno-overriding-option"

.github/workflows/ci_macos.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12"]
+        compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest"]
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -37,12 +37,6 @@ jobs:
         with:
           compiler: ${{ matrix.compiler }}
 
-      - name: Patch M1 GCC
-        if: contains(matrix.compiler, 'gcc') && matrix.compiler != 'gcc-14'
-        uses: seqan/actions/patch-m1-gcc@main
-        with:
-          compiler: ${{ matrix.compiler }}
-
       - name: Configure tests
         run: |
           mkdir build && cd build

cmake/package-lock.cmake

@@ -24,7 +24,7 @@ CPMDeclarePackage (sharg
                    GITHUB_REPOSITORY seqan/sharg-parser
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE
-                   OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
+                   OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING" "SHARG_NO_TDL ON"
 )
 
 # seqan3