[INFRA] Update CI

.codecov.yml

@@ -4,7 +4,6 @@
 
 # See https://docs.codecov.io/docs/codecovyml-reference
 codecov:
-  token: a75b1e95-134c-4ada-adac-5846045f188e
   require_ci_to_pass: no  # codecov reports its results independent of whether CI passed
   notify:
     wait_for_ci: no       # codecov has not to wait until the CI is finished to post its results

.github/workflows/ci_cmake.yml

@@ -35,20 +35,18 @@ jobs:
       matrix:
         include:
           - name: "Non-cyclic tests"
-            compiler: "gcc-14"
+            compiler: "gcc-latest"
             build: unit
             use_include_dependencies: "ON"
             cmake_depends_use_compiler: "OFF"
 
           - name: "External project"
-            compiler: "gcc-14"
+            compiler: "gcc-latest"
             build: external_project
             use_include_dependencies: "OFF"
             cmake_depends_use_compiler: "ON"
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
-      volumes:
-        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4

.github/workflows/ci_coverage.yml

@@ -33,11 +33,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["gcc-14"]
+        compiler: ["gcc-latest"]
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
-      volumes:
-        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -75,18 +73,20 @@ jobs:
                 --filter ${GITHUB_WORKSPACE}/test/include/seqan3/test \
                 --exclude ${GITHUB_WORKSPACE}/include/seqan3/contrib \
                 --exclude ${GITHUB_WORKSPACE}/include/seqan3/std \
-                --exclude-lines-by-pattern '^\s*$' \
-                --exclude-lines-by-pattern '^\s*};$' \
-                --exclude-unreachable-branches \
+                --exclude-lines-by-pattern '^\s*}|^\s*};' \
                 --exclude-throw-branches \
                 --exclude-noncode-lines \
+                --exclude-unreachable-branches \
                 --merge-mode-functions separate \
                 -j \
                 --cobertura \
                 --output ${GITHUB_WORKSPACE}/build/coverage_report.xml
 
       - name: Submit coverage build
-        uses: codecov/codecov-action@v3.1.5
+        uses: codecov/codecov-action@v5.4.3
         with:
-          files: build/coverage_report.xml
+          disable_search: true
           fail_ci_if_error: false
+          files: build/coverage_report.xml
+          plugins: noop
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/ci_license.yml

@@ -27,7 +27,7 @@ defaults:
 jobs:
   check:
     name: REUSE Compliance
-    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'
     steps:

.github/workflows/ci_lint.yml

@@ -16,67 +16,26 @@ defaults:
 
 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
+  cancel_running_workflows:
+    name: Cancel ${{ matrix.workflow}}
+    strategy:
+      fail-fast: false
+      matrix:
+        workflow: ["linux", "macos", "misc", "coverage", "cmake", "documentation"]
     concurrency:
-      group: linux-${{ github.event.pull_request.number }}
+      group: ${{ matrix.workflow }}-${{ github.event.pull_request.number }}
       cancel-in-progress: true
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     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-${{ github.event.pull_request.number }}
-      cancel-in-progress: true
-    runs-on: ubuntu-22.04
-    steps:
-      - name: "Cancel Coverage"
-        run: echo "Cancelling Coverage"
-  cancel_cmake:
-    name: Cancel running Workflows
-    concurrency:
-      group: cmake-${{ github.event.pull_request.number }}
-      cancel-in-progress: true
-    runs-on: ubuntu-22.04
-    steps:
-      - name: "Cancel CMake"
-        run: echo "Cancelling CMake"
-  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 Documentation"
-        run: echo "Cancelling Documentation"
+      - name: "Cancel ${{ matrix.workflow }}"
+        run: echo "Cancelling ${{ matrix.workflow }}"
   lint:
     name: Lint
     concurrency:
       group: lint-${{ github.event.pull_request.number }}
       cancel-in-progress: true
-    needs: [cancel_linux, cancel_macos, cancel_misc, cancel_coverage, cancel_cmake, cancel_documentation]
-    runs-on: ubuntu-22.04
+    needs: cancel_running_workflows
+    runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
       - name: Run lint

.github/workflows/ci_linux.yml

@@ -33,14 +33,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "intel"]
-        include:
-          - compiler: "intel"
-            cxx_flags: "-fp-model=strict -Wno-overriding-option"
+        compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest", "intel"]
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
-      volumes:
-        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -53,8 +48,7 @@ jobs:
           $CXX --version || true
           cmake --version || true
           mkdir build && cd build
-          cmake ../test/unit -DCMAKE_BUILD_TYPE=Release \
-                             -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+          cmake ../test/unit -DCMAKE_BUILD_TYPE=Release
           make gtest_main
 
       - name: Build tests

.github/workflows/ci_macos.yml

@@ -28,12 +28,12 @@ defaults:
 jobs:
   build:
     name: ${{ matrix.compiler }}
-    runs-on: macos-14
+    runs-on: macos-latest
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     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

.github/workflows/ci_misc.yml

@@ -33,15 +33,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-19", "gcc-14", "gcc-12", "intel"]
+        compiler: ["clang-latest", "gcc-latest", "gcc-third-latest", "intel"]
         build: ["snippet", "performance", "header"]
-        include:
-          - compiler: "intel"
-            cxx_flags: "-fp-model=strict -Wno-overriding-option"
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
-      volumes:
-        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -53,7 +48,6 @@ jobs:
         run: |
           mkdir build && cd build
           cmake ../test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=Release \
-                                            -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
                                             -DSEQAN3_BENCHMARK_MIN_TIME=0.01s
           case "${{ matrix.build }}" in
             snippet) make gtest_main;;

.github/workflows/ci_update_cookbook.yml

@@ -23,7 +23,7 @@ defaults:
 jobs:
   update-cookbook:
     name: Update Cookbook
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     if: github.repository_owner == 'seqan'
     timeout-minutes: 15
     steps:

.github/workflows/cron_api.yml

@@ -32,20 +32,17 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["gcc-14", "gcc-13", "gcc-12"]
+        compiler: ["gcc-latest", "gcc-second-latest", "gcc-third-latest"]
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
-      volumes:
-        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Configure tests
         run: |
           mkdir build && cd build
-          cmake ../test/api_stability -DCMAKE_BUILD_TYPE=Release \
-                                      -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+          cmake ../test/api_stability -DCMAKE_BUILD_TYPE=Release
 
       - name: Build tests
         working-directory: build

.github/workflows/cron_avx2.yml

@@ -27,21 +27,16 @@ defaults:
 jobs:
   build:
     name: ${{ matrix.build }} ${{ matrix.compiler }}
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     timeout-minutes: 300
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "intel"]
+        compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest", "intel"]
         build: [unit, snippet, performance, header]
-        include:
-          - compiler: "intel"
-            cxx_flags: "-fp-model=strict -Wno-overriding-option"
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
-      volumes:
-        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -50,7 +45,6 @@ jobs:
         run: |
           mkdir build && cd build
           cmake ../test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=Release \
-                                            -DCMAKE_CXX_FLAGS="-mavx2 ${{ matrix.cxx_flags }}" \
                                             -DSEQAN3_BENCHMARK_MIN_TIME=0.01s
           case "${{ matrix.build }}" in
             unit) make gtest_main;;

.github/workflows/cron_codechecker.yml

@@ -28,8 +28,6 @@ jobs:
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     container:
       image: ghcr.io/seqan/codechecker
-      volumes:
-        - /home/runner:/home/runner
     steps:
       - name: Run CodeChecker
         uses: seqan/actions/codechecker@main

.github/workflows/cron_codeql.yml

@@ -15,6 +15,7 @@ concurrency:
 
 env:
   SEQAN3_NO_VERSION_CHECK: 1
+  CODEQL_EXTRACTOR_CPP_AUTOINSTALL_DEPENDENCIES: false
   TZ: Europe/Berlin
 
 defaults:
@@ -29,9 +30,7 @@ jobs:
     permissions:
       security-events: write
     container:
-      image: ghcr.io/seqan/gcc-14
-      volumes:
-        - /home/runner:/home/runner
+      image: ghcr.io/seqan/gcc-second-latest
     steps:
     - name: Checkout
       uses: actions/checkout@v4

.github/workflows/cron_latest_libraries.yml

@@ -27,21 +27,16 @@ defaults:
 jobs:
   build:
     name: ${{ matrix.build }} ${{ matrix.compiler }}
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     timeout-minutes: 300
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "intel"]
+        compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest", "intel"]
         build: [unit, snippet, performance, header]
-        include:
-          - compiler: "intel"
-            cxx_flags: "-fp-model=strict -Wno-overriding-option"
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
-      volumes:
-        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -59,7 +54,6 @@ jobs:
         run: |
           mkdir build && cd build
           cmake ../test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=Release \
-                                            -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
                                             -DSEQAN3_BENCHMARK_MIN_TIME=0.01s
           case "${{ matrix.build }}" in
             unit) make gtest_main;;

.github/workflows/cron_no_optional_libraries.yml

@@ -31,7 +31,7 @@ jobs:
       # Either all optional dependencies are disabled (true, true, true)
       # Or only Bzip2 is disabled (false, true, false)
       matrix:
-        os: [ubuntu-latest, macos-14]
+        os: [ubuntu-latest, macos-latest]
         build_type: [Release, Debug]
         zlib: [true, false]
         include:
@@ -41,18 +41,16 @@ jobs:
           - zlib: false
             bzip2: true
             cereal: false
-          - os: macos-14
-            compiler: clang-19
+          - os: macos-latest
+            compiler: clang-latest
           - os: ubuntu-latest
-            compiler: gcc-14
-            image: ghcr.io/seqan/gcc-14
+            compiler: gcc-latest
+            image: ghcr.io/seqan/gcc-latest
 
     container:
       # If an image is defined for a matrix entry, use it.
       # Otherwise, use the "empty"/'' image which means do not use a container at all.
       image: ${{ matrix.image || '' }}
-      volumes:
-        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4