Merge branch 'seqan:main' into main

Author: ChristopherAdelmann

.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/config/codechecker.yml

@@ -5,6 +5,7 @@
 analyze:
   - --enable=bugprone
   - --enable=performance
+  - --enable=prefix:clang-diagnostic-shadow
   - --disable=bugprone-easily-swappable-parameters
   - --disable=cert-dcl58-cpp
   - --disable=clang-diagnostic-float-conversion

.github/workflows/README.md

@@ -35,23 +35,21 @@ 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
+        uses: actions/checkout@v6
 
       - name: Configure tests
         run: |

.github/workflows/ci_cmake.yml

@@ -33,25 +33,17 @@ 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
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
-      - name: Load ccache
-        uses: actions/cache@v4
-        with:
-          path: /home/runner/.ccache
-          key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}-${{ github.run_id }}
-          restore-keys: |
-            ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}
-            ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}
+      - name: Setup cache
+        uses: seqan/actions/setup-actions-cache@main
 
       - name: Increase ccache size
         run: echo "CCACHE_MAXSIZE=300M" >> "${GITHUB_ENV}"
@@ -81,17 +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@v5.5.1
         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_coverage.yml

@@ -34,12 +34,12 @@ jobs:
     steps:
       - name: Checkout
         if: github.event_name != 'pull_request_target'
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       # pull_request_target does not checkout the merge commit by default
       - name: Checkout
         if: github.event_name == 'pull_request_target'
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           ref: "refs/pull/${{ github.event.number }}/merge"
 

.github/workflows/ci_documentation.yml

@@ -27,15 +27,15 @@ 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:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: REUSE Compliance Check
-        uses: fsfe/reuse-action@v5
+        uses: fsfe/reuse-action@v6
 
       - name: Check Markdown files for doxygen
         run: ${{ github.workspace }}/test/scripts/check_markdown_doxygen.sh ${{ github.workspace }}

.github/workflows/license_check.yaml .github/workflows/ci_license.yml.github/workflows/license_check.yaml renamed to .github/workflows/ci_license.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_lint.yml

@@ -33,34 +33,22 @@ 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
+        uses: actions/checkout@v6
 
-      - name: Load ccache
-        uses: actions/cache@v4
-        with:
-          path: /home/runner/.ccache
-          key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}-${{ github.run_id }}
-          restore-keys: |
-            ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}
-            ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}
+      - name: Setup cache
+        uses: seqan/actions/setup-actions-cache@main
 
       - name: Configure tests
         run: |
           $CXX --version || true
           cmake --version || true
           mkdir build && cd build
-          cmake ../test/unit -DCMAKE_BUILD_TYPE=Release \
-                             -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+          cmake ../test/unit -DCMAKE_BUILD_TYPE=Release
           make gtest_main
 
       - name: Build tests

.github/workflows/ci_linux.yml

@@ -28,15 +28,15 @@ 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
+        uses: actions/checkout@v6
 
       - name: Setup toolchain
         uses: seqan/actions/setup-toolchain@main