[INFRA] Add CodeChecker and CodeQL

Author: eseiler

.github/config/codechecker.skip

@@ -0,0 +1,6 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
++${GITHUB_WORKSPACE}/*
+-*

.github/config/codechecker.yml

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+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+analyze:
+  - --enable=performance
+  - --enable=bugprone
+  - --enable=clang-diagnostic-shadow
+  - --disable=bugprone-easily-swappable-parameters
+  - --disable=clang-diagnostic-implicit-int-float-conversion
+  - --disable=clang-diagnostic-float-conversion
+  - --disable=clang-diagnostic-implicit-int-conversion
+  - --disable=bugprone-exception-escape
+  - --disable=bugprone-narrowing-conversions
+  - --disable=deadcode.DeadStores
+  - --skip=${GITHUB_WORKSPACE}/.github/config/codechecker.skip
+  - --clean
+
+parse:
+  - --export=html
+  - --output=./html
+  - --skip=${GITHUB_WORKSPACE}/.github/config/codechecker.skip
+  - --trim-path-prefix=${GITHUB_WORKSPACE}/

.github/workflows/cron_codechecker.yml

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+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: CodeChecker
+
+on:
+  schedule:
+    - cron: "0 8 * * MON"
+  workflow_dispatch:
+
+concurrency:
+  group: codechecker-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  SHARG_NO_VERSION_CHECK: 1
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eexuo pipefail {0}
+
+jobs:
+  build:
+    name: CodeChecker
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
+    container:
+      image: ghcr.io/seqan/clang-19
+    steps:
+      - name: Run CodeChecker
+        uses: seqan/actions/codechecker@main
+        with:
+          configure_path: ../test/analyse
+          deploy_host: ${{ secrets.DEPLOY_HOST }}
+          deploy_user: ${{ secrets.DEPLOY_USER }}
+          deploy_ssh_key: ${{ secrets.DEPLOY_SSH_KEY }}
+          deploy_path: ${{ secrets.DEPLOY_CODECHECKER_PATH }}

.github/workflows/cron_codeql.yml

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+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: CodeQL
+
+on:
+  schedule:
+    - cron: "0 21 * * MON"
+  workflow_dispatch:
+
+concurrency:
+  group: codeql-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  SHARG_NO_VERSION_CHECK: 1
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eeuxo pipefail {0}
+
+jobs:
+  codeql:
+    name: CodeQL
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
+    permissions:
+      security-events: write
+    container:
+      image: ghcr.io/seqan/gcc-14
+      volumes:
+        - /home/runner:/home/runner
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: cpp
+        build-mode: manual
+        trap-caching: false
+
+    - name: Build tests
+      run: |
+        cmake test/analyse -DCMAKE_BUILD_TYPE=Release \
+                           -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
+        make -k
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:cpp"

test/analyse/CMakeLists.txt

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+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: BSD-3-Clause
+
+cmake_minimum_required (VERSION 3.20...3.31)
+project (sharg_test_analyze CXX)
+
+include (../sharg-test.cmake)
+
+enable_testing ()
+
+add_subdirectory (../snippet snippet)
+add_subdirectory (../unit unit)