seqan · eseiler · Mar 19, 2025 · Mar 19, 2025 · Mar 19, 2025 · Mar 19, 2025
diff --git a/.github/config/codechecker.skip b/.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
+
++${GITHUB_WORKSPACE}/*
+-*
diff --git a/.github/config/codechecker.yml b/.github/config/codechecker.yml
@@ -0,0 +1,23 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+analyze:
+  - --enable=performance
+  - --enable=bugprone
+  - --enable=clang-diagnostic-shadow
+  - --disable=bugprone-easily-swappable-parameters
+  - --disable=clang-diagnostic-implicit-int-float-conversion
+  - --disable=clang-diagnostic-float-conversion
+  - --disable=clang-diagnostic-implicit-int-conversion
+  - --disable=bugprone-exception-escape
+  - --disable=bugprone-narrowing-conversions
+  - --disable=deadcode.DeadStores
+  - --skip=${GITHUB_WORKSPACE}/.github/config/codechecker.skip
+  - --clean
+
+parse:
+  - --export=html
+  - --output=./html
+  - --skip=${GITHUB_WORKSPACE}/.github/config/codechecker.skip
+  - --trim-path-prefix=${GITHUB_WORKSPACE}/
diff --git a/.github/workflows/ci_license.yml b/.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:

diff --git a/.github/workflows/cron_codechecker.yml b/.github/workflows/cron_codechecker.yml
@@ -0,0 +1,39 @@
+# 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: ${{ secrets.DEPLOY_CODECHECKER_PATH }}
diff --git a/.github/workflows/cron_codeql.yml b/.github/workflows/cron_codeql.yml
@@ -0,0 +1,55 @@
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: CodeQL
+
+on:
+  schedule:
+    - cron: "0 21 * * MON"
+  workflow_dispatch:
+
+concurrency:
+  group: codeql-${{ 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"
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -35,7 +35,7 @@ jobs:
       group: lint-${{ github.event.pull_request.number }}
       cancel-in-progress: true
     needs: cancel_running_workflows
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
       - name: Run lint

diff --git a/.github/workflows/readme_snippet.yml b/.github/workflows/readme_snippet.yml
@@ -8,6 +8,11 @@ on:
   push:
     branches:
       - 'main'
+  workflow_dispatch:
+
+concurrency:
+  group: readme-snippet-${{ github.ref }}
+  cancel-in-progress: true
 
 env:
   TZ: Europe/Berlin
@@ -19,11 +24,9 @@ defaults:
 jobs:
   readme-snippet:
     name: Update README
-    concurrency:
-      group: readme-snippet-${{ github.ref }}
-      cancel-in-progress: false
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     timeout-minutes: 15
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     steps:
       - name: Checkout Sharg
         uses: actions/checkout@v4

diff --git a/.github/workflows/update_cookbook.yml b/.github/workflows/update_cookbook.yml
@@ -2,12 +2,17 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
-name: Sharg lint
+name: Sharg Cookbook
 
 on:
   push:
     branches:
       - 'main'
+  workflow_dispatch:
+
+concurrency:
+  group: update-cookbook-${{ github.ref }}
+  cancel-in-progress: true
 
 env:
   TZ: Europe/Berlin
@@ -19,11 +24,9 @@ defaults:
 jobs:
   update-cookbook:
     name: Update Cookbook
-    concurrency:
-      group: update-cookbook-${{ github.ref }}
-      cancel-in-progress: true
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     timeout-minutes: 15
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     steps:
       - name: Checkout Sharg
         uses: actions/checkout@v4

diff --git a/test/analyse/CMakeLists.txt b/test/analyse/CMakeLists.txt
@@ -0,0 +1,13 @@
+# 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)
diff --git a/test/sharg-test.cmake b/test/sharg-test.cmake
@@ -20,14 +20,21 @@ if (NOT DEFINED CMAKE_CXX_EXTENSIONS)
     set (CMAKE_CXX_EXTENSIONS OFF)
 endif ()
 
+set (SHARG_TEST_CPM_DIR
+     "${CMAKE_CURRENT_LIST_DIR}/../cmake/"
+     CACHE STRING "Path to directory containing CPM.cmake.")
+
+set (CPM_INDENT "CMake Package Manager CPM: ")
+include ("${SHARG_TEST_CPM_DIR}/CPM.cmake")
+CPMUsePackageLock ("${SHARG_TEST_CPM_DIR}/package-lock.cmake")
+
+include (${CMAKE_CURRENT_LIST_DIR}/cmake/sharg_require_ccache.cmake)
+
 # require Sharg package
 find_package (Sharg REQUIRED HINTS ${CMAKE_CURRENT_LIST_DIR}/../cmake)
 
 enable_testing ()
 
-set (CPM_INDENT "CMake Package Manager CPM: ")
-CPMUsePackageLock ("${CMAKE_CURRENT_LIST_DIR}/../cmake/package-lock.cmake")
-
 include (CheckCXXSourceCompiles)
 include (FindPackageHandleStandardArgs)
 include (FindPackageMessage)
@@ -115,5 +122,4 @@ list (APPEND SHARG_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_VERBOSE_MAKEFILE=${CMAKE
 
 include (sharg_test_component)
 include (sharg_test_files)
-include (sharg_require_ccache)
 include (add_subdirectories)