[INFRA] More refactoring

.github/dependabot.yml

@@ -0,0 +1,9 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/ci_coverage.yml

@@ -64,15 +64,15 @@ jobs:
           mkdir build
           cd build
           cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
-          make -j2 gtest_main benchmark_main yaml-cpp
+          make -j2 -k gtest_main yaml-cpp
 
       - name: Build tests
         env:
           CCACHE_IGNOREOPTIONS: "-fprofile-abs-path"
         run: |
           ccache -z
           cd build
-          CMAKE_BUILD_PARALLEL_LEVEL=2 cmake --build . -- -k test
+          make -j2 -k check
           ccache -sv
 
       - name: Generate coverage report

.github/workflows/ci_linux.yml

@@ -71,14 +71,14 @@ jobs:
           cd build
           cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
                    -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
-          make -j2 gtest_main benchmark_main yaml-cpp
+          make -j2 -k gtest_main yaml-cpp
 
       - name: Build application
         run: |
           cd build
-          CMAKE_BUILD_PARALLEL_LEVEL=2 cmake --build . -- -k
+          make -j2 -k
 
       - name: Build and run tests
         run: |
           cd build
-          CMAKE_BUILD_PARALLEL_LEVEL=2 cmake --build . -- -k test
+          make -j2 -k check

.github/workflows/ci_macos.yml

@@ -71,14 +71,14 @@ jobs:
           cd build
           cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
                    -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
-          make -j3 gtest_main benchmark_main yaml-cpp
+          make -j3 -k gtest_main yaml-cpp
 
       - name: Build application
         run: |
           cd build
-          CMAKE_BUILD_PARALLEL_LEVEL=3 cmake --build . -- -k
+          make -j3 -k
 
       - name: Build and run tests
         run: |
           cd build
-          CMAKE_BUILD_PARALLEL_LEVEL=3 cmake --build . -- -k test
+          make -j3 -k check

.github/workflows/lint.yml

@@ -0,0 +1,46 @@
+name: Lint
+
+on:
+  workflow_dispatch:
+
+env:
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eeuxo pipefail {0}
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-22.04
+    timeout-minutes: 30
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+          submodules: false
+
+      - name: Run clang-format
+        uses: DoozyX/[email protected]
+        with:
+          clangFormatVersion: 17
+          inplace: True
+
+      - name: Run cmake-format
+        uses: PuneetMatharu/[email protected]
+        with:
+          args: --config-files .cmake-format.yaml --in-place
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v5
+        with:
+          commit-message: '[MISC] Automatic linting'
+          committer: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
+          author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
+          body: Automatic linting
+          signoff: false
+          branch: actions/lint
+          delete-branch: true
+          title: '[MISC] Automatic linting'

CMakeLists.txt

@@ -25,12 +25,14 @@ string (ASCII 27 Esc)
 set (FontBold "${Esc}[1m")
 set (FontReset "${Esc}[m")
 
+# Allow to include CMake scripts from the app-template.
 list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
 
 # Use ccache.
 include (ccache)
 require_ccache ()
 
+# Add packages.
 set (CPM_INDENT "  CMake Package Manager CPM: ")
 include (CPM)
 include (CPMGetSystemPackage)
@@ -40,20 +42,11 @@ CPMUsePackageLock (${CMAKE_CURRENT_LIST_DIR}/cmake/package-lock.cmake)
 CPMGetSystemPackage (sharg)
 CPMGetSystemPackage (seqan3)
 
-# Allow to include CMake scripts from seqan3.
-list (APPEND CMAKE_MODULE_PATH "${seqan3_SOURCE_DIR}/test/cmake/")
-# Allow to include CMake scripts from the app-template.
-list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/test/cmake/")
-
 # Add the application.
 add_subdirectory (src)
 message (STATUS "${FontBold}You can run `make` to build the application.${FontReset}")
 
-## DOCUMENTATION
-
-add_subdirectory (doc EXCLUDE_FROM_ALL)
-
 ## TEST
-
+list (APPEND CMAKE_CTEST_ARGUMENTS "--output-on-failure") # Must be before `enable_testing ()`.
 enable_testing ()
 add_subdirectory (test EXCLUDE_FROM_ALL)

cmake/package-lock.cmake

@@ -35,16 +35,6 @@ CPMDeclarePackage (seqan3
                    SYSTEM TRUE
                    OPTIONS "INSTALL_SEQAN3 OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
-# benchmark
-set (BENCHMARK_VERSION 1.8.3)
-CPMDeclarePackage (benchmark
-                   NAME benchmark
-                   VERSION ${BENCHMARK_VERSION}
-                   GITHUB_REPOSITORY google/benchmark
-                   SYSTEM TRUE
-                   OPTIONS "BENCHMARK_ENABLE_TESTING OFF" "BENCHMARK_ENABLE_WERROR OFF"
-                           "CMAKE_MESSAGE_LOG_LEVEL WARNING"
-)
 # googletest
 set (GOOGLETEST_VERSION 1.14.0)
 CPMDeclarePackage (googletest