[INFRA] ccache, fmindex, CI

.github/workflows/ci_coverage.yml

@@ -11,10 +11,9 @@ on:
 
 concurrency:
   group: coverage-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: false
+  cancel-in-progress: ${{ github.event_name != 'push' }}
 
 env:
-  SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 
 defaults:
@@ -34,16 +33,10 @@ jobs:
             compiler: "gcc-13"
 
     steps:
-      # How many commits do we need to fetch to also fetch the branch point?
-      - name: Get fetch depth
-        id: fetch_depth
-        run: echo "depth=$(( ${{ github.event.pull_request.commits }} + 2 ))" >> $GITHUB_OUTPUT
-
       - name: Checkout
         uses: actions/checkout@v4
         with:
-          fetch-depth: ${{ steps.fetch_depth.outputs.depth }}
-          submodules: false
+          fetch-depth: 0
 
       - name: Setup toolchain
         uses: seqan/actions/setup-toolchain@main
@@ -61,7 +54,7 @@ jobs:
           sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/${CC/gcc/gcov} 100
           pip install gcovr==6.0
 
-      - name: Configure tests
+      - name: Configure
         run: |
           mkdir build
           cd build
@@ -70,24 +63,19 @@ jobs:
                    -DCMAKE_C_FLAGS="--coverage -fprofile-arcs -ftest-coverage -Werror" \
                    -DCMAKE_EXE_LINKER_FLAGS="-Wl,-lgcov" \
                    -DCMAKE_SHARED_LINKER_FLAGS="-Wl,-lgcov"
-          make -j2 -k gtest_main yaml-cpp
 
-      - name: Build tests
+      - name: Build and run tests
         run: |
-          ccache -z
           cd build
           make -j2 -k check
-          ccache -sv
 
       - name: Generate coverage report
         run: |
           gcovr --gcov-executable ${{ github.workspace }}/.github/workflows/scripts/gcov.sh \
-                --root ${{ github.workspace }}/test \
+                --root ${{ github.workspace }} \
                 ${{ github.workspace }}/build \
                 --filter ${{ github.workspace }}/include \
                 --filter ${{ github.workspace }}/src \
-                --exclude-lines-by-pattern '^\s*$' \
-                --exclude-lines-by-pattern '^\s*};$' \
                 --exclude-unreachable-branches \
                 --exclude-throw-branches \
                 --exclude-noncode-lines \

.github/workflows/ci_linux.yml

@@ -14,7 +14,6 @@ concurrency:
   cancel-in-progress: ${{ github.event_name != 'push' }}
 
 env:
-  SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 
 defaults:
@@ -32,31 +31,24 @@ jobs:
         include:
           - name: "clang17"
             compiler: "clang-17"
-            build: unit
             build_type: Release
             cxx_flags: "-stdlib=libc++"
 
           - name: "gcc13"
             compiler: "gcc-13"
-            build: unit
             build_type: Release
 
           - name: "gcc12"
             compiler: "gcc-12"
-            build: unit
             build_type: Release
 
           - name: "gcc11"
             compiler: "gcc-11"
-            build: unit
             build_type: Release
 
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 1
-          submodules: false
 
       - name: Setup toolchain
         uses: seqan/actions/setup-toolchain@main
@@ -75,12 +67,6 @@ jobs:
           cd build
           cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
                    -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Werror"
-          make -j2 -k gtest_main yaml-cpp
-
-      - name: Build application
-        run: |
-          cd build
-          make -j2 -k
 
       - name: Build and run tests
         run: |

.github/workflows/ci_macos.yml

@@ -14,7 +14,6 @@ concurrency:
   cancel-in-progress: ${{ github.event_name != 'push' }}
 
 env:
-  SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 
 defaults:
@@ -32,31 +31,24 @@ jobs:
         include:
           - name: "clang17"
             compiler: "clang-17"
-            build: unit
             build_type: Release
             cxx_flags: "-stdlib=libc++" # For verbosity. This is already the default.
 
           - name: "gcc13"
             compiler: "gcc-13"
-            build: unit
             build_type: Release
 
           - name: "gcc12"
             compiler: "gcc-12"
-            build: unit
             build_type: Release
 
           - name: "gcc11"
             compiler: "gcc-11"
-            build: unit
             build_type: Release
 
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 1
-          submodules: false
 
       - name: Setup toolchain
         uses: seqan/actions/setup-toolchain@main
@@ -75,12 +67,6 @@ jobs:
           cd build
           cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
                    -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Werror"
-          make -j3 -k gtest_main yaml-cpp
-
-      - name: Build application
-        run: |
-          cd build
-          make -j3 -k
 
       - name: Build and run tests
         run: |

.github/workflows/lint.yml

@@ -22,9 +22,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 1
-          submodules: false
 
       - name: Run clang-format
         uses: DoozyX/[email protected]

CMakeLists.txt

@@ -14,21 +14,21 @@ project (app-template
 # This allows including `*.cmake` files from the `cmake` directory without specifying the full path.
 list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
 
-# Use ccache if available. This speeds up the build process by caching files that have been compiled before.
-include (ccache)
-
 # Specify the directories where to store the built archives, libraries and executables.
 include (output_directories)
 
 # Add packages.
 # We use CPM for package management: https://github.com/cpm-cmake/CPM.cmake
-# The added packages (hibf, sharg, seqan3) are defined in the `cmake/package-locj.cmake` file.
+# The added packages (e.g., hibf, sharg, seqan3) are defined in the `cmake/package-lock.cmake` file.
 include (CPM)
 CPMUsePackageLock (${CMAKE_CURRENT_LIST_DIR}/cmake/package-lock.cmake)
 
+# Use ccache if available. This speeds up the build process by caching files that have been compiled before.
+CPMGetPackage (use_ccache)
 CPMGetPackage (hibf)
 CPMGetPackage (sharg)
 CPMGetPackage (seqan3)
+CPMGetPackage (fmindex)
 
 # Add the application. This will include `src/CMakeLists.txt`.
 add_subdirectory (src)

cmake/package-lock.cmake

@@ -15,6 +15,7 @@ CPMDeclarePackage (hibf
                    EXCLUDE_FROM_ALL TRUE
                    OPTIONS "INSTALL_HIBF OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
+
 # sharg
 set (SHARG_VERSION 01f848eeb6dbac3d50a718a8ee26bcf695edf5a8)
 CPMDeclarePackage (sharg
@@ -25,6 +26,7 @@ CPMDeclarePackage (sharg
                    EXCLUDE_FROM_ALL TRUE
                    OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
+
 # seqan3
 set (SEQAN3_VERSION fee3fb8e5976b455e848dd68c57f64fd3f67c3c2)
 CPMDeclarePackage (seqan3
@@ -35,6 +37,18 @@ CPMDeclarePackage (seqan3
                    EXCLUDE_FROM_ALL TRUE
                    OPTIONS "INSTALL_SEQAN3 OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
+
+# fmindex
+set (FMINDEX_VERSION 822d4d1aa6fa725f7d34e1ea819e9c23a2b6ebc2)
+CPMDeclarePackage (fmindex
+                   NAME fmindex
+                   GIT_TAG ${FMINDEX_VERSION}
+                   GITHUB_REPOSITORY SGSSGene/fmindex-collection
+                   SYSTEM TRUE
+                   EXCLUDE_FROM_ALL TRUE
+                   OPTIONS "CMAKE_MESSAGE_LOG_LEVEL WARNING"
+)
+
 # googletest
 set (GOOGLETEST_VERSION 1.14.0)
 CPMDeclarePackage (googletest
@@ -45,3 +59,14 @@ CPMDeclarePackage (googletest
                    EXCLUDE_FROM_ALL TRUE
                    OPTIONS "BUILD_GMOCK OFF" "INSTALL_GTEST OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
+
+# use_ccache
+set (USE_CCACHE_VERSION d2a54ef555b6fc2d496a4c9506dbeb7cf899ce37)
+CPMDeclarePackage (use_ccache
+                   NAME use_ccache
+                   GIT_TAG ${USE_CCACHE_VERSION}
+                   GITHUB_REPOSITORY seqan/cmake-scripts
+                   SOURCE_SUBDIR ccache
+                   SYSTEM TRUE
+                   EXCLUDE_FROM_ALL TRUE
+)

src/CMakeLists.txt

@@ -8,7 +8,9 @@ cmake_minimum_required (VERSION 3.25)
 # You can add more external include paths of other projects that are needed for your project.
 add_library ("${PROJECT_NAME}_lib" STATIC fastq_conversion.cpp)
 target_include_directories ("${PROJECT_NAME}_lib" PUBLIC "${${PROJECT_NAME}_SOURCE_DIR}/include")
-target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC seqan3::seqan3 sharg::sharg seqan::hibf)
+target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC seqan3::seqan3 sharg::sharg seqan::hibf
+                                                    fmindex-collection::fmindex-collection
+)
 target_compile_options ("${PROJECT_NAME}_lib" PUBLIC "-pedantic" "-Wall" "-Wextra")
 
 # Add the application.