[INFRA] Simplify

.cmake-format.yaml

@@ -29,6 +29,14 @@ parse:
   _help_additional_commands:
   - Specify structure for custom cmake functions
   additional_commands:
+    declare_datasource:
+      pargs:
+        nargs: '*'
+        flags: []
+      kwargs:
+        FILE: 1
+        URL: '*'
+        URL_HASH: 1
     cpmgetpackage:
       pargs: 1
       spelling: CPMGetPackage

.github/workflows/ci_coverage.yml

@@ -32,8 +32,6 @@ jobs:
         include:
           - name: "gcc13"
             compiler: "gcc-13"
-            build: coverage
-            build_type: Coverage
 
     steps:
       # How many commits do we need to fetch to also fetch the branch point?
@@ -56,7 +54,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Install gcovr
         run: |
@@ -67,12 +65,14 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
+          cmake .. -DCMAKE_BUILD_TYPE=Debug \
+                   -DCMAKE_CXX_FLAGS="--coverage -fprofile-arcs -ftest-coverage -Werror" \
+                   -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
-        env:
-          CCACHE_IGNOREOPTIONS: "-fprofile-abs-path"
         run: |
           ccache -z
           cd build
@@ -82,7 +82,7 @@ jobs:
       - name: Generate coverage report
         run: |
           gcovr --gcov-executable ${{ github.workspace }}/.github/workflows/scripts/gcov.sh \
-                --root ${{ github.workspace }}/test/coverage \
+                --root ${{ github.workspace }}/test \
                 ${{ github.workspace }}/build \
                 --filter ${{ github.workspace }}/include \
                 --filter ${{ github.workspace }}/src \

.github/workflows/ci_license.yml

@@ -20,7 +20,7 @@ jobs:
   check:
     name: REUSE Compliance
     runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    timeout-minutes: 5
     steps:
       - name: Checkout
         uses: actions/checkout@v4

.github/workflows/ci_linux.yml

@@ -67,14 +67,14 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Configure
         run: |
           mkdir build
           cd build
           cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Werror"
           make -j2 -k gtest_main yaml-cpp
 
       - name: Build application

.github/workflows/ci_macos.yml

@@ -67,14 +67,14 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Configure
         run: |
           mkdir build
           cd build
           cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Werror"
           make -j3 -k gtest_main yaml-cpp
 
       - name: Build application

CMakeLists.txt

@@ -2,61 +2,45 @@
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
-cmake_minimum_required (VERSION 3.16)
-
-## CUSTOMISE
+cmake_minimum_required (VERSION 3.25)
 
 # Define the application name and version.
-project (app-template VERSION 1.0.0)
-
-# Needed for CPM
-find_package (Git REQUIRED)
-
-## BUILD
-
-# Make Release default build type
-if (NOT CMAKE_BUILD_TYPE)
-    set (CMAKE_BUILD_TYPE
-         Release
-         CACHE STRING "Choose the type of build, options are: Debug Release Coverage RelWithDebInfo MinSizeRel." FORCE
-    )
-endif ()
+project (app-template
+         LANGUAGES CXX
+         VERSION 1.0.0
+         DESCRIPTION "My application description"
+)
 
-# Specify the directories where to store the built archives, libraries and executables
-set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
-set (CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
-set (CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
-
-# Messages
-string (ASCII 27 Esc)
-set (FontBold "${Esc}[1m")
-set (FontReset "${Esc}[m")
-
-# Allow to include CMake scripts from the app-template.
+# This allows including `*.cmake` files from the `cmake` directory without specifying the full path.
 list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
 
-# Use ccache.
+# Use ccache if available. This speeds up the build process by caching files that have been compiled before.
 include (ccache)
-require_ccache ()
+
+# Specify the directories where to store the built archives, libraries and executables.
+include (output_directories)
 
 # Add packages.
-set (CPM_INDENT "  CMake Package Manager CPM: ")
+# 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.
 include (CPM)
-include (CPMGetSystemPackage)
 CPMUsePackageLock (${CMAKE_CURRENT_LIST_DIR}/cmake/package-lock.cmake)
 
-CPMGetSystemPackage (hibf)
-CPMGetSystemPackage (sharg)
-CPMGetSystemPackage (seqan3)
+CPMGetPackage (hibf)
+CPMGetPackage (sharg)
+CPMGetPackage (seqan3)
 
-# Add the application.
+# Add the application. This will include `src/CMakeLists.txt`.
 add_subdirectory (src)
-message (STATUS "${FontBold}You can run `make` to build the application.${FontReset}")
 
-## TEST
+# An option to disable configuring and building the tests. Tests are enabled by default.
+# If your project-name (line 8 of this file) is `app-template`, the option will be `app-template_TEST`.
+# It can be used when calling CMake: `cmake .. -Dapp-template_TEST=OFF`.
+# It is good practice to allow disabling tests. If another project includes your application,
+# it might not want to build your tests.
 option (${PROJECT_NAME}_TEST "Enable testing for ${PROJECT_NAME}." ON)
+
 if (${PROJECT_NAME}_TEST)
-    list (APPEND CMAKE_CTEST_ARGUMENTS "--output-on-failure") # Must be before `enable_testing ()`.
-    enable_testing ()
+    # Add the tests. This will include `test/CMakeLists.txt`.
     add_subdirectory (test EXCLUDE_FROM_ALL)
 endif ()

cmake/ccache.cmake

@@ -1,8 +1,6 @@
 # SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
 # SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
-# SPDX-License-Identifier: BSD-3-Clause
-
-cmake_minimum_required (VERSION 3.21)
+# SPDX-License-Identifier: CC0-1.0
 
 include (FindPackageMessage)
 
@@ -11,25 +9,20 @@ include (FindPackageMessage)
 # See also
 # * https://ccache.dev/
 # * https://cmake.org/cmake/help/latest/variable/CMAKE_LANG_COMPILER_LAUNCHER.html
-macro (require_ccache)
-    option (USE_CCACHE "Use ccache if available." ON)
-    set (FPROFILE_ABS_PATH "-fprofile-abs-path")
-    if (USE_CCACHE)
-        find_program (CCACHE_PROGRAM ccache)
+option (USE_CCACHE "Use ccache if available." ON)
 
-        if (NOT CCACHE_PROGRAM)
-            find_package_message (CCACHE_PROGRAM "  Ccache program:             not available" "[${CCACHE_PROGRAM}]")
-        else ()
-            find_package_message (CCACHE_PROGRAM "  Ccache program:             available" "[${CCACHE_PROGRAM}]")
-            set (FPROFILE_ABS_PATH "--ccache-skip -fprofile-abs-path")
+if (USE_CCACHE)
+    find_program (CCACHE_PROGRAM ccache)
 
-            list (PREPEND CMAKE_CXX_COMPILER_LAUNCHER "${CCACHE_PROGRAM}")
-            list (PREPEND CMAKE_C_COMPILER_LAUNCHER "${CCACHE_PROGRAM}")
+    if (NOT CCACHE_PROGRAM)
+        find_package_message (CCACHE_PROGRAM "Ccache program:             not available" "[${CCACHE_PROGRAM}]")
+    else ()
+        find_package_message (CCACHE_PROGRAM "Ccache program:             available" "[${CCACHE_PROGRAM}]")
 
-            list (PREPEND CMAKE_CXX_LINKER_LAUNCHER "${CCACHE_PROGRAM}")
-            list (PREPEND CMAKE_C_LINKER_LAUNCHER "${CCACHE_PROGRAM}")
-        endif ()
+        list (PREPEND CMAKE_CXX_COMPILER_LAUNCHER "${CCACHE_PROGRAM}")
+        list (PREPEND CMAKE_C_COMPILER_LAUNCHER "${CCACHE_PROGRAM}")
 
-        unset (CCACHE_PROGRAM)
+        list (PREPEND CMAKE_CXX_LINKER_LAUNCHER "${CCACHE_PROGRAM}")
+        list (PREPEND CMAKE_C_LINKER_LAUNCHER "${CCACHE_PROGRAM}")
     endif ()
-endmacro ()
+endif ()

cmake/output_directories.cmake

@@ -0,0 +1,7 @@
+# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
+set (CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
+set (CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}")

cmake/package-lock.cmake

@@ -12,6 +12,7 @@ CPMDeclarePackage (hibf
                    GIT_TAG ${HIBF_VERSION}
                    GITHUB_REPOSITORY seqan/hibf
                    SYSTEM TRUE
+                   EXCLUDE_FROM_ALL TRUE
                    OPTIONS "INSTALL_HIBF OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 # sharg
@@ -21,6 +22,7 @@ CPMDeclarePackage (sharg
                    GIT_TAG ${SHARG_VERSION}
                    GITHUB_REPOSITORY seqan/sharg-parser
                    SYSTEM TRUE
+                   EXCLUDE_FROM_ALL TRUE
                    OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 # seqan3
@@ -30,6 +32,7 @@ CPMDeclarePackage (seqan3
                    GIT_TAG ${SEQAN3_VERSION}
                    GITHUB_REPOSITORY seqan/seqan3
                    SYSTEM TRUE
+                   EXCLUDE_FROM_ALL TRUE
                    OPTIONS "INSTALL_SEQAN3 OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 # googletest
@@ -39,5 +42,6 @@ CPMDeclarePackage (googletest
                    VERSION ${GOOGLETEST_VERSION}
                    GITHUB_REPOSITORY google/googletest
                    SYSTEM TRUE
+                   EXCLUDE_FROM_ALL TRUE
                    OPTIONS "BUILD_GMOCK OFF" "INSTALL_GTEST OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )

cmake/test/add_local_data.cmake

@@ -0,0 +1,23 @@
+# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+set (DATASOURCES_DATA_DIR "${${PROJECT_NAME}_SOURCE_DIR}/test/data")
+
+file (GLOB_RECURSE datasources
+      LIST_DIRECTORIES false
+      RELATIVE ${DATASOURCES_DATA_DIR}
+      CONFIGURE_DEPENDS ${DATASOURCES_DATA_DIR}/*
+)
+list (REMOVE_ITEM datasources datasources.cmake README.md)
+list (FILTER datasources EXCLUDE REGEX "\.license")
+
+foreach (datasource IN LISTS datasources)
+    get_filename_component (datasource_name "${datasource}" NAME)
+    file (SHA256 ${DATASOURCES_DATA_DIR}/${datasource} datasource_hash)
+
+    declare_datasource (FILE ${datasource_name}
+                        URL ${DATASOURCES_DATA_DIR}/${datasource}
+                        URL_HASH SHA256=${datasource_hash}
+    )
+endforeach ()