[INFRA] Simplify

.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" \
+                   -DCMAKE_C_FLAGS="--coverage -fprofile-arcs -ftest-coverage" \
+                   -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

@@ -67,7 +67,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Configure
         run: |

.github/workflows/ci_macos.yml

@@ -67,7 +67,7 @@ jobs:
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.21.7
+          cmake: 3.25.3
 
       - name: Configure
         run: |

CMakeLists.txt

@@ -4,34 +4,9 @@
 
 cmake_minimum_required (VERSION 3.16)
 
-## CUSTOMISE
-
 # 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 ()
-
-# 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 "${Esc}[m")
-
 # Allow to include CMake scripts from the app-template.
 list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
 
@@ -42,16 +17,29 @@ require_ccache ()
 # Add packages.
 set (CPM_INDENT "  CMake Package Manager CPM: ")
 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_subdirectory (src)
-message (STATUS "${FontBold}You can run `make` to build the application.${FontReset}")
+# A interface to reuse common properties.
+# You can add more external include paths of other projects that are needed for your project.
+add_library ("${PROJECT_NAME}_interface" INTERFACE)
+target_link_libraries ("${PROJECT_NAME}_interface" INTERFACE seqan3::seqan3)
+target_link_libraries ("${PROJECT_NAME}_interface" INTERFACE sharg::sharg)
+target_link_libraries ("${PROJECT_NAME}_interface" INTERFACE seqan::hibf)
+target_include_directories ("${PROJECT_NAME}_interface" INTERFACE "include")
+target_compile_options ("${PROJECT_NAME}_interface" INTERFACE "-pedantic" "-Wall" "-Wextra")
+
+# An object library (without main) to be used in multiple targets.
+add_library ("${PROJECT_NAME}_lib" STATIC src/fastq_conversion.cpp)
+target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC "${PROJECT_NAME}_interface")
+
+add_executable ("${PROJECT_NAME}" src/main.cpp)
+target_link_libraries ("${PROJECT_NAME}" PRIVATE "${PROJECT_NAME}_lib")
+
 
 ## TEST
 option (${PROJECT_NAME}_TEST "Enable testing for ${PROJECT_NAME}." ON)

cmake/test_config.cmake

@@ -0,0 +1,63 @@
+# 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
+
+# Add googletest.
+CPMGetPackage (googletest)
+include (GoogleTest OPTIONAL)
+
+# Set directories for test output files, input data and binaries.
+file (MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/output)
+add_definitions (-DOUTPUTDIR=\"${CMAKE_CURRENT_BINARY_DIR}/output/\")
+add_definitions (-DDATADIR=\"${CMAKE_CURRENT_BINARY_DIR}/data/\")
+add_definitions (-DBINDIR=\"${CMAKE_CURRENT_BINARY_DIR}/../\")
+add_definitions (-DAPPNAME=\"${PROJECT_NAME}\")
+
+# # Test executables and libraries should not mix with the application files.
+# # This must happen after setting the output directories.
+# unset (CMAKE_ARCHIVE_OUTPUT_DIRECTORY)
+# unset (CMAKE_LIBRARY_OUTPUT_DIRECTORY)
+# unset (CMAKE_RUNTIME_OUTPUT_DIRECTORY)
+
+# Add the test interface library.
+if (NOT TARGET ${PROJECT_NAME}_test)
+    add_library (${PROJECT_NAME}_test INTERFACE)
+    target_compile_options (${PROJECT_NAME}_test INTERFACE "-pedantic" "-Wall" "-Wextra" "-Werror")
+
+    # GCC12 and above: Disable warning about std::hardware_destructive_interference_size not being ABI-stable.
+    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+        if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 12)
+            target_compile_options (${PROJECT_NAME}_test INTERFACE "-Wno-interference-size")
+        endif ()
+    endif ()
+
+    # GCC12 has some bogus warnings. They will not be fixed in googletest.
+    # https://github.com/google/googletest/issues/4232
+    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+        if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 12 AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 13)
+            target_compile_options (${PROJECT_NAME}_test INTERFACE "-Wno-restrict")
+        endif ()
+    endif ()
+
+    target_link_libraries (${PROJECT_NAME}_test INTERFACE "${PROJECT_NAME}_lib" "GTest::gtest_main")
+    add_library (${PROJECT_NAME}::test ALIAS ${PROJECT_NAME}_test)
+endif ()
+
+# Add the check target that builds and runs tests.
+add_custom_target (check COMMAND ${CMAKE_CTEST_COMMAND} ${CMAKE_CTEST_ARGUMENTS})
+
+macro (add_app_test test_filename)
+    file (RELATIVE_PATH source_file "${CMAKE_SOURCE_DIR}" "${CMAKE_CURRENT_LIST_DIR}/${test_filename}")
+    get_filename_component (target "${source_file}" NAME_WE)
+
+    add_executable (${target} ${test_filename})
+    target_link_libraries (${target} ${PROJECT_NAME}::test)
+
+    add_dependencies (${target} ${PROJECT_NAME})
+    add_dependencies (check ${target})
+
+    add_test (NAME ${target} COMMAND ${target})
+
+    unset (source_file)
+    unset (target)
+endmacro ()

test/CMakeLists.txt

@@ -4,83 +4,12 @@
 
 cmake_minimum_required (VERSION 3.16)
 
-# Add googletest.
-CPMGetSystemPackage (googletest)
-include (GoogleTest OPTIONAL)
-
-# 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}/cmake/")
-
-# Set directories for test output files, input data and binaries.
-file (MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/output)
-add_definitions (-DOUTPUTDIR=\"${CMAKE_CURRENT_BINARY_DIR}/output/\")
-add_definitions (-DDATADIR=\"${CMAKE_CURRENT_BINARY_DIR}/data/\")
-add_definitions (-DBINDIR=\"${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/\")
-add_definitions (-DAPPNAME=\"${PROJECT_NAME}\")
-
-# Test executables and libraries should not mix with the application files.
-# This must happen after setting the output directories.
-unset (CMAKE_ARCHIVE_OUTPUT_DIRECTORY)
-unset (CMAKE_LIBRARY_OUTPUT_DIRECTORY)
-unset (CMAKE_RUNTIME_OUTPUT_DIRECTORY)
-
-# Add the test interface library.
-if (NOT TARGET ${PROJECT_NAME}_test)
-    add_library (${PROJECT_NAME}_test INTERFACE)
-    target_compile_options (${PROJECT_NAME}_test INTERFACE "-pedantic" "-Wall" "-Wextra" "-Werror")
-
-    # GCC12 and above: Disable warning about std::hardware_destructive_interference_size not being ABI-stable.
-    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-        if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 12)
-            target_compile_options (${PROJECT_NAME}_test INTERFACE "-Wno-interference-size")
-        endif ()
-    endif ()
-
-    # GCC12 has some bogus warnings. They will not be fixed in googletest.
-    # https://github.com/google/googletest/issues/4232
-    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-        if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 12 AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 13)
-            target_compile_options (${PROJECT_NAME}_test INTERFACE "-Wno-restrict")
-        endif ()
-    endif ()
-
-    target_link_libraries (${PROJECT_NAME}_test INTERFACE "${PROJECT_NAME}_lib" "GTest::gtest_main")
-    target_include_directories (${PROJECT_NAME}_test INTERFACE "${seqan3_SOURCE_DIR}/test/include")
-    add_library (${PROJECT_NAME}::test ALIAS ${PROJECT_NAME}_test)
-endif ()
-
-# Add the check target that builds and runs tests.
-add_custom_target (check COMMAND ${CMAKE_CTEST_COMMAND} ${CMAKE_CTEST_ARGUMENTS})
-
-include (seqan3_test_component)
-# A macro that adds an api or cli test.
-macro (add_app_test test_filename)
-    # Extract the test target name.
-    file (RELATIVE_PATH source_file "${CMAKE_SOURCE_DIR}" "${CMAKE_CURRENT_LIST_DIR}/${test_filename}")
-    seqan3_test_component (target "${source_file}" TARGET_NAME)
-    seqan3_test_component (test_name "${source_file}" TEST_NAME)
-
-    # Create the test target.
-    add_executable (${target} ${test_filename})
-    target_link_libraries (${target} ${PROJECT_NAME}::test)
-    add_dependencies (${target} ${PROJECT_NAME})
-    add_dependencies (check ${target})
-
-    # Generate and set the test name.
-    add_test (NAME "${test_name}" COMMAND ${target})
+include (test_config)
+include (data/datasources.cmake)
 
-    unset (source_file)
-    unset (target)
-    unset (test_name)
-endmacro ()
+message (STATUS "You can run `make check` to build and run tests.")
 
-# Fetch data and add the tests.
-include (data/datasources.cmake)
-add_subdirectory (api)
-add_subdirectory (cli)
-add_subdirectory (header)
-add_subdirectory (coverage)
+add_app_test (api_fastq_coversion_test.cpp)
+add_app_test (cli_fastq_coversion_test.cpp)
 
-message (STATUS "${FontBold}You can run `make check` to build and run tests.${FontReset}")
+target_use_datasources (check FILES in.fastq out.fasta)

test/api/convert_fastq_test.cpp → test/api_fastq_coversion_test.cpp

@@ -4,8 +4,9 @@
 
 #include <gtest/gtest.h>
 
-#include "../app_test.hpp"
-#include "fastq_conversion.hpp"
+#include <fastq_conversion.hpp>
+
+#include "app_test.hpp"
 
 // To prevent issues when running multiple API tests in parallel, give each API test unique names:
 struct fastq_to_fasta : public app_test