patch: removing test and doc

doc/CMakeLists.txt

-cmake_minimum_required (VERSION 3.8)
-
-# Find doxygen.
-find_package (Doxygen QUIET)
-
-if (${DOXYGEN_FOUND})
-    message (STATUS "Found Doxygen: ${DOXYGEN_EXECUTABLE}")
-
-    # Configure doxygen options.
-    set (APP_TEMPLATE_DOXYFILE_IN ${CMAKE_SOURCE_DIR}/doc/doxygen_cfg)
-    set (APP_TEMPLATE_DOXYGEN_OUTPUT_DIR "${PROJECT_BINARY_DIR}/doc")
-    set (APP_TEMPLATE_DOXYGEN_EXCLUDE_SYMBOLS "")
-    set (APP_TEMPLATE_DOXYGEN_PREDEFINED_NDEBUG "")
-    set (APP_TEMPLATE_DOXYGEN_ENABLED_SECTIONS "DEV")
-    set (APP_TEMPLATE_DOXYGEN_EXTRACT_PRIVATE "YES")
-
-    configure_file (${APP_TEMPLATE_DOXYFILE_IN} ${APP_TEMPLATE_DOXYGEN_OUTPUT_DIR}/Doxyfile)
-    add_custom_target (doc
-                       COMMAND ${DOXYGEN_EXECUTABLE}
-                       WORKING_DIRECTORY ${APP_TEMPLATE_DOXYGEN_OUTPUT_DIR}
-                       COMMENT "Generating (developer) API documentation with Doxygen."
-                       VERBATIM)
-    message (STATUS "${FontBold}You can run `make doc` to build api documentation.${FontReset}")
-else ()
-    message (STATUS "Doxygen not found.")
-endif ()

doc/README.md

-# Documentation
-
-To build the API documentation, you need to install `doxygen`. We use Doxygen version 1.8.17.
-Run `make doc` and open the API documentation via `open doc/html/index.html`.
-
-You can run `doxygen -u doxygen_cfg` to convert the configuration file to its verbose version.
-`doxygen -u -s doxygen_cfg` will convert it back to its compact version.

doc/doxygen_cfg

-# Doxyfile 1.9.1
-
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-DOXYFILE_ENCODING      = UTF-8
-PROJECT_NAME           = fastq_to_fasta
-PROJECT_NUMBER         =
-PROJECT_BRIEF          = "A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app."
-PROJECT_LOGO           =
-OUTPUT_DIRECTORY       = ${APP_TEMPLATE_DOXYGEN_OUTPUT_DIR}
-CREATE_SUBDIRS         = NO
-ALLOW_UNICODE_NAMES    = NO
-OUTPUT_LANGUAGE        = English
-OUTPUT_TEXT_DIRECTION  = None
-BRIEF_MEMBER_DESC      = YES
-REPEAT_BRIEF           = YES
-ABBREVIATE_BRIEF       = "The $name class" \
-                         "The $name widget" \
-                         "The $name file" \
-                         is \
-                         provides \
-                         specifies \
-                         contains \
-                         represents \
-                         a \
-                         an \
-                         the
-ALWAYS_DETAILED_SEC    = NO
-INLINE_INHERITED_MEMB  = NO
-FULL_PATH_NAMES        = YES
-STRIP_FROM_PATH        = ${CMAKE_SOURCE_DIR}
-STRIP_FROM_INC_PATH    = ${CMAKE_SOURCE_DIR}/include
-SHORT_NAMES            = NO
-JAVADOC_AUTOBRIEF      = NO
-JAVADOC_BANNER         = NO
-QT_AUTOBRIEF           = NO
-MULTILINE_CPP_IS_BRIEF = NO
-PYTHON_DOCSTRING       = YES
-INHERIT_DOCS           = YES
-SEPARATE_MEMBER_PAGES  = NO
-TAB_SIZE               = 4
-ALIASES                =
-OPTIMIZE_OUTPUT_FOR_C  = NO
-OPTIMIZE_OUTPUT_JAVA   = NO
-OPTIMIZE_FOR_FORTRAN   = NO
-OPTIMIZE_OUTPUT_VHDL   = NO
-OPTIMIZE_OUTPUT_SLICE  = NO
-EXTENSION_MAPPING      =
-MARKDOWN_SUPPORT       = YES
-TOC_INCLUDE_HEADINGS   = 5
-AUTOLINK_SUPPORT       = YES
-BUILTIN_STL_SUPPORT    = NO
-CPP_CLI_SUPPORT        = NO
-SIP_SUPPORT            = NO
-IDL_PROPERTY_SUPPORT   = YES
-DISTRIBUTE_GROUP_DOC   = NO
-GROUP_NESTED_COMPOUNDS = NO
-SUBGROUPING            = YES
-INLINE_GROUPED_CLASSES = NO
-INLINE_SIMPLE_STRUCTS  = NO
-TYPEDEF_HIDES_STRUCT   = NO
-LOOKUP_CACHE_SIZE      = 0
-NUM_PROC_THREADS       = 1
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-EXTRACT_ALL            = YES
-EXTRACT_PRIVATE        = NO
-EXTRACT_PRIV_VIRTUAL   = NO
-EXTRACT_PACKAGE        = NO
-EXTRACT_STATIC         = NO
-EXTRACT_LOCAL_CLASSES  = YES
-EXTRACT_LOCAL_METHODS  = NO
-EXTRACT_ANON_NSPACES   = NO
-RESOLVE_UNNAMED_PARAMS = YES
-HIDE_UNDOC_MEMBERS     = NO
-HIDE_UNDOC_CLASSES     = NO
-HIDE_FRIEND_COMPOUNDS  = NO
-HIDE_IN_BODY_DOCS      = NO
-INTERNAL_DOCS          = NO
-CASE_SENSE_NAMES       = NO
-HIDE_SCOPE_NAMES       = NO
-HIDE_COMPOUND_REFERENCE= NO
-SHOW_INCLUDE_FILES     = YES
-SHOW_GROUPED_MEMB_INC  = NO
-FORCE_LOCAL_INCLUDES   = NO
-INLINE_INFO            = YES
-SORT_MEMBER_DOCS       = YES
-SORT_BRIEF_DOCS        = NO
-SORT_MEMBERS_CTORS_1ST = NO
-SORT_GROUP_NAMES       = NO
-SORT_BY_SCOPE_NAME     = NO
-STRICT_PROTO_MATCHING  = NO
-GENERATE_TODOLIST      = YES
-GENERATE_TESTLIST      = YES
-GENERATE_BUGLIST       = YES
-GENERATE_DEPRECATEDLIST= YES
-ENABLED_SECTIONS       =
-MAX_INITIALIZER_LINES  = 30
-SHOW_USED_FILES        = YES
-SHOW_FILES             = YES
-SHOW_NAMESPACES        = YES
-FILE_VERSION_FILTER    =
-LAYOUT_FILE            =
-CITE_BIB_FILES         =
-#---------------------------------------------------------------------------
-# Configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-QUIET                  = NO
-WARNINGS               = YES
-WARN_IF_UNDOCUMENTED   = YES
-WARN_IF_DOC_ERROR      = YES
-WARN_NO_PARAMDOC       = NO
-WARN_AS_ERROR          = NO
-WARN_FORMAT            = "$file:$line: $text"
-WARN_LOGFILE           =
-#---------------------------------------------------------------------------
-# Configuration options related to the input files
-#---------------------------------------------------------------------------
-INPUT                  = ${CMAKE_SOURCE_DIR}/include \
-                         ${CMAKE_SOURCE_DIR}/src \
-                         ${CMAKE_SOURCE_DIR}/LICENSE.md
-INPUT_ENCODING         = UTF-8
-FILE_PATTERNS          = *.c \
-                         *.cc \
-                         *.cxx \
-                         *.cpp \
-                         *.c++ \
-                         *.java \
-                         *.ii \
-                         *.ixx \
-                         *.ipp \
-                         *.i++ \
-                         *.inl \
-                         *.idl \
-                         *.ddl \
-                         *.odl \
-                         *.h \
-                         *.hh \
-                         *.hxx \
-                         *.hpp \
-                         *.h++ \
-                         *.cs \
-                         *.d \
-                         *.php \
-                         *.php4 \
-                         *.php5 \
-                         *.phtml \
-                         *.inc \
-                         *.m \
-                         *.markdown \
-                         *.md \
-                         *.mm \
-                         *.dox \
-                         *.doc \
-                         *.txt \
-                         *.py \
-                         *.pyw \
-                         *.f90 \
-                         *.f95 \
-                         *.f03 \
-                         *.f08 \
-                         *.f \
-                         *.for \
-                         *.tcl \
-                         *.vhd \
-                         *.vhdl \
-                         *.ucf \
-                         *.qsf \
-                         *.ice
-RECURSIVE              = YES
-EXCLUDE                =
-EXCLUDE_SYMLINKS       = NO
-EXCLUDE_PATTERNS       =
-EXCLUDE_SYMBOLS        =
-EXAMPLE_PATH           =
-EXAMPLE_PATTERNS       = *
-EXAMPLE_RECURSIVE      = NO
-IMAGE_PATH             =
-INPUT_FILTER           =
-FILTER_PATTERNS        =
-FILTER_SOURCE_FILES    = NO
-FILTER_SOURCE_PATTERNS =
-USE_MDFILE_AS_MAINPAGE =
-#---------------------------------------------------------------------------
-# Configuration options related to source browsing
-#---------------------------------------------------------------------------
-SOURCE_BROWSER         = NO
-INLINE_SOURCES         = NO
-STRIP_CODE_COMMENTS    = YES
-REFERENCED_BY_RELATION = NO
-REFERENCES_RELATION    = NO
-REFERENCES_LINK_SOURCE = YES
-SOURCE_TOOLTIPS        = YES
-USE_HTAGS              = NO
-VERBATIM_HEADERS       = YES
-CLANG_ASSISTED_PARSING = NO
-CLANG_ADD_INC_PATHS    = YES
-CLANG_OPTIONS          =
-CLANG_DATABASE_PATH    =
-#---------------------------------------------------------------------------
-# Configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-ALPHABETICAL_INDEX     = YES
-IGNORE_PREFIX          =
-#---------------------------------------------------------------------------
-# Configuration options related to the HTML output
-#---------------------------------------------------------------------------
-GENERATE_HTML          = YES
-HTML_OUTPUT            = html
-HTML_FILE_EXTENSION    = .html
-HTML_HEADER            =
-HTML_FOOTER            =
-HTML_STYLESHEET        =
-HTML_EXTRA_STYLESHEET  =
-HTML_EXTRA_FILES       =
-HTML_COLORSTYLE_HUE    = 220
-HTML_COLORSTYLE_SAT    = 100
-HTML_COLORSTYLE_GAMMA  = 80
-HTML_TIMESTAMP         = NO
-HTML_DYNAMIC_MENUS     = YES
-HTML_DYNAMIC_SECTIONS  = NO
-HTML_INDEX_NUM_ENTRIES = 100
-GENERATE_DOCSET        = NO
-DOCSET_FEEDNAME        = "Doxygen generated docs"
-DOCSET_BUNDLE_ID       = org.doxygen.Project
-DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
-DOCSET_PUBLISHER_NAME  = Publisher
-GENERATE_HTMLHELP      = NO
-CHM_FILE               =
-HHC_LOCATION           =
-GENERATE_CHI           = NO
-CHM_INDEX_ENCODING     =
-BINARY_TOC             = NO
-TOC_EXPAND             = NO
-GENERATE_QHP           = NO
-QCH_FILE               =
-QHP_NAMESPACE          = org.doxygen.Project
-QHP_VIRTUAL_FOLDER     = doc
-QHP_CUST_FILTER_NAME   =
-QHP_CUST_FILTER_ATTRS  =
-QHP_SECT_FILTER_ATTRS  =
-QHG_LOCATION           =
-GENERATE_ECLIPSEHELP   = NO
-ECLIPSE_DOC_ID         = org.doxygen.Project
-DISABLE_INDEX          = NO
-GENERATE_TREEVIEW      = NO
-ENUM_VALUES_PER_LINE   = 4
-TREEVIEW_WIDTH         = 250
-EXT_LINKS_IN_WINDOW    = NO
-HTML_FORMULA_FORMAT    = png
-FORMULA_FONTSIZE       = 10
-FORMULA_TRANSPARENT    = YES
-FORMULA_MACROFILE      =
-USE_MATHJAX            = NO
-MATHJAX_FORMAT         = HTML-CSS
-MATHJAX_RELPATH        = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/
-MATHJAX_EXTENSIONS     =
-MATHJAX_CODEFILE       =
-SEARCHENGINE           = YES
-SERVER_BASED_SEARCH    = NO
-EXTERNAL_SEARCH        = NO
-SEARCHENGINE_URL       =
-SEARCHDATA_FILE        = searchdata.xml
-EXTERNAL_SEARCH_ID     =
-EXTRA_SEARCH_MAPPINGS  =
-#---------------------------------------------------------------------------
-# Configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-GENERATE_LATEX         = YES
-LATEX_OUTPUT           = latex
-LATEX_CMD_NAME         =
-MAKEINDEX_CMD_NAME     = makeindex
-LATEX_MAKEINDEX_CMD    = makeindex
-COMPACT_LATEX          = NO
-PAPER_TYPE             = a4
-EXTRA_PACKAGES         =
-LATEX_HEADER           =
-LATEX_FOOTER           =
-LATEX_EXTRA_STYLESHEET =
-LATEX_EXTRA_FILES      =
-PDF_HYPERLINKS         = YES
-USE_PDFLATEX           = YES
-LATEX_BATCHMODE        = NO
-LATEX_HIDE_INDICES     = NO
-LATEX_SOURCE_CODE      = NO
-LATEX_BIB_STYLE        = plain
-LATEX_TIMESTAMP        = NO
-LATEX_EMOJI_DIRECTORY  =
-#---------------------------------------------------------------------------
-# Configuration options related to the RTF output
-#---------------------------------------------------------------------------
-GENERATE_RTF           = NO
-RTF_OUTPUT             = rtf
-COMPACT_RTF            = NO
-RTF_HYPERLINKS         = NO
-RTF_STYLESHEET_FILE    =
-RTF_EXTENSIONS_FILE    =
-RTF_SOURCE_CODE        = NO
-#---------------------------------------------------------------------------
-# Configuration options related to the man page output
-#---------------------------------------------------------------------------
-GENERATE_MAN           = NO
-MAN_OUTPUT             = man
-MAN_EXTENSION          = .3
-MAN_SUBDIR             =
-MAN_LINKS              = NO
-#---------------------------------------------------------------------------
-# Configuration options related to the XML output
-#---------------------------------------------------------------------------
-GENERATE_XML           = NO
-XML_OUTPUT             = xml
-XML_PROGRAMLISTING     = YES
-XML_NS_MEMB_FILE_SCOPE = NO
-#---------------------------------------------------------------------------
-# Configuration options related to the DOCBOOK output
-#---------------------------------------------------------------------------
-GENERATE_DOCBOOK       = NO
-DOCBOOK_OUTPUT         = docbook
-DOCBOOK_PROGRAMLISTING = NO
-#---------------------------------------------------------------------------
-# Configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-GENERATE_AUTOGEN_DEF   = NO
-#---------------------------------------------------------------------------
-# Configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-GENERATE_PERLMOD       = NO
-PERLMOD_LATEX          = NO
-PERLMOD_PRETTY         = YES
-PERLMOD_MAKEVAR_PREFIX =
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor
-#---------------------------------------------------------------------------
-ENABLE_PREPROCESSING   = YES
-MACRO_EXPANSION        = NO
-EXPAND_ONLY_PREDEF     = NO
-SEARCH_INCLUDES        = YES
-INCLUDE_PATH           = ${CMAKE_SOURCE_DIR}/include
-INCLUDE_FILE_PATTERNS  =
-PREDEFINED             =
-EXPAND_AS_DEFINED      =
-SKIP_FUNCTION_MACROS   = YES
-#---------------------------------------------------------------------------
-# Configuration options related to external references
-#---------------------------------------------------------------------------
-TAGFILES               =
-GENERATE_TAGFILE       =
-ALLEXTERNALS           = NO
-EXTERNAL_GROUPS        = YES
-EXTERNAL_PAGES         = YES
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool
-#---------------------------------------------------------------------------
-CLASS_DIAGRAMS         = YES
-DIA_PATH               =
-HIDE_UNDOC_RELATIONS   = YES
-HAVE_DOT               = NO
-DOT_NUM_THREADS        = 0
-DOT_FONTNAME           = Helvetica
-DOT_FONTSIZE           = 10
-DOT_FONTPATH           =
-CLASS_GRAPH            = YES
-COLLABORATION_GRAPH    = YES
-GROUP_GRAPHS           = YES
-UML_LOOK               = NO
-UML_LIMIT_NUM_FIELDS   = 10
-DOT_UML_DETAILS        = NO
-DOT_WRAP_THRESHOLD     = 17
-TEMPLATE_RELATIONS     = NO
-INCLUDE_GRAPH          = YES
-INCLUDED_BY_GRAPH      = YES
-CALL_GRAPH             = NO
-CALLER_GRAPH           = NO
-GRAPHICAL_HIERARCHY    = YES
-DIRECTORY_GRAPH        = YES
-DOT_IMAGE_FORMAT       = png
-INTERACTIVE_SVG        = NO
-DOT_PATH               =
-DOTFILE_DIRS           =
-MSCFILE_DIRS           =
-DIAFILE_DIRS           =
-PLANTUML_JAR_PATH      =
-PLANTUML_CFG_FILE      =
-PLANTUML_INCLUDE_PATH  =
-DOT_GRAPH_MAX_NODES    = 50
-MAX_DOT_GRAPH_DEPTH    = 0
-DOT_TRANSPARENT        = NO
-DOT_MULTI_TARGETS      = NO
-GENERATE_LEGEND        = YES
-DOT_CLEANUP            = YES

test/CMakeLists.txt

-cmake_minimum_required (VERSION 3.8)
-
-# 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}/\")
-
-# Define cmake configuration flags to configure and build external projects with the same flags as specified for
-# this project.
-# We also pass the C_COMPILER such that googletest is built with the corresponding GCC.
-# Otherwise, it might happen that the app is built with, e.g., g++-11, but gtest with gcc-7, which might cause trouble.
-set (SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "")
-list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}")
-list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}")
-list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}")
-list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR}")
-list (APPEND SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS "-DCMAKE_VERBOSE_MAKEFILE=${CMAKE_VERBOSE_MAKEFILE}")
-set (SEQAN3_TEST_CLONE_DIR "${PROJECT_BINARY_DIR}/vendor/googletest")
-
-include (seqan3_require_test)
-seqan3_require_test ()
-
-# Build tests just before their execution, because they have not been built with "all" target.
-# The trick is here to provide a cmake file as a directory property that executes the build command.
-file (WRITE "${CMAKE_CURRENT_BINARY_DIR}/build_test_targets.cmake"
-            "execute_process (COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target api_test)\n"
-            "execute_process (COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target cli_test)\n"
-            "execute_process (COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target header_test)\n")
-set_directory_properties (PROPERTIES TEST_INCLUDE_FILE "${CMAKE_CURRENT_BINARY_DIR}/build_test_targets.cmake")
-
-# Test executables and libraries should not mix with the application files.
-unset (CMAKE_ARCHIVE_OUTPUT_DIRECTORY)
-unset (CMAKE_LIBRARY_OUTPUT_DIRECTORY)
-unset (CMAKE_RUNTIME_OUTPUT_DIRECTORY)
-
-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} "${PROJECT_NAME}_lib" seqan3::seqan3 gtest gtest_main)
-
-    # Make seqan3::test available for both cli and api tests.
-    target_include_directories (${target} PUBLIC "${SEQAN3_CLONE_DIR}/test/include")
-    target_include_directories (${target} PUBLIC "${SEQAN3_TEST_CLONE_DIR}/googletest/include/")
-
-    # Generate and set the test name.
-    add_test (NAME "${test_name}" COMMAND ${target})
-
-    unset (source_file)
-    unset (target)
-    unset (test_name)
-endmacro ()
-
-string (TOUPPER ${PROJECT_NAME} uppercase_project_name)
-set (${uppercase_project_name}_HEADER_TEST_ONLY OFF CACHE BOOL "Only build header test.")
-
-if (${uppercase_project_name}_HEADER_TEST_ONLY)
-    add_subdirectory (header)
-else ()
-    # Fetch data and add the tests.
-    include (data/datasources.cmake)
-    add_subdirectory (api)
-    add_subdirectory (cli)
-    add_subdirectory (coverage)
-endif ()
-
-message (STATUS "${FontBold}You can run `make test` to build and run tests.${FontReset}")

test/api/CMakeLists.txt

-cmake_minimum_required (VERSION 3.8)
-
-add_custom_target (api_test ALL)
-
-macro (add_api_test test_filename)
-    add_app_test (${test_filename})
-
-    seqan3_test_component (target "${test_filename}" TARGET_NAME)
-    add_dependencies (api_test ${target})
-endmacro ()
-
-add_api_test (convert_fastq_test.cpp)
-target_use_datasources (convert_fastq_test FILES in.fastq)

test/api/README.md

-# API Test
-
-Here are test files for API tests, i.e. the internal functions of the app are executed with different input parameters.
-The test then validates whether the functions work correctly.
-Attention: The default `make` target does not build tests.
-Please invoke the build with `make api_test` or use `make test` to build and run all kinds of tests.

test/api/convert_fastq_test.cpp

-#include <gtest/gtest.h>
-
-#include <seqan3/alphabet/nucleotide/dna5.hpp>
-#include <seqan3/core/detail/debug_stream_alphabet.hpp>
-#include <seqan3/io/sequence_file/input.hpp>
-#include <seqan3/test/expect_range_eq.hpp>
-
-#include "fastq_conversion.hpp"
-
-TEST(group1, out_empty)
-{
-    std::string expected{"> seq1\nACGTTTGATTCGCG\n> seq2\nTCGGGGGATTCGCG\n"};
-    testing::internal::CaptureStdout();
-    convert_fastq(DATADIR"in.fastq", "");
-    std::string std_cout = testing::internal::GetCapturedStdout();
-    EXPECT_RANGE_EQ(expected, std_cout);
-}
-
-TEST(group1, out_not_empty)
-{
-    std::filesystem::path tmp_dir = std::filesystem::temp_directory_path(); // get the temp directory
-    convert_fastq(DATADIR"in.fastq", tmp_dir/"out.fasta");                 // create out.fasta
-
-    // Check if out.fasta is correct
-    using seqan3::operator""_dna5;
-    std::vector<seqan3::dna5_vector> expected_seqs = {"ACGTTTGATTCGCG"_dna5, "TCGGGGGATTCGCG"_dna5};
-    std::vector<std::string> expected_ids{"seq1", "seq2"};
-    std::vector<seqan3::dna5_vector> seqs{};
-    std::vector<std::string> ids{};
-    seqan3::sequence_file_input fin{tmp_dir/"out.fasta"};
-
-    for (auto & [seq, id, qual] : fin)
-    {
-        ids.push_back(id);
-        seqs.push_back(seq);
-    }
-    EXPECT_RANGE_EQ(seqs, expected_seqs);
-    EXPECT_RANGE_EQ(ids, expected_ids);
-}

test/benchmark/README.md

-# Benchmarks
-
-Here are test files for benchmarks with respect to time, space consumption and memory.
-They are usually based on the command-line interface, but you can also add micro benchmark if you wish.
-
-The benchmark tests are not yet implemented.

test/cli/CMakeLists.txt

-cmake_minimum_required (VERSION 3.8)

test/cli/README.md

-# CLI Test
-
-Here are test files for command line interface tests, i.e. the app is executed with defined input files and parameters.
-The test then validates whether the output is correct.
-
-Each test fixture should be inherited from the `cli_test` class: It provides the functionality of executing the app,
-finding the input files, capturing the output and creating individual test directories.
-We provide a new test macro `EXPECT_RANGE_EQ` for the comparison of whole ranges.
-It provides more insights about differences than an implementation with `EXPECT_TRUE(std::ranges::equal())`.
-The test output files are stored in the directory `test/output`.
-
-To prevent issues when running multiple CLI tests in parallel, each CLI should use its own derived test fixture.
-For example, if two CLI tests run a test called `my_test` and both use the `cli_test` test fixture, there may
-be issues because both tests will use the same working directory. Instead, define different test fixtures for both
-tests, e.g. `struct my_test_fixture : public cli_test {};`.
-
-Attention: The default `make` target does not build tests.
-Please invoke the build with `make cli_test` or use `make test` to build and run all kinds of tests.

test/cli/cli_test.hpp

-#include <gtest/gtest.h>
-
-#include <cstdlib>               // system calls
-#include <seqan3/std/filesystem> // test directory creation
-#include <sstream>               // ostringstream
-#include <string>                // strings
-
-#pragma once
-
-// Provides functions for CLI test implementation.
-struct cli_test : public ::testing::Test
-{
-private:
-
-    // Holds the original work directory where Gtest has been started.
-    std::filesystem::path original_workdir{};
-
-protected:
-
-    // Result struct for captured streams and exit code.
-    struct cli_test_result
-    {
-        std::string out{};
-        std::string err{};
-        int exit_code{};
-    };
-
-    // Invoke the app execution. The command line call should be given as separate parameters.
-    template <typename... CommandItemTypes>
-    cli_test_result execute_app(CommandItemTypes &&... command_items)
-    {
-        cli_test_result result{};
-
-        // Assemble the command string and disable version check.
-        std::ostringstream command{};
-        command << "SEQAN3_NO_VERSION_CHECK=1 " << BINDIR;
-        int a[] = {0, ((void)(command << command_items << ' '), 0) ... };
-        (void) a;
-
-        // Always capture the output streams.
-        testing::internal::CaptureStdout();
-        testing::internal::CaptureStderr();
-
-        // Run the command and return results.
-        result.exit_code = std::system(command.str().c_str());
-        result.out = testing::internal::GetCapturedStdout();
-        result.err = testing::internal::GetCapturedStderr();
-        return result;
-    }
-
-    // Generate the full path of a test input file that is provided in the data directory.
-    static std::filesystem::path data(std::string const & filename)
-    {
-        return std::filesystem::path{std::string{DATADIR}}.concat(filename);
-    }
-
-    // Create an individual work directory for the current test.
-    void SetUp() override
-    {
-        // Assemble the directory name.
-        ::testing::TestInfo const * const info = ::testing::UnitTest::GetInstance()->current_test_info();
-        std::filesystem::path const test_dir{std::string{OUTPUTDIR} +
-                                             std::string{info->test_case_name()} +
-                                             std::string{"."} +
-                                             std::string{info->name()}};
-        try
-        {
-            std::filesystem::remove_all(test_dir);              // delete the directory if it exists
-            std::filesystem::create_directories(test_dir);      // create the new empty directory
-            original_workdir = std::filesystem::current_path(); // store original work dir path
-            std::filesystem::current_path(test_dir);            // change the work dir
-        }
-        catch (std::exception const & exc)
-        {
-            FAIL() << "Failed to set up the test directory " << test_dir << ":\n" << exc.what();
-        }
-    }
-
-    // Switch back to the initial work directory.
-    void TearDown() override
-    {
-        try
-        {
-            std::filesystem::current_path(original_workdir);    // restore the original work dir
-        }
-        catch (std::exception const & exc)
-        {
-            FAIL() << "Failed to set the work directory to " << original_workdir << ":\n" << exc.what();
-        }
-    }
-};

test/cli/fastq_to_fasta_options_test.cpp

-#include <seqan3/std/ranges>     // range comparisons
-#include <string>                // strings
-#include <vector>                // vectors
-
-#include <seqan3/alphabet/nucleotide/dna5.hpp>
-#include <seqan3/core/detail/debug_stream_alphabet.hpp>
-#include <seqan3/core/detail/debug_stream_tuple.hpp>
-#include <seqan3/core/detail/debug_stream_type.hpp>
-#include <seqan3/io/sequence_file/input.hpp>
-
-// Include the EXPECT_RANGE_EQ macro for better information if range elements differ.
-#include <seqan3/test/expect_range_eq.hpp>
-
-#include "cli_test.hpp"
-
-// To prevent issues when running multiple CLI tests in parallel, give each CLI test unique names:
-struct fastq_to_fasta : public cli_test {};
-
-TEST_F(fastq_to_fasta, no_options)
-{
-    cli_test_result result = execute_app("app-template");
-    std::string expected
-    {
-        "Fastq-to-Fasta-Converter\n"
-        "========================\n"
-        "    Try -h or --help for more information.\n"
-    };
-    EXPECT_EQ(result.exit_code, 0);
-    EXPECT_EQ(result.out, expected);
-    EXPECT_EQ(result.err, std::string{});
-}
-
-TEST_F(fastq_to_fasta, fail_no_argument)
-{
-    cli_test_result result = execute_app("app-template", "-v");
-    std::string expected
-    {
-        "Parsing error. Not enough positional arguments provided (Need at least 1). "
-        "See -h/--help for more information.\n"
-    };
-    EXPECT_NE(result.exit_code, 0);
-    EXPECT_EQ(result.out, std::string{});
-    EXPECT_EQ(result.err, expected);
-}
-
-TEST_F(fastq_to_fasta, with_argument)
-{
-    cli_test_result result = execute_app("app-template", data("in.fastq"));
-    EXPECT_EQ(result.exit_code, 0);
-    EXPECT_EQ(result.out, "> seq1\nACGTTTGATTCGCG\n> seq2\nTCGGGGGATTCGCG\n");
-    EXPECT_EQ(result.err, std::string{});
-}
-
-TEST_F(fastq_to_fasta, with_argument_verbose)
-{
-    cli_test_result result = execute_app("app-template", data("in.fastq"), "-v");
-    EXPECT_EQ(result.exit_code, 0);
-    EXPECT_EQ(result.out, "> seq1\nACGTTTGATTCGCG\n> seq2\nTCGGGGGATTCGCG\n");
-    EXPECT_EQ(result.err, "Conversion was a success. Congrats!\n");
-}
-
-TEST_F(fastq_to_fasta, with_out_file)
-{
-    cli_test_result result = execute_app("app-template", data("in.fastq"), "-o", "out.fasta");
-    seqan3::sequence_file_input fin{"out.fasta", seqan3::fields<seqan3::field::seq, seqan3::field::id>{}};
-
-    // create records to compare
-    using record_type = typename decltype(fin)::record_type;
-    using seqan3::operator""_dna5;
-    std::vector<record_type> records{};
-    records.emplace_back("ACGTTTGATTCGCG"_dna5, std::string{"seq1"});
-    records.emplace_back("TCGGGGGATTCGCG"_dna5, std::string{"seq2"});
-
-    EXPECT_RANGE_EQ(fin, records);
-    EXPECT_EQ(result.exit_code, 0);
-    EXPECT_EQ(result.out, std::string{});
-    EXPECT_EQ(result.err, std::string{});
-}

test/cmake/app_datasources.cmake

-include (ExternalProject)
-
-# Example call:
-#
-# ```cmake
-# declare_datasource (
-#   FILE pdb100d.ent.gz # build/data/pdb100d.ent.gz
-#   URL ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/00/pdb100d.ent.gz # 16KiloByte
-#   URL_HASH SHA256=c2b8f884568b07f58519966e256e2f3aa440508e8013bd10e0ee338e138e62a0)
-# ```
-#
-# Options:
-#
-# declare_datasource (FILE <datasource name> URL <url1> [<url2>...] [URL_HASH <algo>=<hashValue>] [<option>...])
-#
-# FILE <datasource name> (required):
-#    The name of the downloaded file (must be unique across all declared datasources).
-#    This will put the file into the ``<build>/data/<datasource name>`` folder.
-#
-# URL <url1> [<url2>...] (required):
-#    List of paths and/or URL(s) of the external datasource. When more than one URL is given, they are tried in
-#    turn until one succeeds. A URL may be an ordinary path in the local file system (in which case it must be the only
-#    URL provided) or any downloadable URL supported by the file(DOWNLOAD) command. A local filesystem path may refer to
-#    either an existing directory or to an archive file, whereas a URL is expected to point to a file which can be
-#    treated as an archive.
-#
-# URL_HASH <algo>=<hashValue> (optional):
-#    Hash of the archive file to be downloaded. The argument should be of the form <algo>=<hashValue> where algo can be
-#    any of the hashing algorithms supported by the file() command. Specifying this option is strongly recommended for
-#    URL downloads, as it ensures the integrity of the downloaded content. It is also used as a check for a previously
-#    downloaded file, allowing connection to the remote location to be avoided altogether if the local directory already
-#    has a file from an earlier download that matches the specified hash.
-#
-# This uses under the hood ExternalProject's and you can pass any viable option of ExternalProject to this function and
-# overwrite the default behaviour. See https://cmake.org/cmake/help/latest/module/ExternalProject.html for more
-# information.
-function (declare_datasource)
-    set (options "")
-    set (one_value_args FILE URL_HASH)
-    set (multi_value_args URL)
-
-    cmake_parse_arguments (ARG "${options}" "${one_value_args}" "${multi_value_args}" ${ARGN})
-
-    string (TOLOWER "datasource--${ARG_FILE}" datasource_name)
-
-    # create data folder
-    file (MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/data)
-
-    ExternalProject_Add (
-        "${datasource_name}"
-        URL "${ARG_URL}"
-        URL_HASH "${ARG_URL_HASH}"
-        DOWNLOAD_NAME "${ARG_FILE}"
-        CONFIGURE_COMMAND ""
-        BUILD_COMMAND ""
-        INSTALL_COMMAND
-            ${CMAKE_COMMAND} -E create_symlink <DOWNLOADED_FILE> ${CMAKE_CURRENT_BINARY_DIR}/data/${ARG_FILE}
-        TEST_COMMAND ""
-        PREFIX "${CMAKE_CURRENT_BINARY_DIR}/_datasources"
-        DOWNLOAD_NO_EXTRACT TRUE # don't extract archive files like .tar.gz.
-        ${ARG_UNPARSED_ARGUMENTS}
-    )
-endfunction ()
-
-# Example call:
-#
-# ```cmake
-# # my_app uses and needs the files RF00001.fa.gz, pdb100d.ent.gz, and GRCh38_latest_clinvar.vcf.gz.
-# target_use_datasources (my_app FILES RF00001.fa.gz pdb100d.ent.gz GRCh38_latest_clinvar.vcf.gz)
-# ```
-#
-# Options:
-#
-# target_use_datasources (<target> FILES <file1> [<file2>...])
-#
-# It declares that a <target> uses and depends on the following files.
-#
-# This also sets the build requirement that the files must be downloaded before the <target> will be build.
-#
-# The named <target> must have been created by a command such as add_executable() or add_library().
-function (target_use_datasources target)
-    set (options "")
-    set (one_value_args)
-    set (multi_value_args "FILES")
-
-    cmake_parse_arguments (ARG "${options}" "${one_value_args}" "${multi_value_args}" ${ARGN})
-
-    foreach (filename ${ARG_FILES})
-        string (TOLOWER "datasource--${filename}" datasource_name)
-        add_dependencies ("${target}" "${datasource_name}")
-    endforeach ()
-endfunction ()

test/coverage/CMakeLists.txt

-cmake_minimum_required (VERSION 3.8)
-
-# Add a custom build type: Coverage
-
-set (CMAKE_CXX_FLAGS_COVERAGE
-     "${CMAKE_CXX_FLAGS_DEBUG} --coverage -fprofile-arcs -ftest-coverage" CACHE STRING
-     "Flags used by the C++ compiler during coverage builds."
-     FORCE)
-set (CMAKE_C_FLAGS_COVERAGE
-     "${CMAKE_C_FLAGS_DEBUG} --coverage -fprofile-arcs -ftest-coverage" CACHE STRING
-     "Flags used by the C compiler during coverage builds."
-     FORCE)
-set (CMAKE_EXE_LINKER_FLAGS_COVERAGE
-     "${CMAKE_EXE_LINKER_FLAGS_DEBUG} -Wl,-lgcov" CACHE STRING
-     "Flags used for linking binaries during coverage builds."
-     FORCE)
-set (CMAKE_SHARED_LINKER_FLAGS_COVERAGE
-     "${CMAKE_SHARED_LINKER_FLAGS_DEBUG} -Wl,-lgcov" CACHE STRING
-     "Flags used by the shared libraries linker during coverage builds."
-     FORCE)
-
-mark_as_advanced (
-    CMAKE_CXX_FLAGS_COVERAGE
-    CMAKE_C_FLAGS_COVERAGE
-    CMAKE_EXE_LINKER_FLAGS_COVERAGE
-    CMAKE_SHARED_LINKER_FLAGS_COVERAGE)

test/coverage/README.md

-# Coverage Test
-
-This is the test for the code coverage.
-It reaches 100% if each code line is executed at least once through the app tests.
-
-Coverage tests are not yet part of the CMake configuration like it is in SeqAn3.
-However, the CI tests code coverage by running gcov and uploading the results to codecov.
-
-The custom build type `Coverage` can be used to configure the project such that coverage reports are possible.

test/data/README.md

-# Data Directory
-
-Store the data here that should be used as input files for the tests.
-Large files (>50kb) should not be stored here, but rather fetched from a webserver.
-Register each file (from external or internal storage) in the `datasources.cmake` file.

test/data/datasources.cmake

-cmake_minimum_required (VERSION 3.8)
-
-include (cmake/app_datasources.cmake)
-
-# copies file to <build>/data/in.fastq
-declare_datasource (FILE in.fastq
-                    URL ${CMAKE_SOURCE_DIR}/test/data/in.fastq
-                    URL_HASH SHA256=6e30fc35f908a36fe0c68a7a35c47f51f9570da16622fb0c072a20e6a9ba5b3e)

test/data/in.fastq

-@seq1
-ACGTTTGATTCGCG
-+
-!**55CCF>>>>>C
-@seq2
-TCGGGGGATTCGCG
-+
-!**65CCF>CF>>C

test/header/CMakeLists.txt

-cmake_minimum_required (VERSION 3.8)
-
-include (seqan3_test_files)
-include (seqan3_test_component)
-
-add_library ("${PROJECT_NAME}_header_test_lib" INTERFACE)
-target_link_libraries ("${PROJECT_NAME}_header_test_lib" INTERFACE "${PROJECT_NAME}_interface" gtest gtest_main)
-target_include_directories ("${PROJECT_NAME}_header_test_lib" INTERFACE "${SEQAN3_TEST_CLONE_DIR}/googletest/include/")
-# SeqAn3 script adds an include for <bechmark/benchmark.h>
-target_include_directories ("${PROJECT_NAME}_header_test_lib" INTERFACE ./dummy_include)
-set (target "header_test")
-
-set (header_base_path "${CMAKE_CURRENT_LIST_DIR}/../../include/")
-
-file (GLOB_RECURSE header_files RELATIVE "${header_base_path}" "${header_base_path}/*.hpp")
-
-file (WRITE "${PROJECT_BINARY_DIR}/${target}.cpp" "")
-add_executable (${target} ${PROJECT_BINARY_DIR}/${target}.cpp)
-target_link_libraries (${target} ${PROJECT_NAME}_header_test_lib)
-add_test (NAME "header/${target}" COMMAND ${target})
-
-foreach (header ${header_files})
-    seqan3_test_component (header_test_name "${header}" TEST_NAME)
-    seqan3_test_component (header_target_name "${header}" TARGET_UNIQUE_NAME)
-
-    foreach (header_sub_test "header-guard" "no-self-include")
-        set (header_target_source "${PROJECT_BINARY_DIR}/${target}_files/${header_test_name}.hpp-${header_sub_test}.cpp")
-        set (header_target "${target}--${header_target_name}-${header_sub_test}")
-
-        string (REPLACE "-" "__" header_test_name_safe "${target}, ${header_target}")
-
-        # we use add_custom_command to detect changes to a header file, which will update the generated source file
-        add_custom_command (OUTPUT "${header_target_source}"
-                            COMMAND "${CMAKE_COMMAND}"
-                                    "-DHEADER_FILE_ABSOLUTE=${header_base_path}/${header}"
-                                    "-DHEADER_FILE_INCLUDE=${header}"
-                                    "-DHEADER_TARGET_SOURCE=${header_target_source}"
-                                    "-DHEADER_TEST_NAME_SAFE=${header_test_name_safe}"
-                                    "-DHEADER_COMPONENT=${PROJECT_NAME}"
-                                    "-DHEADER_SUB_TEST=${header_sub_test}"
-                                    "-P"
-                                    "${SEQAN3_CLONE_DIR}/test/header/generate_header_source.cmake"
-                            DEPENDS "${header_base_path}/${header}"
-                                    "${SEQAN3_CLONE_DIR}/test/header/generate_header_source.cmake")
-
-        add_library (${header_target} OBJECT "${header_target_source}")
-
-        # NOTE: a simple target_link_libraries (${header_target} ${PROJECT_NAME}_header_test_lib)
-        # is not possible for OBJECT libraries before cmake 3.12
-        if (CMAKE_VERSION VERSION_LESS 3.12)
-            target_compile_options (${header_target} PRIVATE $<TARGET_PROPERTY:${PROJECT_NAME}_header_test_lib,INTERFACE_COMPILE_OPTIONS>)
-            target_compile_definitions (${header_target} PRIVATE $<TARGET_PROPERTY:${PROJECT_NAME}_header_test_lib,INTERFACE_COMPILE_DEFINITIONS>)
-            target_include_directories (${header_target} PRIVATE $<TARGET_PROPERTY:${PROJECT_NAME}_header_test_lib,INTERFACE_INCLUDE_DIRECTORIES>)
-            add_dependencies (${header_target} "${PROJECT_NAME}_interface" gtest gtest_main)
-        else ()
-            target_link_libraries (${header_target} ${PROJECT_NAME}_header_test_lib)
-        endif ()
-
-        target_sources (${target} PRIVATE $<TARGET_OBJECTS:${header_target}>)
-    endforeach ()
-endforeach ()

test/header/dummy_include/benchmark/benchmark.h

-#pragma once