Implement hyperparameters

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "lib/json"]
+	path = lib/json
+	url = https://github.com/nlohmann/json.git

CMakeLists.txt

@@ -1,15 +1,29 @@
-cmake_minimum_required(VERSION 3.5)
+cmake_minimum_required(VERSION 3.20)
-project(PyWrap)
 
+project(PyWrap
+  VERSION 0.1.0
+  DESCRIPTION "Wrap Python classifiers."
+  HOMEPAGE_URL "https://github.com/rmontanana/pywrap"
+  LANGUAGES CXX
+)
+
+# Global CMake variables
+# ----------------------
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}")
 
+# CMakes modules
+# --------------
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules ${CMAKE_MODULE_PATH})
+include(AddGitSubmodule)
+
+# Libraries
+# ---------
 find_package(Python3 3.11...3.11.9 COMPONENTS Interpreter Development REQUIRED)
 find_package(Torch REQUIRED)
 find_package(Boost REQUIRED COMPONENTS python3 numpy3)
 
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}")
-
 # Temporary patch while find_package(Torch) is not fixed
 file(
         GLOB
@@ -19,5 +33,11 @@ file(
 )
 message(STATUS "TORCH Libraries: ${LIBTORCH_PYTHON}")
 
+# External libraries - dependencies of BayesNet
+# ---------------------------------------------
+add_git_submodule("lib/json")
 add_subdirectory(lib/Files)
+
+# Include directories
+# -------------------
 add_subdirectory(src)

Makefile

@@ -4,7 +4,7 @@ SHELL := /bin/bash
 
 f_release = build_release
 f_debug = build_debug
-app_targets = main example
+app_targets = main
 test_targets = unit_tests_bayesnet unit_tests_platform
 n_procs = -j 16
 

cmake/modules/AddGitSubmodule.cmake

@@ -0,0 +1,12 @@
+
+function(add_git_submodule dir)
+  find_package(Git REQUIRED) 
+
+  if(NOT EXISTS ${dir}/CMakeLists.txt)
+    message(STATUS "🚨 Adding git submodule => ${dir}")
+    execute_process(COMMAND ${GIT_EXECUTABLE}
+      submodule update --init --recursive -- ${dir}
+      WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}) 
+  endif()
+  add_subdirectory(${dir})
+endfunction(add_git_submodule)

cmake/modules/CodeCoverage.cmake

@@ -0,0 +1,742 @@
+# Copyright (c) 2012 - 2017, Lars Bilke
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification,
+# are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its contributors
+#    may be used to endorse or promote products derived from this software without
+#    specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# CHANGES:
+#
+# 2012-01-31, Lars Bilke
+# - Enable Code Coverage
+#
+# 2013-09-17, Joakim Söderberg
+# - Added support for Clang.
+# - Some additional usage instructions.
+#
+# 2016-02-03, Lars Bilke
+# - Refactored functions to use named parameters
+#
+# 2017-06-02, Lars Bilke
+# - Merged with modified version from github.com/ufz/ogs
+#
+# 2019-05-06, Anatolii Kurotych
+# - Remove unnecessary --coverage flag
+#
+# 2019-12-13, FeRD (Frank Dana)
+# - Deprecate COVERAGE_LCOVR_EXCLUDES and COVERAGE_GCOVR_EXCLUDES lists in favor
+#   of tool-agnostic COVERAGE_EXCLUDES variable, or EXCLUDE setup arguments.
+# - CMake 3.4+: All excludes can be specified relative to BASE_DIRECTORY
+# - All setup functions: accept BASE_DIRECTORY, EXCLUDE list
+# - Set lcov basedir with -b argument
+# - Add automatic --demangle-cpp in lcovr, if 'c++filt' is available (can be
+#   overridden with NO_DEMANGLE option in setup_target_for_coverage_lcovr().)
+# - Delete output dir, .info file on 'make clean'
+# - Remove Python detection, since version mismatches will break gcovr
+# - Minor cleanup (lowercase function names, update examples...)
+#
+# 2019-12-19, FeRD (Frank Dana)
+# - Rename Lcov outputs, make filtered file canonical, fix cleanup for targets
+#
+# 2020-01-19, Bob Apthorpe
+# - Added gfortran support
+#
+# 2020-02-17, FeRD (Frank Dana)
+# - Make all add_custom_target()s VERBATIM to auto-escape wildcard characters
+#   in EXCLUDEs, and remove manual escaping from gcovr targets
+#
+# 2021-01-19, Robin Mueller
+# - Add CODE_COVERAGE_VERBOSE option which will allow to print out commands which are run
+# - Added the option for users to set the GCOVR_ADDITIONAL_ARGS variable to supply additional
+#   flags to the gcovr command
+#
+# 2020-05-04, Mihchael Davis
+#     - Add -fprofile-abs-path to make gcno files contain absolute paths
+#     - Fix BASE_DIRECTORY not working when defined
+#     - Change BYPRODUCT from folder to index.html to stop ninja from complaining about double defines
+#
+# 2021-05-10, Martin Stump
+#     - Check if the generator is multi-config before warning about non-Debug builds
+#
+# 2022-02-22, Marko Wehle
+#     - Change gcovr output from -o <filename> for --xml <filename> and --html <filename> output respectively.
+#       This will allow for Multiple Output Formats at the same time by making use of GCOVR_ADDITIONAL_ARGS, e.g. GCOVR_ADDITIONAL_ARGS "--txt".
+#
+# 2022-09-28, Sebastian Mueller
+#     - fix append_coverage_compiler_flags_to_target to correctly add flags
+#     - replace "-fprofile-arcs -ftest-coverage" with "--coverage" (equivalent)
+#
+# USAGE:
+#
+# 1. Copy this file into your cmake modules path.
+#
+# 2. Add the following line to your CMakeLists.txt (best inside an if-condition
+#    using a CMake option() to enable it just optionally):
+#      include(CodeCoverage)
+#
+# 3. Append necessary compiler flags for all supported source files:
+#      append_coverage_compiler_flags()
+#    Or for specific target:
+#      append_coverage_compiler_flags_to_target(YOUR_TARGET_NAME)
+#
+# 3.a (OPTIONAL) Set appropriate optimization flags, e.g. -O0, -O1 or -Og
+#
+# 4. If you need to exclude additional directories from the report, specify them
+#    using full paths in the COVERAGE_EXCLUDES variable before calling
+#    setup_target_for_coverage_*().
+#    Example:
+#      set(COVERAGE_EXCLUDES
+#          '${PROJECT_SOURCE_DIR}/src/dir1/*'
+#          '/path/to/my/src/dir2/*')
+#    Or, use the EXCLUDE argument to setup_target_for_coverage_*().
+#    Example:
+#      setup_target_for_coverage_lcov(
+#          NAME coverage
+#          EXECUTABLE testrunner
+#          EXCLUDE "${PROJECT_SOURCE_DIR}/src/dir1/*" "/path/to/my/src/dir2/*")
+#
+# 4.a NOTE: With CMake 3.4+, COVERAGE_EXCLUDES or EXCLUDE can also be set
+#     relative to the BASE_DIRECTORY (default: PROJECT_SOURCE_DIR)
+#     Example:
+#       set(COVERAGE_EXCLUDES "dir1/*")
+#       setup_target_for_coverage_gcovr_html(
+#           NAME coverage
+#           EXECUTABLE testrunner
+#           BASE_DIRECTORY "${PROJECT_SOURCE_DIR}/src"
+#           EXCLUDE "dir2/*")
+#
+# 5. Use the functions described below to create a custom make target which
+#    runs your test executable and produces a code coverage report.
+#
+# 6. Build a Debug build:
+#      cmake -DCMAKE_BUILD_TYPE=Debug ..
+#      make
+#      make my_coverage_target
+#
+
+include(CMakeParseArguments)
+
+option(CODE_COVERAGE_VERBOSE "Verbose information" FALSE)
+
+# Check prereqs
+find_program( GCOV_PATH gcov )
+find_program( LCOV_PATH  NAMES lcov lcov.bat lcov.exe lcov.perl)
+find_program( FASTCOV_PATH NAMES fastcov fastcov.py )
+find_program( GENHTML_PATH NAMES genhtml genhtml.perl genhtml.bat )
+find_program( GCOVR_PATH gcovr PATHS ${CMAKE_SOURCE_DIR}/scripts/test)
+find_program( CPPFILT_PATH NAMES c++filt )
+
+if(NOT GCOV_PATH)
+    message(FATAL_ERROR "gcov not found! Aborting...")
+endif() # NOT GCOV_PATH
+
+# Check supported compiler (Clang, GNU and Flang)
+get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
+foreach(LANG ${LANGUAGES})
+  if("${CMAKE_${LANG}_COMPILER_ID}" MATCHES "(Apple)?[Cc]lang")
+    if("${CMAKE_${LANG}_COMPILER_VERSION}" VERSION_LESS 3)
+      message(FATAL_ERROR "Clang version must be 3.0.0 or greater! Aborting...")
+    endif()
+  elseif(NOT "${CMAKE_${LANG}_COMPILER_ID}" MATCHES "GNU"
+         AND NOT "${CMAKE_${LANG}_COMPILER_ID}" MATCHES "(LLVM)?[Ff]lang")
+    message(FATAL_ERROR "Compiler is not GNU or Flang! Aborting...")
+  endif()
+endforeach()
+
+set(COVERAGE_COMPILER_FLAGS "-g --coverage"
+    CACHE INTERNAL "")
+if(CMAKE_CXX_COMPILER_ID MATCHES "(GNU|Clang)")
+    include(CheckCXXCompilerFlag)
+    check_cxx_compiler_flag(-fprofile-abs-path HAVE_fprofile_abs_path)
+    if(HAVE_fprofile_abs_path)
+        set(COVERAGE_COMPILER_FLAGS "${COVERAGE_COMPILER_FLAGS} -fprofile-abs-path")
+    endif()
+endif()
+
+set(CMAKE_Fortran_FLAGS_COVERAGE
+    ${COVERAGE_COMPILER_FLAGS}
+    CACHE STRING "Flags used by the Fortran compiler during coverage builds."
+    FORCE )
+set(CMAKE_CXX_FLAGS_COVERAGE
+    ${COVERAGE_COMPILER_FLAGS}
+    CACHE STRING "Flags used by the C++ compiler during coverage builds."
+    FORCE )
+set(CMAKE_C_FLAGS_COVERAGE
+    ${COVERAGE_COMPILER_FLAGS}
+    CACHE STRING "Flags used by the C compiler during coverage builds."
+    FORCE )
+set(CMAKE_EXE_LINKER_FLAGS_COVERAGE
+    ""
+    CACHE STRING "Flags used for linking binaries during coverage builds."
+    FORCE )
+set(CMAKE_SHARED_LINKER_FLAGS_COVERAGE
+    ""
+    CACHE STRING "Flags used by the shared libraries linker during coverage builds."
+    FORCE )
+mark_as_advanced(
+    CMAKE_Fortran_FLAGS_COVERAGE
+    CMAKE_CXX_FLAGS_COVERAGE
+    CMAKE_C_FLAGS_COVERAGE
+    CMAKE_EXE_LINKER_FLAGS_COVERAGE
+    CMAKE_SHARED_LINKER_FLAGS_COVERAGE )
+
+get_property(GENERATOR_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
+if(NOT (CMAKE_BUILD_TYPE STREQUAL "Debug" OR GENERATOR_IS_MULTI_CONFIG))
+    message(WARNING "Code coverage results with an optimised (non-Debug) build may be misleading")
+endif() # NOT (CMAKE_BUILD_TYPE STREQUAL "Debug" OR GENERATOR_IS_MULTI_CONFIG)
+
+if(CMAKE_C_COMPILER_ID STREQUAL "GNU" OR CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
+    link_libraries(gcov)
+endif()
+
+# Defines a target for running and collection code coverage information
+# Builds dependencies, runs the given executable and outputs reports.
+# NOTE! The executable should always have a ZERO as exit code otherwise
+# the coverage generation will not complete.
+#
+# setup_target_for_coverage_lcov(
+#     NAME testrunner_coverage                    # New target name
+#     EXECUTABLE testrunner -j ${PROCESSOR_COUNT} # Executable in PROJECT_BINARY_DIR
+#     DEPENDENCIES testrunner                     # Dependencies to build first
+#     BASE_DIRECTORY "../"                        # Base directory for report
+#                                                 #  (defaults to PROJECT_SOURCE_DIR)
+#     EXCLUDE "src/dir1/*" "src/dir2/*"           # Patterns to exclude (can be relative
+#                                                 #  to BASE_DIRECTORY, with CMake 3.4+)
+#     NO_DEMANGLE                                 # Don't demangle C++ symbols
+#                                                 #  even if c++filt is found
+# )
+function(setup_target_for_coverage_lcov)
+
+    set(options NO_DEMANGLE SONARQUBE)
+    set(oneValueArgs BASE_DIRECTORY NAME)
+    set(multiValueArgs EXCLUDE EXECUTABLE EXECUTABLE_ARGS DEPENDENCIES LCOV_ARGS GENHTML_ARGS)
+    cmake_parse_arguments(Coverage "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+    if(NOT LCOV_PATH)
+        message(FATAL_ERROR "lcov not found! Aborting...")
+    endif() # NOT LCOV_PATH
+
+    if(NOT GENHTML_PATH)
+        message(FATAL_ERROR "genhtml not found! Aborting...")
+    endif() # NOT GENHTML_PATH
+
+    # Set base directory (as absolute path), or default to PROJECT_SOURCE_DIR
+    if(DEFINED Coverage_BASE_DIRECTORY)
+        get_filename_component(BASEDIR ${Coverage_BASE_DIRECTORY} ABSOLUTE)
+    else()
+        set(BASEDIR ${PROJECT_SOURCE_DIR})
+    endif()
+
+    # Collect excludes (CMake 3.4+: Also compute absolute paths)
+    set(LCOV_EXCLUDES "")
+    foreach(EXCLUDE ${Coverage_EXCLUDE} ${COVERAGE_EXCLUDES} ${COVERAGE_LCOV_EXCLUDES})
+        if(CMAKE_VERSION VERSION_GREATER 3.4)
+            get_filename_component(EXCLUDE ${EXCLUDE} ABSOLUTE BASE_DIR ${BASEDIR})
+        endif()
+        list(APPEND LCOV_EXCLUDES "${EXCLUDE}")
+    endforeach()
+    list(REMOVE_DUPLICATES LCOV_EXCLUDES)
+
+    # Conditional arguments
+    if(CPPFILT_PATH AND NOT ${Coverage_NO_DEMANGLE})
+      set(GENHTML_EXTRA_ARGS "--demangle-cpp")
+    endif()
+
+    # Setting up commands which will be run to generate coverage data.
+    # Cleanup lcov
+    set(LCOV_CLEAN_CMD
+        ${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} -directory .
+        -b ${BASEDIR} --zerocounters
+    )
+    # Create baseline to make sure untouched files show up in the report
+    set(LCOV_BASELINE_CMD
+        ${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} -c -i -d . -b
+        ${BASEDIR} -o ${Coverage_NAME}.base
+    )
+    # Run tests
+    set(LCOV_EXEC_TESTS_CMD
+        ${Coverage_EXECUTABLE} ${Coverage_EXECUTABLE_ARGS}
+    )
+    # Capturing lcov counters and generating report
+    set(LCOV_CAPTURE_CMD
+        ${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} --directory . -b
+        ${BASEDIR} --capture --output-file ${Coverage_NAME}.capture
+    )
+    # add baseline counters
+    set(LCOV_BASELINE_COUNT_CMD
+        ${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} -a ${Coverage_NAME}.base
+        -a ${Coverage_NAME}.capture --output-file ${Coverage_NAME}.total
+    )
+    # filter collected data to final coverage report
+    set(LCOV_FILTER_CMD
+        ${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} --remove
+        ${Coverage_NAME}.total ${LCOV_EXCLUDES} --output-file ${Coverage_NAME}.info
+    )
+    # Generate HTML output
+    set(LCOV_GEN_HTML_CMD
+        ${GENHTML_PATH} ${GENHTML_EXTRA_ARGS} ${Coverage_GENHTML_ARGS} -o
+        ${Coverage_NAME} ${Coverage_NAME}.info
+    )
+    if(${Coverage_SONARQUBE})
+        # Generate SonarQube output
+        set(GCOVR_XML_CMD
+            ${GCOVR_PATH} --sonarqube ${Coverage_NAME}_sonarqube.xml -r ${BASEDIR} ${GCOVR_ADDITIONAL_ARGS}
+            ${GCOVR_EXCLUDE_ARGS} --object-directory=${PROJECT_BINARY_DIR}
+        )
+        set(GCOVR_XML_CMD_COMMAND
+            COMMAND ${GCOVR_XML_CMD}
+        )
+        set(GCOVR_XML_CMD_BYPRODUCTS ${Coverage_NAME}_sonarqube.xml)
+        set(GCOVR_XML_CMD_COMMENT COMMENT "SonarQube code coverage info report saved in ${Coverage_NAME}_sonarqube.xml.")
+    endif()
+
+
+    if(CODE_COVERAGE_VERBOSE)
+        message(STATUS "Executed command report")
+        message(STATUS "Command to clean up lcov: ")
+        string(REPLACE ";" " " LCOV_CLEAN_CMD_SPACED "${LCOV_CLEAN_CMD}")
+        message(STATUS "${LCOV_CLEAN_CMD_SPACED}")
+
+        message(STATUS "Command to create baseline: ")
+        string(REPLACE ";" " " LCOV_BASELINE_CMD_SPACED "${LCOV_BASELINE_CMD}")
+        message(STATUS "${LCOV_BASELINE_CMD_SPACED}")
+
+        message(STATUS "Command to run the tests: ")
+        string(REPLACE ";" " " LCOV_EXEC_TESTS_CMD_SPACED "${LCOV_EXEC_TESTS_CMD}")
+        message(STATUS "${LCOV_EXEC_TESTS_CMD_SPACED}")
+
+        message(STATUS "Command to capture counters and generate report: ")
+        string(REPLACE ";" " " LCOV_CAPTURE_CMD_SPACED "${LCOV_CAPTURE_CMD}")
+        message(STATUS "${LCOV_CAPTURE_CMD_SPACED}")
+
+        message(STATUS "Command to add baseline counters: ")
+        string(REPLACE ";" " " LCOV_BASELINE_COUNT_CMD_SPACED "${LCOV_BASELINE_COUNT_CMD}")
+        message(STATUS "${LCOV_BASELINE_COUNT_CMD_SPACED}")
+
+        message(STATUS "Command to filter collected data: ")
+        string(REPLACE ";" " " LCOV_FILTER_CMD_SPACED "${LCOV_FILTER_CMD}")
+        message(STATUS "${LCOV_FILTER_CMD_SPACED}")
+
+        message(STATUS "Command to generate lcov HTML output: ")
+        string(REPLACE ";" " " LCOV_GEN_HTML_CMD_SPACED "${LCOV_GEN_HTML_CMD}")
+        message(STATUS "${LCOV_GEN_HTML_CMD_SPACED}")
+
+        if(${Coverage_SONARQUBE})
+            message(STATUS "Command to generate SonarQube XML output: ")
+            string(REPLACE ";" " " GCOVR_XML_CMD_SPACED "${GCOVR_XML_CMD}")
+            message(STATUS "${GCOVR_XML_CMD_SPACED}")
+        endif()
+    endif()
+
+    # Setup target
+    add_custom_target(${Coverage_NAME}
+        COMMAND ${LCOV_CLEAN_CMD}
+        COMMAND ${LCOV_BASELINE_CMD}
+        COMMAND ${LCOV_EXEC_TESTS_CMD}
+        COMMAND ${LCOV_CAPTURE_CMD}
+        COMMAND ${LCOV_BASELINE_COUNT_CMD}
+        COMMAND ${LCOV_FILTER_CMD}
+        COMMAND ${LCOV_GEN_HTML_CMD}
+        ${GCOVR_XML_CMD_COMMAND}
+
+        # Set output files as GENERATED (will be removed on 'make clean')
+        BYPRODUCTS
+            ${Coverage_NAME}.base
+            ${Coverage_NAME}.capture
+            ${Coverage_NAME}.total
+            ${Coverage_NAME}.info
+            ${GCOVR_XML_CMD_BYPRODUCTS}
+            ${Coverage_NAME}/index.html
+        WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+        DEPENDS ${Coverage_DEPENDENCIES}
+        VERBATIM # Protect arguments to commands
+        COMMENT "Resetting code coverage counters to zero.\nProcessing code coverage counters and generating report."
+    )
+
+    # Show where to find the lcov info report
+    add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
+        COMMAND ;
+        COMMENT "Lcov code coverage info report saved in ${Coverage_NAME}.info."
+        ${GCOVR_XML_CMD_COMMENT}
+    )
+
+    # Show info where to find the report
+    add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
+        COMMAND ;
+        COMMENT "Open ./${Coverage_NAME}/index.html in your browser to view the coverage report."
+    )
+
+endfunction() # setup_target_for_coverage_lcov
+
+# Defines a target for running and collection code coverage information
+# Builds dependencies, runs the given executable and outputs reports.
+# NOTE! The executable should always have a ZERO as exit code otherwise
+# the coverage generation will not complete.
+#
+# setup_target_for_coverage_gcovr_xml(
+#     NAME ctest_coverage                    # New target name
+#     EXECUTABLE ctest -j ${PROCESSOR_COUNT} # Executable in PROJECT_BINARY_DIR
+#     DEPENDENCIES executable_target         # Dependencies to build first
+#     BASE_DIRECTORY "../"                   # Base directory for report
+#                                            #  (defaults to PROJECT_SOURCE_DIR)
+#     EXCLUDE "src/dir1/*" "src/dir2/*"      # Patterns to exclude (can be relative
+#                                            #  to BASE_DIRECTORY, with CMake 3.4+)
+# )
+# The user can set the variable GCOVR_ADDITIONAL_ARGS to supply additional flags to the
+# GCVOR command.
+function(setup_target_for_coverage_gcovr_xml)
+
+    set(options NONE)
+    set(oneValueArgs BASE_DIRECTORY NAME)
+    set(multiValueArgs EXCLUDE EXECUTABLE EXECUTABLE_ARGS DEPENDENCIES)
+    cmake_parse_arguments(Coverage "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+    if(NOT GCOVR_PATH)
+        message(FATAL_ERROR "gcovr not found! Aborting...")
+    endif() # NOT GCOVR_PATH
+
+    # Set base directory (as absolute path), or default to PROJECT_SOURCE_DIR
+    if(DEFINED Coverage_BASE_DIRECTORY)
+        get_filename_component(BASEDIR ${Coverage_BASE_DIRECTORY} ABSOLUTE)
+    else()
+        set(BASEDIR ${PROJECT_SOURCE_DIR})
+    endif()
+
+    # Collect excludes (CMake 3.4+: Also compute absolute paths)
+    set(GCOVR_EXCLUDES "")
+    foreach(EXCLUDE ${Coverage_EXCLUDE} ${COVERAGE_EXCLUDES} ${COVERAGE_GCOVR_EXCLUDES})
+        if(CMAKE_VERSION VERSION_GREATER 3.4)
+            get_filename_component(EXCLUDE ${EXCLUDE} ABSOLUTE BASE_DIR ${BASEDIR})
+        endif()
+        list(APPEND GCOVR_EXCLUDES "${EXCLUDE}")
+    endforeach()
+    list(REMOVE_DUPLICATES GCOVR_EXCLUDES)
+
+    # Combine excludes to several -e arguments
+    set(GCOVR_EXCLUDE_ARGS "")
+    foreach(EXCLUDE ${GCOVR_EXCLUDES})
+        list(APPEND GCOVR_EXCLUDE_ARGS "-e")
+        list(APPEND GCOVR_EXCLUDE_ARGS "${EXCLUDE}")
+    endforeach()
+
+    # Set up commands which will be run to generate coverage data
+    # Run tests
+    set(GCOVR_XML_EXEC_TESTS_CMD
+        ${Coverage_EXECUTABLE} ${Coverage_EXECUTABLE_ARGS}
+    )
+    # Running gcovr
+    set(GCOVR_XML_CMD
+        ${GCOVR_PATH} --xml ${Coverage_NAME}.xml -r ${BASEDIR} ${GCOVR_ADDITIONAL_ARGS}
+        ${GCOVR_EXCLUDE_ARGS} --object-directory=${PROJECT_BINARY_DIR}
+    )
+
+    if(CODE_COVERAGE_VERBOSE)
+        message(STATUS "Executed command report")
+
+        message(STATUS "Command to run tests: ")
+        string(REPLACE ";" " " GCOVR_XML_EXEC_TESTS_CMD_SPACED "${GCOVR_XML_EXEC_TESTS_CMD}")
+        message(STATUS "${GCOVR_XML_EXEC_TESTS_CMD_SPACED}")
+
+        message(STATUS "Command to generate gcovr XML coverage data: ")
+        string(REPLACE ";" " " GCOVR_XML_CMD_SPACED "${GCOVR_XML_CMD}")
+        message(STATUS "${GCOVR_XML_CMD_SPACED}")
+    endif()
+
+    add_custom_target(${Coverage_NAME}
+        COMMAND ${GCOVR_XML_EXEC_TESTS_CMD}
+        COMMAND ${GCOVR_XML_CMD}
+
+        BYPRODUCTS ${Coverage_NAME}.xml
+        WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+        DEPENDS ${Coverage_DEPENDENCIES}
+        VERBATIM # Protect arguments to commands
+        COMMENT "Running gcovr to produce Cobertura code coverage report."
+    )
+
+    # Show info where to find the report
+    add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
+        COMMAND ;
+        COMMENT "Cobertura code coverage report saved in ${Coverage_NAME}.xml."
+    )
+endfunction() # setup_target_for_coverage_gcovr_xml
+
+# Defines a target for running and collection code coverage information
+# Builds dependencies, runs the given executable and outputs reports.
+# NOTE! The executable should always have a ZERO as exit code otherwise
+# the coverage generation will not complete.
+#
+# setup_target_for_coverage_gcovr_html(
+#     NAME ctest_coverage                    # New target name
+#     EXECUTABLE ctest -j ${PROCESSOR_COUNT} # Executable in PROJECT_BINARY_DIR
+#     DEPENDENCIES executable_target         # Dependencies to build first
+#     BASE_DIRECTORY "../"                   # Base directory for report
+#                                            #  (defaults to PROJECT_SOURCE_DIR)
+#     EXCLUDE "src/dir1/*" "src/dir2/*"      # Patterns to exclude (can be relative
+#                                            #  to BASE_DIRECTORY, with CMake 3.4+)
+# )
+# The user can set the variable GCOVR_ADDITIONAL_ARGS to supply additional flags to the
+# GCVOR command.
+function(setup_target_for_coverage_gcovr_html)
+
+    set(options NONE)
+    set(oneValueArgs BASE_DIRECTORY NAME)
+    set(multiValueArgs EXCLUDE EXECUTABLE EXECUTABLE_ARGS DEPENDENCIES)
+    cmake_parse_arguments(Coverage "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+    if(NOT GCOVR_PATH)
+        message(FATAL_ERROR "gcovr not found! Aborting...")
+    endif() # NOT GCOVR_PATH
+
+    # Set base directory (as absolute path), or default to PROJECT_SOURCE_DIR
+    if(DEFINED Coverage_BASE_DIRECTORY)
+        get_filename_component(BASEDIR ${Coverage_BASE_DIRECTORY} ABSOLUTE)
+    else()
+        set(BASEDIR ${PROJECT_SOURCE_DIR})
+    endif()
+
+    # Collect excludes (CMake 3.4+: Also compute absolute paths)
+    set(GCOVR_EXCLUDES "")
+    foreach(EXCLUDE ${Coverage_EXCLUDE} ${COVERAGE_EXCLUDES} ${COVERAGE_GCOVR_EXCLUDES})
+        if(CMAKE_VERSION VERSION_GREATER 3.4)
+            get_filename_component(EXCLUDE ${EXCLUDE} ABSOLUTE BASE_DIR ${BASEDIR})
+        endif()
+        list(APPEND GCOVR_EXCLUDES "${EXCLUDE}")
+    endforeach()
+    list(REMOVE_DUPLICATES GCOVR_EXCLUDES)
+
+    # Combine excludes to several -e arguments
+    set(GCOVR_EXCLUDE_ARGS "")
+    foreach(EXCLUDE ${GCOVR_EXCLUDES})
+        list(APPEND GCOVR_EXCLUDE_ARGS "-e")
+        list(APPEND GCOVR_EXCLUDE_ARGS "${EXCLUDE}")
+    endforeach()
+
+    # Set up commands which will be run to generate coverage data
+    # Run tests
+    set(GCOVR_HTML_EXEC_TESTS_CMD
+        ${Coverage_EXECUTABLE} ${Coverage_EXECUTABLE_ARGS}
+    )
+    # Create folder
+    set(GCOVR_HTML_FOLDER_CMD
+        ${CMAKE_COMMAND} -E make_directory ${PROJECT_BINARY_DIR}/${Coverage_NAME}
+    )
+    # Running gcovr
+    set(GCOVR_HTML_CMD
+        ${GCOVR_PATH} --html ${Coverage_NAME}/index.html --html-details -r ${BASEDIR} ${GCOVR_ADDITIONAL_ARGS}
+        ${GCOVR_EXCLUDE_ARGS} --object-directory=${PROJECT_BINARY_DIR}
+    )
+
+    if(CODE_COVERAGE_VERBOSE)
+        message(STATUS "Executed command report")
+
+        message(STATUS "Command to run tests: ")
+        string(REPLACE ";" " " GCOVR_HTML_EXEC_TESTS_CMD_SPACED "${GCOVR_HTML_EXEC_TESTS_CMD}")
+        message(STATUS "${GCOVR_HTML_EXEC_TESTS_CMD_SPACED}")
+
+        message(STATUS "Command to create a folder: ")
+        string(REPLACE ";" " " GCOVR_HTML_FOLDER_CMD_SPACED "${GCOVR_HTML_FOLDER_CMD}")
+        message(STATUS "${GCOVR_HTML_FOLDER_CMD_SPACED}")
+
+        message(STATUS "Command to generate gcovr HTML coverage data: ")
+        string(REPLACE ";" " " GCOVR_HTML_CMD_SPACED "${GCOVR_HTML_CMD}")
+        message(STATUS "${GCOVR_HTML_CMD_SPACED}")
+    endif()
+
+    add_custom_target(${Coverage_NAME}
+        COMMAND ${GCOVR_HTML_EXEC_TESTS_CMD}
+        COMMAND ${GCOVR_HTML_FOLDER_CMD}
+        COMMAND ${GCOVR_HTML_CMD}
+
+        BYPRODUCTS ${PROJECT_BINARY_DIR}/${Coverage_NAME}/index.html  # report directory
+        WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+        DEPENDS ${Coverage_DEPENDENCIES}
+        VERBATIM # Protect arguments to commands
+        COMMENT "Running gcovr to produce HTML code coverage report."
+    )
+
+    # Show info where to find the report
+    add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
+        COMMAND ;
+        COMMENT "Open ./${Coverage_NAME}/index.html in your browser to view the coverage report."
+    )
+
+endfunction() # setup_target_for_coverage_gcovr_html
+
+# Defines a target for running and collection code coverage information
+# Builds dependencies, runs the given executable and outputs reports.
+# NOTE! The executable should always have a ZERO as exit code otherwise
+# the coverage generation will not complete.
+#
+# setup_target_for_coverage_fastcov(
+#     NAME testrunner_coverage                    # New target name
+#     EXECUTABLE testrunner -j ${PROCESSOR_COUNT} # Executable in PROJECT_BINARY_DIR
+#     DEPENDENCIES testrunner                     # Dependencies to build first
+#     BASE_DIRECTORY "../"                        # Base directory for report
+#                                                 #  (defaults to PROJECT_SOURCE_DIR)
+#     EXCLUDE "src/dir1/" "src/dir2/"             # Patterns to exclude.
+#     NO_DEMANGLE                                 # Don't demangle C++ symbols
+#                                                 #  even if c++filt is found
+#     SKIP_HTML                                   # Don't create html report
+#     POST_CMD perl -i -pe s!${PROJECT_SOURCE_DIR}/!!g ctest_coverage.json  # E.g. for stripping source dir from file paths
+# )
+function(setup_target_for_coverage_fastcov)
+
+    set(options NO_DEMANGLE SKIP_HTML)
+    set(oneValueArgs BASE_DIRECTORY NAME)
+    set(multiValueArgs EXCLUDE EXECUTABLE EXECUTABLE_ARGS DEPENDENCIES FASTCOV_ARGS GENHTML_ARGS POST_CMD)
+    cmake_parse_arguments(Coverage "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+    if(NOT FASTCOV_PATH)
+        message(FATAL_ERROR "fastcov not found! Aborting...")
+    endif()
+
+    if(NOT Coverage_SKIP_HTML AND NOT GENHTML_PATH)
+        message(FATAL_ERROR "genhtml not found! Aborting...")
+    endif()
+
+    # Set base directory (as absolute path), or default to PROJECT_SOURCE_DIR
+    if(Coverage_BASE_DIRECTORY)
+        get_filename_component(BASEDIR ${Coverage_BASE_DIRECTORY} ABSOLUTE)
+    else()
+        set(BASEDIR ${PROJECT_SOURCE_DIR})
+    endif()
+
+    # Collect excludes (Patterns, not paths, for fastcov)
+    set(FASTCOV_EXCLUDES "")
+    foreach(EXCLUDE ${Coverage_EXCLUDE} ${COVERAGE_EXCLUDES} ${COVERAGE_FASTCOV_EXCLUDES})
+        list(APPEND FASTCOV_EXCLUDES "${EXCLUDE}")
+    endforeach()
+    list(REMOVE_DUPLICATES FASTCOV_EXCLUDES)
+
+    # Conditional arguments
+    if(CPPFILT_PATH AND NOT ${Coverage_NO_DEMANGLE})
+        set(GENHTML_EXTRA_ARGS "--demangle-cpp")
+    endif()
+
+    # Set up commands which will be run to generate coverage data
+    set(FASTCOV_EXEC_TESTS_CMD ${Coverage_EXECUTABLE} ${Coverage_EXECUTABLE_ARGS})
+
+    set(FASTCOV_CAPTURE_CMD ${FASTCOV_PATH} ${Coverage_FASTCOV_ARGS} --gcov ${GCOV_PATH}
+        --search-directory ${BASEDIR}
+        --process-gcno
+        --output ${Coverage_NAME}.json
+        --exclude ${FASTCOV_EXCLUDES}
+    )
+
+    set(FASTCOV_CONVERT_CMD ${FASTCOV_PATH}
+        -C ${Coverage_NAME}.json --lcov --output ${Coverage_NAME}.info
+    )
+
+    if(Coverage_SKIP_HTML)
+        set(FASTCOV_HTML_CMD ";")
+    else()
+        set(FASTCOV_HTML_CMD ${GENHTML_PATH} ${GENHTML_EXTRA_ARGS} ${Coverage_GENHTML_ARGS}
+            -o ${Coverage_NAME} ${Coverage_NAME}.info
+        )
+    endif()
+
+    set(FASTCOV_POST_CMD ";")
+    if(Coverage_POST_CMD)
+        set(FASTCOV_POST_CMD ${Coverage_POST_CMD})
+    endif()
+
+    if(CODE_COVERAGE_VERBOSE)
+        message(STATUS "Code coverage commands for target ${Coverage_NAME} (fastcov):")
+
+        message("   Running tests:")
+        string(REPLACE ";" " " FASTCOV_EXEC_TESTS_CMD_SPACED "${FASTCOV_EXEC_TESTS_CMD}")
+        message("     ${FASTCOV_EXEC_TESTS_CMD_SPACED}")
+
+        message("   Capturing fastcov counters and generating report:")
+        string(REPLACE ";" " " FASTCOV_CAPTURE_CMD_SPACED "${FASTCOV_CAPTURE_CMD}")
+        message("     ${FASTCOV_CAPTURE_CMD_SPACED}")
+
+        message("   Converting fastcov .json to lcov .info:")
+        string(REPLACE ";" " " FASTCOV_CONVERT_CMD_SPACED "${FASTCOV_CONVERT_CMD}")
+        message("     ${FASTCOV_CONVERT_CMD_SPACED}")
+
+        if(NOT Coverage_SKIP_HTML)
+            message("   Generating HTML report: ")
+            string(REPLACE ";" " " FASTCOV_HTML_CMD_SPACED "${FASTCOV_HTML_CMD}")
+            message("     ${FASTCOV_HTML_CMD_SPACED}")
+        endif()
+        if(Coverage_POST_CMD)
+            message("   Running post command: ")
+            string(REPLACE ";" " " FASTCOV_POST_CMD_SPACED "${FASTCOV_POST_CMD}")
+            message("     ${FASTCOV_POST_CMD_SPACED}")
+        endif()
+    endif()
+
+    # Setup target
+    add_custom_target(${Coverage_NAME}
+
+        # Cleanup fastcov
+        COMMAND ${FASTCOV_PATH} ${Coverage_FASTCOV_ARGS} --gcov ${GCOV_PATH}
+            --search-directory ${BASEDIR}
+            --zerocounters
+
+        COMMAND ${FASTCOV_EXEC_TESTS_CMD}
+        COMMAND ${FASTCOV_CAPTURE_CMD}
+        COMMAND ${FASTCOV_CONVERT_CMD}
+        COMMAND ${FASTCOV_HTML_CMD}
+        COMMAND ${FASTCOV_POST_CMD}
+
+        # Set output files as GENERATED (will be removed on 'make clean')
+        BYPRODUCTS
+             ${Coverage_NAME}.info
+             ${Coverage_NAME}.json
+             ${Coverage_NAME}/index.html  # report directory
+
+        WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+        DEPENDS ${Coverage_DEPENDENCIES}
+        VERBATIM # Protect arguments to commands
+        COMMENT "Resetting code coverage counters to zero. Processing code coverage counters and generating report."
+    )
+
+    set(INFO_MSG "fastcov code coverage info report saved in ${Coverage_NAME}.info and ${Coverage_NAME}.json.")
+    if(NOT Coverage_SKIP_HTML)
+        string(APPEND INFO_MSG " Open ${PROJECT_BINARY_DIR}/${Coverage_NAME}/index.html in your browser to view the coverage report.")
+    endif()
+    # Show where to find the fastcov info report
+    add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
+        COMMAND ${CMAKE_COMMAND} -E echo ${INFO_MSG}
+    )
+
+endfunction() # setup_target_for_coverage_fastcov
+
+function(append_coverage_compiler_flags)
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${COVERAGE_COMPILER_FLAGS}" PARENT_SCOPE)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${COVERAGE_COMPILER_FLAGS}" PARENT_SCOPE)
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${COVERAGE_COMPILER_FLAGS}" PARENT_SCOPE)
+    message(STATUS "Appending code coverage compiler flags: ${COVERAGE_COMPILER_FLAGS}")
+endfunction() # append_coverage_compiler_flags
+
+# Setup coverage for specific library
+function(append_coverage_compiler_flags_to_target name)
+    separate_arguments(_flag_list NATIVE_COMMAND "${COVERAGE_COMPILER_FLAGS}")
+    target_compile_options(${name} PRIVATE ${_flag_list})
+    if(CMAKE_C_COMPILER_ID STREQUAL "GNU" OR CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
+        target_link_libraries(${name} PRIVATE gcov)
+    endif()
+endfunction()

cmake/modules/StaticAnalyzers.cmake

@@ -0,0 +1,22 @@
+if(ENABLE_CLANG_TIDY)
+    find_program(CLANG_TIDY_COMMAND NAMES clang-tidy)
+
+    if(NOT CLANG_TIDY_COMMAND)
+        message(WARNING "🔴 CMake_RUN_CLANG_TIDY is ON but clang-tidy is not found!")
+        set(CMAKE_CXX_CLANG_TIDY "" CACHE STRING "" FORCE)
+    else()
+    
+        message(STATUS "🟢 CMake_RUN_CLANG_TIDY is ON")
+        set(CLANGTIDY_EXTRA_ARGS
+            "-extra-arg=-Wno-unknown-warning-option"
+        )
+        set(CMAKE_CXX_CLANG_TIDY "${CLANG_TIDY_COMMAND};-p=${CMAKE_BINARY_DIR};${CLANGTIDY_EXTRA_ARGS}" CACHE STRING "" FORCE)
+
+        add_custom_target(clang-tidy
+            COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target ${CMAKE_PROJECT_NAME}
+            COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target clang-tidy
+            COMMENT "Running clang-tidy..."
+        )
+       set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+    endif()
+endif(ENABLE_CLANG_TIDY)

lib/Files/ArffFiles.cc

@@ -4,11 +4,9 @@
 #include <map>
 #include <iostream>
 
-using namespace std;
-
 ArffFiles::ArffFiles() = default;
 
-vector<string> ArffFiles::getLines() const
+std::vector<std::string> ArffFiles::getLines() const
 {
     return lines;
 }
@@ -18,48 +16,48 @@ unsigned long int ArffFiles::getSize() const
     return lines.size();
 }
 
-vector<pair<string, string>> ArffFiles::getAttributes() const
+std::vector<std::pair<std::string, std::string>> ArffFiles::getAttributes() const
 {
     return attributes;
 }
 
-string ArffFiles::getClassName() const
+std::string ArffFiles::getClassName() const
 {
     return className;
 }
 
-string ArffFiles::getClassType() const
+std::string ArffFiles::getClassType() const
 {
     return classType;
 }
 
-vector<vector<float>>& ArffFiles::getX()
+std::vector<std::vector<float>>& ArffFiles::getX()
 {
     return X;
 }
 
-vector<int>& ArffFiles::getY()
+std::vector<int>& ArffFiles::getY()
 {
     return y;
 }
 
-void ArffFiles::loadCommon(string fileName)
+void ArffFiles::loadCommon(std::string fileName)
 {
-    ifstream file(fileName);
+    std::ifstream file(fileName);
     if (!file.is_open()) {
-        throw invalid_argument("Unable to open file");
+        throw std::invalid_argument("Unable to open file");
     }
-    string line;
+    std::string line;
-    string keyword;
+    std::string keyword;
-    string attribute;
+    std::string attribute;
-    string type;
+    std::string type;
-    string type_w;
+    std::string type_w;
     while (getline(file, line)) {
         if (line.empty() || line[0] == '%' || line == "\r" || line == " ") {
             continue;
         }
-        if (line.find("@attribute") != string::npos || line.find("@ATTRIBUTE") != string::npos) {
+        if (line.find("@attribute") != std::string::npos || line.find("@ATTRIBUTE") != std::string::npos) {
-            stringstream ss(line);
+            std::stringstream ss(line);
             ss >> keyword >> attribute;
             type = "";
             while (ss >> type_w)
@@ -74,35 +72,35 @@ void ArffFiles::loadCommon(string fileName)
     }
     file.close();
     if (attributes.empty())
-        throw invalid_argument("No attributes found");
+        throw std::invalid_argument("No attributes found");
 }
 
-void ArffFiles::load(const string& fileName, bool classLast)
+void ArffFiles::load(const std::string& fileName, bool classLast)
 {
     int labelIndex;
     loadCommon(fileName);
     if (classLast) {
-        className = get<0>(attributes.back());
+        className = std::get<0>(attributes.back());
-        classType = get<1>(attributes.back());
+        classType = std::get<1>(attributes.back());
         attributes.pop_back();
         labelIndex = static_cast<int>(attributes.size());
     } else {
-        className = get<0>(attributes.front());
+        className = std::get<0>(attributes.front());
-        classType = get<1>(attributes.front());
+        classType = std::get<1>(attributes.front());
         attributes.erase(attributes.begin());
         labelIndex = 0;
     }
     generateDataset(labelIndex);
 }
-void ArffFiles::load(const string& fileName, const string& name)
+void ArffFiles::load(const std::string& fileName, const std::string& name)
 {
     int labelIndex;
     loadCommon(fileName);
     bool found = false;
     for (int i = 0; i < attributes.size(); ++i) {
         if (attributes[i].first == name) {
-            className = get<0>(attributes[i]);
+            className = std::get<0>(attributes[i]);
-            classType = get<1>(attributes[i]);
+            classType = std::get<1>(attributes[i]);
             attributes.erase(attributes.begin() + i);
             labelIndex = i;
             found = true;
@@ -110,19 +108,19 @@ void ArffFiles::load(const string& fileName, const string& name)
         }
     }
     if (!found) {
-        throw invalid_argument("Class name not found");
+        throw std::invalid_argument("Class name not found");
     }
     generateDataset(labelIndex);
 }
 
 void ArffFiles::generateDataset(int labelIndex)
 {
-    X = vector<vector<float>>(attributes.size(), vector<float>(lines.size()));
+    X = std::vector<std::vector<float>>(attributes.size(), std::vector<float>(lines.size()));
-    auto yy = vector<string>(lines.size(), "");
+    auto yy = std::vector<std::string>(lines.size(), "");
-    auto removeLines = vector<int>(); // Lines with missing values
+    auto removeLines = std::vector<int>(); // Lines with missing values
     for (size_t i = 0; i < lines.size(); i++) {
-        stringstream ss(lines[i]);
+        std::stringstream ss(lines[i]);
-        string value;
+        std::string value;
         int pos = 0;
         int xIndex = 0;
         while (getline(ss, value, ',')) {
@@ -146,21 +144,21 @@ void ArffFiles::generateDataset(int labelIndex)
     y = factorize(yy);
 }
 
-string ArffFiles::trim(const string& source)
+std::string ArffFiles::trim(const std::string& source)
 {
-    string s(source);
+    std::string s(source);
     s.erase(0, s.find_first_not_of(" '\n\r\t"));
     s.erase(s.find_last_not_of(" '\n\r\t") + 1);
     return s;
 }
 
-vector<int> ArffFiles::factorize(const vector<string>& labels_t)
+std::vector<int> ArffFiles::factorize(const std::vector<std::string>& labels_t)
 {
-    vector<int> yy;
+    std::vector<int> yy;
     yy.reserve(labels_t.size());
-    map<string, int> labelMap;
+    std::map<std::string, int> labelMap;
     int i = 0;
-    for (const string& label : labels_t) {
+    for (const std::string& label : labels_t) {
         if (labelMap.find(label) == labelMap.end()) {
             labelMap[label] = i++;
         }

lib/Files/ArffFiles.h

@@ -4,31 +4,29 @@
 #include <string>
 #include <vector>
 
-using namespace std;
-
 class ArffFiles {
 private:
-    vector<string> lines;
+    std::vector<std::string> lines;
-    vector<pair<string, string>> attributes;
+    std::vector<std::pair<std::string, std::string>> attributes;
-    string className;
+    std::string className;
-    string classType;
+    std::string classType;
-    vector<vector<float>> X;
+    std::vector<std::vector<float>> X;
-    vector<int> y;
+    std::vector<int> y;
     void generateDataset(int);
-    void loadCommon(string);
+    void loadCommon(std::string);
 public:
     ArffFiles();
-    void load(const string&, bool = true);
+    void load(const std::string&, bool = true);
-    void load(const string&, const string&);
+    void load(const std::string&, const std::string&);
-    vector<string> getLines() const;
+    std::vector<std::string> getLines() const;
     unsigned long int getSize() const;
-    string getClassName() const;
+    std::string getClassName() const;
-    string getClassType() const;
+    std::string getClassType() const;
-    static string trim(const string&);
+    static std::string trim(const std::string&);
-    vector<vector<float>>& getX();
+    std::vector<std::vector<float>>& getX();
-    vector<int>& getY();
+    std::vector<int>& getY();
-    vector<pair<string, string>> getAttributes() const;
+    std::vector<std::pair<std::string, std::string>> getAttributes() const;
-    static vector<int> factorize(const vector<string>& labels_t);
+    static std::vector<int> factorize(const std::vector<std::string>& labels_t);
 };
 
 #endif

src/CMakeLists.txt

@@ -1,9 +1,8 @@
 include_directories(${PyWrap_SOURCE_DIR}/lib/Files)
+include_directories(${PyWrap_SOURCE_DIR}/lib/json/include)
 include_directories(${Python3_INCLUDE_DIRS})
 include_directories(${TORCH_INCLUDE_DIRS})
 
 add_executable(main main.cc STree.cc SVC.cc RandomForest.cc PyClassifier.cc PyWrap.cc)
-add_executable(example example.cpp PyWrap.cc)
 
 target_link_libraries(main ${Python3_LIBRARIES} "${TORCH_LIBRARIES}" ${LIBTORCH_PYTHON} Boost::boost Boost::python Boost::numpy ArffFiles)
-target_link_libraries(example ${Python3_LIBRARIES} "${TORCH_LIBRARIES}" ${LIBTORCH_PYTHON} Boost::boost Boost::python Boost::numpy ArffFiles)

src/Classifier.h

@@ -0,0 +1,13 @@
+#ifndef CLASSIFER_H
+#define CLASSIFER_H
+#include <nlohmann/json.hpp>
+
+namespace pywrap {
+    class Classifier {
+    public:
+        Classifier() = default;
+        virtual ~Classifier() = default;
+        virtual void setHyperparameters(const nlohmann::json& hyperparameters) = 0;
+    };
+} /* namespace pywrap */
+#endif /* CLASSIFER_H */

src/PyClassifier.cc

@@ -1,9 +1,10 @@
 #include "PyClassifier.h"
+#include <iostream>
 
 namespace pywrap {
     namespace bp = boost::python;
     namespace np = boost::python::numpy;
-    PyClassifier::PyClassifier(const std::string& module, const std::string& className) : module(module), className(className)
+    PyClassifier::PyClassifier(const std::string& module, const std::string& className) : module(module), className(className), fitted(false)
     {
         pyWrap = PyWrap::GetInstance();
         pyWrap->importClass(module, className);
@@ -36,10 +37,14 @@ namespace pywrap {
     }
     PyClassifier& PyClassifier::fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states)
     {
+        if (!fitted && hyperparameters.size() > 0) {
+            std::cout << "Setting hyperparameters" << std::endl;
+        }
         auto [Xn, yn] = tensors2numpy(X, y);
         CPyObject Xp = bp::incref(bp::object(Xn).ptr());
         CPyObject yp = bp::incref(bp::object(yn).ptr());
         pyWrap->fit(module, this->className, Xp, yp);
+        fitted = true;
         return *this;
     }
     torch::Tensor PyClassifier::predict(torch::Tensor& X)
@@ -69,4 +74,19 @@ namespace pywrap {
         auto result = pyWrap->score(module, className, Xp, yp);
         return result;
     }
+    void PyClassifier::setHyperparameters(const nlohmann::json& hyperparameters)
+    {
+        // Check if hyperparameters are valid, default is no hyperparameters
+        const std::vector<std::string> validKeys = { };
+        checkHyperparameters(validKeys, hyperparameters);
+        this->hyperparameters = hyperparameters;
+    }
+    void PyClassifier::checkHyperparameters(const std::vector<std::string>& validKeys, const nlohmann::json& hyperparameters)
+    {
+        for (const auto& item : hyperparameters.items()) {
+            if (find(validKeys.begin(), validKeys.end(), item.key()) == validKeys.end()) {
+                throw std::invalid_argument("Hyperparameter " + item.key() + " is not valid");
+            }
+        }
+    }
 } /* namespace pywrap */

src/PyClassifier.h

@@ -2,15 +2,17 @@
 #define PYCLASSIFER_H
 #include "boost/python/detail/wrap_python.hpp"
 #include <boost/python/numpy.hpp>
+#include <nlohmann/json.hpp>
 #include <string>
 #include <map>
 #include <vector>
 #include <utility>
 #include <torch/torch.h>
 #include "PyWrap.h"
+#include "Classifier.h"
 
 namespace pywrap {
-    class PyClassifier {
+    class PyClassifier : public Classifier {
     public:
         PyClassifier(const std::string& module, const std::string& className);
         virtual ~PyClassifier();
@@ -19,11 +21,15 @@ namespace pywrap {
         double score(torch::Tensor& X, torch::Tensor& y);
         std::string version();
         std::string callMethodString(const std::string& method);
+        void setHyperparameters(const nlohmann::json& hyperparameters) override;
+    protected:
+        void checkHyperparameters(const std::vector<std::string>& validKeys, const nlohmann::json& hyperparameters);
+        nlohmann::json hyperparameters;
     private:
         PyWrap* pyWrap;
         std::string module;
         std::string className;
+        bool fitted;
     };
-
 } /* namespace pywrap */
 #endif /* PYCLASSIFER_H */

src/STree.cc

@@ -5,4 +5,11 @@ namespace pywrap {
     {
         return callMethodString("graph");
     }
+    void STree::setHyperparameters(const nlohmann::json& hyperparameters)
+    {
+        // Check if hyperparameters are valid
+        const std::vector<std::string> validKeys = { "C", "n_jobs", "kernel", "max_iter", "max_depth", "random_state", "multiclass_strategy" };
+        checkHyperparameters(validKeys, hyperparameters);
+        this->hyperparameters = hyperparameters;
+    }
 } /* namespace pywrap */

src/STree.h

@@ -1,5 +1,6 @@
 #ifndef STREE_H
 #define STREE_H
+#include "nlohmann/json.hpp"
 #include "PyClassifier.h"
 
 namespace pywrap {
@@ -8,6 +9,7 @@ namespace pywrap {
         STree() : PyClassifier("stree", "Stree") {};
         ~STree() = default;
         std::string graph();
+        void setHyperparameters(const nlohmann::json& hyperparameters) override;
     };
 } /* namespace pywrap */
 #endif /* STREE_H */

src/example.cpp

@@ -1,257 +0,0 @@
-#include "boost/python/detail/wrap_python.hpp"
-#include <boost/python/numpy.hpp>
-#include <torch/torch.h>
-#include <torch/csrc/utils/tensor_numpy.h>
-#include <string>
-#include <iostream>
-#include "ArffFiles.h"
-#include "PyHelper.hpp"
-#include "PyWrap.h"
-
-
-void errorAbort(const std::string& message)
-{
-    std::cerr << message << std::endl;
-    PyErr_Print();
-    exit(1);
-}
-void print_array(pywrap::np::ndarray& array)
-{
-    std::cout << "Array: " << std::endl;
-    std::cout << pywrap::p::extract<char const*>(pywrap::p::str(array)) << std::endl;
-}
-// np::ndarray to_numpy_matrix(torch::Tensor& input_data, np::dtype numpy_dtype)
-// {
-//     p::tuple shape = p::make_tuple(input_data.size(0), input_data.size(1));
-//     auto tensor_dtype = input_data.dtype();
-//     p::tuple stride = p::make_tuple(sizeof(tensor_dtype) * input_data.size(1), sizeof(tensor_dtype));
-//     auto dito = input_data.transpose(1, 0);
-//     np::ndarray result = np::from_data(dito.data_ptr(), numpy_dtype, shape, stride, p::object());
-//     return result;
-// }
-// np::ndarray to_numpy_vector(torch::Tensor& input_data, np::dtype numpy_dtype)
-// {
-//     p::tuple shape = p::make_tuple(input_data.size(0));
-//     auto tensor_dtype = input_data.dtype();
-//     p::tuple stride = p::make_tuple(sizeof(tensor_dtype), sizeof(tensor_dtype));
-//     np::ndarray result = np::from_data(input_data.data_ptr(), numpy_dtype, shape, stride, p::object());
-//     return result;
-// }
-
-class Paths {
-public:
-    static string datasets()
-    {
-        return "../discretizbench/datasets/";
-    }
-};
-
-tuple<torch::Tensor, torch::Tensor, vector<string>, string, map<string, vector<int>>> loadDataset(const string& name, bool class_last)
-{
-    auto handler = ArffFiles();
-    handler.load(Paths::datasets() + static_cast<string>(name) + ".arff", class_last);
-    // Get Dataset X, y
-    vector<vector<float>> X = handler.getX();
-    vector<int> y = handler.getY();
-    // Get className & Features
-    auto className = handler.getClassName();
-    vector<string> features;
-    auto attributes = handler.getAttributes();
-    transform(attributes.begin(), attributes.end(), back_inserter(features), [](const auto& pair) { return pair.first; });
-    torch::Tensor Xd;
-    auto states = map<string, vector<int>>();
-    Xd = torch::zeros({ static_cast<int>(X.size()), static_cast<int>(X[0].size()) }, torch::kFloat32);
-    for (int i = 0; i < features.size(); ++i) {
-        Xd.index_put_({ i, "..." }, torch::tensor(X[i], torch::kFloat32));
-    }
-    return { Xd, torch::tensor(y, torch::kInt32), features, className, states };
-}
-
-using namespace pywrap;
-np::ndarray tensor2numpy(torch::Tensor& X)
-{
-    int m = X.size(0);
-    int n = X.size(1);
-    auto Xn = np::from_data(X.data_ptr(), np::dtype::get_builtin<float>(), p::make_tuple(m, n), p::make_tuple(sizeof(X.dtype()) * 2 * n, sizeof(X.dtype()) * 2), p::object());
-    Xn = Xn.transpose();
-    return Xn;
-}
-pair<np::ndarray, np::ndarray> tensors2numpy(torch::Tensor& X, torch::Tensor& y)
-{
-    int n = X.size(1);
-    auto yn = np::from_data(y.data_ptr(), np::dtype::get_builtin<int32_t>(), p::make_tuple(n), p::make_tuple(sizeof(y.dtype()) * 2), p::object());
-    return { tensor2numpy(X), yn };
-}
-pair<np::ndarray, np::ndarray> getData(const string& dataset)
-{
-    auto [X, y, featuresx, classNamex, statesx] = loadDataset(dataset, true);
-    auto [Xn, yn] = tensors2numpy(X, y);
-    auto Xn_shapes = Xn.get_shape();
-    auto yn_shapes = yn.get_shape();
-    cout << "Xn_shapes: " << Xn_shapes[0] << ", " << Xn_shapes[1] << endl;
-    cout << "yn_shapes: " << yn_shapes[0] << endl;
-    cout << "X shapes: " << X.sizes() << endl;
-    cout << "y shapes: " << y.sizes() << endl;
-    assert(Xn_shapes[0] == X.sizes()[0]);
-    assert(Xn_shapes[1] == X.sizes()[1]);
-    assert(yn_shapes[0] == y.sizes()[0]);
-
-    return { Xn, yn };
-}
-int main(int argc, char** argv)
-{
-    cout << "* Begin." << endl;
-    {
-        PyWrap* wrapper = PyWrap::GetInstance();
-        string dataset = "iris";
-        // Convert Tensor to numpy array
-        // auto [Xn, yn] = tensors2numpy(X, y);
-        // cout << "Numpy array data: " << endl;
-        // print_array(Xn);
-        // cout << "Numpy array labels: " << endl;
-        // print_array(yn);
-        // Import module
-        string moduleName = "stree";
-        string className = "Stree";
-        // Import
-        {
-            cout << "--Import Phase--" << endl;
-            wrapper->importClass(moduleName, className);
-            cout << "--Import Phase end--" << endl;
-        }
-        // Version
-        {
-            cout << "--Version Phase--" << endl;
-            auto version = wrapper->version(moduleName, className);
-            cout << "Version: " << version << endl;
-            cout << "--Version Phase end--" << endl;
-        }
-        // Fit
-        {
-            cout << "--Fit Phase--" << endl;
-            auto [Xn, yn] = getData(dataset);
-            auto Xn_shapes = Xn.get_shape();
-            auto yn_shapes = yn.get_shape();
-            CPyObject Xp = boost::python::incref(boost::python::object(Xn).ptr());
-            CPyObject yp = boost::python::incref(boost::python::object(yn).ptr());
-            //print_array(yn);
-            // Call fit
-            cout << "Calling fit" << endl;
-            wrapper->fit(moduleName, className, Xp, yp);
-            cout << "--Fit Phase end--" << endl;
-        }
-        // Score
-        {
-            cout << "--Score Phase--" << endl;
-            auto [Xn, yn] = getData(dataset);
-            auto Xn_shapes = Xn.get_shape();
-            auto yn_shapes = yn.get_shape();
-            CPyObject Xp = boost::python::incref(boost::python::object(Xn).ptr());
-            CPyObject yp = boost::python::incref(boost::python::object(yn).ptr());
-            //print_array(yn);
-            // Call score
-            cout << "Calling score" << endl;
-            auto result = wrapper->score(moduleName, className, Xp, yp);
-            cout << "Score: " << result << endl;
-            cout << "--Score Phase end--" << endl;
-        }
-        // Call score
-        // {
-        //     np::initialize();
-        //     cout << "--Score Phase--" << endl;
-        //     auto [X, y, featuresx, classNamex, statesx] = loadDataset(dataset, true);
-        //     auto [Xn, yn] = tensors2numpy(X, y);
-        //     auto Xn_shapes = Xn.get_shape();
-        //     auto yn_shapes = yn.get_shape();
-        //     cout << "Xn_shapes: " << Xn_shapes[0] << ", " << Xn_shapes[1] << endl;
-        //     cout << "yn_shapes: " << yn_shapes[0] << endl;
-        //     cout << "X shapes: " << X.sizes() << endl;
-        //     cout << "y shapes: " << y.sizes() << endl;
-        //     assert(Xn_shapes[0] == X.sizes()[0]);
-        //     assert(Xn_shapes[1] == X.sizes()[1]);
-        //     assert(yn_shapes[0] == y.sizes()[0]);
-        //     CPyObject Xp = Xn.ptr();
-        //     CPyObject yp = yn.ptr();
-        //     print_array(yn);
-        //     cout << "Calling score" << endl;
-        //     auto instance = wrapper->getClass(moduleName, className);
-        //     CPyObject result;
-        //     if (!(result = PyObject_CallMethod(instance, "score", "OO", Xp.getObject(), yp.getObject())))
-        //         errorAbort("Couldn't call method score");
-        //     auto score = PyFloat_AsDouble(result);
-        //     //auto score = wrapper->score(moduleName, className, Xp, yp);
-        //     cout << "Score: " << score << endl;
-        //     cout << "--Score Phase end--" << endl;
-        // }
-        // Clean module
-        {
-            cout << "--Clean Phase--" << endl;
-            wrapper->clean(moduleName, className);
-            cout << "--Clean Phase end--" << endl;
-        }
-    }
-    cout << "* End." << endl;
-}
-// int main(int argc, char** argv)
-// {
-//     auto [data_tensor, y_label, featuresx, classNamex, statesx] = loadDataset("iris", true);
-//     // CPyInstance pInstance;
-//     // auto wrapper = PyWrap();
-//     PyWrap* wrapper = PyWrap::GetInstance();
-//     // PyWrap* wrapper = PyWrap::GetInstance();
-//     int m = data_tensor.size(0);
-//     int n = data_tensor.size(1);
-//     auto data_numpy = np::from_data(data_tensor.data_ptr(), np::dtype::get_builtin<float>(), p::make_tuple(m, n), p::make_tuple(sizeof(data_tensor.dtype()) * 2 * n, sizeof(data_tensor.dtype()) * 2), p::object());
-//     data_numpy = data_numpy.transpose();
-//     auto y_numpy = np::from_data(y_label.data_ptr(), np::dtype::get_builtin<int32_t>(), p::make_tuple(n), p::make_tuple(sizeof(y_label.dtype()) * 2), p::object());
-//     cout << "Numpy array data: " << endl;
-//     print_array(data_numpy);
-//     cout << "Numpy array labels: " << endl;
-//     print_array(y_numpy);
-//     cout << "primero" << endl;
-//     CPyObject p = data_numpy.ptr();
-//     CPyObject yp = y_numpy.ptr();
-//     string moduleName = "sklearn.svm";
-//     string className = "SVC";
-//     string method = "_repr_html_";
-//     // CPyObject module = PyImport_ImportModule(moduleName.c_str());
-//     // if (PyErr_Occurred()) {
-//     //     errorAbort("Could't import module " + moduleName);
-//     // }
-//     // CPyObject classObject = PyObject_GetAttrString(module, className.c_str());
-//     // if (PyErr_Occurred()) {
-//     //     errorAbort("Couldn't find class " + className);
-//     // }
-//     // CPyObject instance = PyObject_CallObject(classObject, NULL);
-//     // if (PyErr_Occurred()) {
-//     //     errorAbort("Couldn't create instance of class " + className);
-//     // }
-//     // wrapper.moduleClassMap.insert({ { moduleName, className }, { module, classObject, instance } });
-//     wrapper->importClass(moduleName, className);
-//     PyObject* instance = wrapper->getClass(moduleName, className);
-//     CPyObject result;
-//     if (!(result = PyObject_CallMethod(instance, method.c_str(), NULL)))
-//         errorAbort("Couldn't call method " + method);
-//     std::string value = PyUnicode_AsUTF8(result);
-//     cout << "Version: " << value << endl;
-//     cout << "Calling fit" << endl;
-//     p.AddRef();
-//     yp.AddRef();
-//     method = "fit";
-//     wrapper->fit(moduleName, className, p, yp);
-//     // PyObject* instance2 = wrapper->getClass(moduleName, className);
-//     // if (!(result = PyObject_CallMethodObjArgs(instance2, PyUnicode_FromString(method.c_str()), p.getObject(), yp.getObject(), NULL)))
-//         // errorAbort("Couldn't call method fit");
-//     // method = "fit";
-//     // if (!(result = PyObject_CallMethodObjArgs(instance, PyUnicode_FromString(method.c_str()), p.getObject(), yp.getObject(), NULL)))
-//     //     errorAbort("Couldn't call method fit");
-//     cout << "Calling score" << endl;
-//     // method = "score";
-//     // if (!(result = PyObject_CallMethodObjArgs(instance, PyUnicode_FromString(method.c_str()), p.getObject(), yp.getObject(), NULL)))
-//     //     errorAbort("Couldn't call method score");
-//     // float score = PyFloat_AsDouble(result);
-//     auto score = wrapper->score(moduleName, className, p, yp);
-//     cout << "Score: " << score << endl;
-//     wrapper->clean(moduleName, className);
-//     return 0;
-// }

src/main.cc

@@ -52,6 +52,8 @@ int main(int argc, char* argv[])
         cout << "X: " << X.sizes() << endl;
         cout << "y: " << y.sizes() << endl;
         auto clf = pywrap::STree();
+        auto hyperparameters = nlohmann::json({ "max_depth": 3, "C" : 0.7 });
+        clf.setHyperparameters(hyperparameters);
         cout << "STree Version: " << clf.version() << endl;
         auto svc = pywrap::SVC();
         svc.fit(X, y, features, className, states);