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Implement hyperparameters

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This commit is contained in:
Ricardo Montañana Gómez
2023-11-08 10:35:38 +01:00
parent 1f46fc6c24
commit 331381930a
17 changed files with 913 additions and 325 deletions
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3
.gitmodules vendored Normal file
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@@ -0,0 +1,3 @@
[submodule "lib/json"]
path = lib/json
url = https://github.com/nlohmann/json.git

28
CMakeLists.txt
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@@ -1,15 +1,29 @@
cmake_minimum_required(VERSION 3.5)
project(PyWrap)
cmake_minimum_required(VERSION 3.20)
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)

2
Makefile
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@@ -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

12
cmake/modules/AddGitSubmodule.cmake Normal file
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@@ -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)

742
cmake/modules/CodeCoverage.cmake Normal file
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@@ -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()

22
cmake/modules/StaticAnalyzers.cmake Normal file
View File

@@ -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)

76
lib/Files/ArffFiles.cc
View File

@@ -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;
string keyword;
string attribute;
string type;
string type_w;
std::string line;
std::string keyword;
std::string attribute;
std::string type;
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) {
stringstream ss(line);
if (line.find("@attribute") != std::string::npos || line.find("@ATTRIBUTE") != std::string::npos) {
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());
classType = get<1>(attributes.back());
className = std::get<0>(attributes.back());
classType = std::get<1>(attributes.back());
attributes.pop_back();
labelIndex = static_cast<int>(attributes.size());
} else {
className = get<0>(attributes.front());
classType = get<1>(attributes.front());
className = std::get<0>(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]);
classType = get<1>(attributes[i]);
className = std::get<0>(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()));
auto yy = vector<string>(lines.size(), "");
auto removeLines = vector<int>(); // Lines with missing values
X = std::vector<std::vector<float>>(attributes.size(), std::vector<float>(lines.size()));
auto yy = std::vector<std::string>(lines.size(), "");
auto removeLines = std::vector<int>(); // Lines with missing values
for (size_t i = 0; i < lines.size(); i++) {
stringstream ss(lines[i]);
string value;
std::stringstream ss(lines[i]);
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++;
}

36
lib/Files/ArffFiles.h
View File

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

1
lib/json Submodule

Submodule lib/json added at 6eab7a2b18

3
src/CMakeLists.txt
View File

@@ -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)

13
src/Classifier.h Normal file
View File

@@ -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 */

22
src/PyClassifier.cc
View File

@@ -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 */

10
src/PyClassifier.h
View File

@@ -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 */

7
src/STree.cc
View File

@@ -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 */

2
src/STree.h
View File

@@ -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 */

257
src/example.cpp
View File

@@ -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;
// }

2
src/main.cc
View File

@@ -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);