Add BayesNet library to PyClassifiers library

CMakeLists.txt

@@ -25,6 +25,7 @@ set(CMAKE_CXX_EXTENSIONS                  OFF)
 set(CMAKE_EXPORT_COMPILE_COMMANDS          ON)
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}")
 SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
+
 # Options
 # -------
 option(ENABLE_TESTING "Unit testing build"                        OFF)
@@ -36,8 +37,8 @@ set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF) 
 find_package(Boost 1.66.0 REQUIRED COMPONENTS python3 numpy3) 
 if(Boost_FOUND)
-    message("Boost_INCLUDE_DIRS=${Boost_INCLUDE_DIRS}")
+  message("Boost_INCLUDE_DIRS=${Boost_INCLUDE_DIRS}")
-    include_directories(${Boost_INCLUDE_DIRS}) 
+  include_directories(${Boost_INCLUDE_DIRS}) 
 endif()
 
 # Python
@@ -50,11 +51,11 @@ set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules ${CMAKE_MODULE_P
 include(AddGitSubmodule)
 
 if (CODE_COVERAGE)
-    enable_testing()
+  enable_testing()
-    include(CodeCoverage)
+  include(CodeCoverage)
-    MESSAGE("Code coverage enabled")
+  MESSAGE("Code coverage enabled")
-    set(CMAKE_CXX_FLAGS " ${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage -O0 -g")
+  set(CMAKE_CXX_FLAGS " ${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage -O0 -g")
-    SET(GCC_COVERAGE_LINK_FLAGS " ${GCC_COVERAGE_LINK_FLAGS} -lgcov --coverage")
+  SET(GCC_COVERAGE_LINK_FLAGS " ${GCC_COVERAGE_LINK_FLAGS} -lgcov --coverage")
 endif (CODE_COVERAGE)
 
 if (ENABLE_CLANG_TIDY)
@@ -63,19 +64,18 @@ endif (ENABLE_CLANG_TIDY)
 
 # External libraries - dependencies of PyClassifiers
 # --------------------------------------------------
-# include(FetchContent)
 add_git_submodule("lib/BayesNet")
 
 # Subdirectories
 # --------------
+file(GLOB PyClassifiers_SOURCES CONFIGURE_DEPENDS ${PyClassifiers_SOURCE_DIR}/src/PyClassifiers/*.cc ${PyClassifiers_SOURCE_DIR}/src/PyClassifiers/*.hpp)
 add_subdirectory(config)
 add_subdirectory(src/PyClassifiers)
 
 # Testing
 # -------
-
 if (ENABLE_TESTING)
   MESSAGE("Testing enabled")
   include(CTest)
   add_subdirectory(tests)
-endif (ENABLE_TESTING)
+endif (ENABLE_TESTING)

Makefile

@@ -1,10 +1,7 @@
-SHELL := /bin/bash
+f_release = build_release
-.DEFAULT_GOAL := help
-.PHONY: help build test clean debug
-
 f_debug = build_debug
 app_targets = PyClassifiers
-test_targets = unit_tests_pyclassifiers
+test_targets = unit_tests_pyclassifiers 
 n_procs = -j 16
 
 define ClearTests
@@ -20,27 +17,49 @@ define ClearTests
 	fi ; 
 endef
 
-submodules: ## Update submodules
+
-	@echo ">>> Updating submodules...";
+setup: ## Install dependencies for tests and coverage
-	@git submodule update --init --recursive
+	@if [ "$(shell uname)" = "Darwin" ]; then \
-	@echo ">>> Done";
+		brew install gcovr; \
+		brew install lcov; \
+	fi
+	@if [ "$(shell uname)" = "Linux" ]; then \
+		pip install gcovr; \
+	fi
+
+dependency: ## Create a dependency graph diagram of the project (build/dependency.png)
+	@echo ">>> Creating dependency graph diagram of the project...";
+	$(MAKE) debug
+	cd $(f_debug) && cmake .. --graphviz=dependency.dot && dot -Tpng dependency.dot -o dependency.png
+
+buildd: ## Build the debug targets
+	cmake --build $(f_debug) -t $(app_targets) $(n_procs)
+
+buildr: ## Build the release targets
+	cmake --build $(f_release) -t $(app_targets) $(n_procs)
 
 clean: ## Clean the tests info
 	@echo ">>> Cleaning Debug PyClassifiers tests...";
 	$(call ClearTests)
 	@echo ">>> Done";
 
-build: ## Build a version of the project
+debug: ## Build a debug version of the project
 	@echo ">>> Building Debug PyClassifiers...";
 	@if [ -d ./$(f_debug) ]; then rm -rf ./$(f_debug); fi
 	@mkdir $(f_debug); 
 	@cmake -S . -B $(f_debug) -D CMAKE_BUILD_TYPE=Debug -D ENABLE_TESTING=ON -D CODE_COVERAGE=ON
-	@cmake --build $(f_debug) $(n_procs)
+	@echo ">>> Done";
+
+release: ## Build a Release version of the project
+	@echo ">>> Building Release PyClassifiers...";
+	@if [ -d ./$(f_release) ]; then rm -rf ./$(f_release); fi
+	@mkdir $(f_release); 
+	@cmake -S . -B $(f_release) -D CMAKE_BUILD_TYPE=Release
 	@echo ">>> Done";	
 
 opt = ""
 test: ## Run tests (opt="-s") to verbose output the tests, (opt="-c='Test Maximum Spanning Tree'") to run only that section
-	@echo ">>> Running PyClassifiers & Platform tests...";
+	@echo ">>> Running PyClassifiers tests...";
 	@$(MAKE) clean
 	@cmake --build $(f_debug) -t $(test_targets) $(n_procs)
 	@for t in $(test_targets); do \
@@ -52,10 +71,9 @@ test: ## Run tests (opt="-s") to verbose output the tests, (opt="-c='Test Maximu
 	@echo ">>> Done";
 
 coverage: ## Run tests and generate coverage report (build/index.html)
-	@echo ">>> Building tests with coverage...";
+	@echo ">>> Building tests with coverage..."
 	@$(MAKE) test
-	@cd $(f_debug) ; \
+	@gcovr $(f_debug)/tests
-	gcovr --config ../gcovr.cfg tests ;
 	@echo ">>> Done";	
 
 

gcovr.cfg

@@ -0,0 +1,4 @@
+filter = src/
+exclude-directories = build_debug/lib/
+print-summary = yes
+sort-percentage = yes

src/PyClassifiers/CMakeLists.txt

@@ -6,6 +6,6 @@ include_directories(
     ${Python3_INCLUDE_DIRS}
     ${TORCH_INCLUDE_DIRS}
 )
-add_library(PyClassifiers SHARED PyWrap.cc STree.cc ODTE.cc SVC.cc RandomForest.cc PyClassifier.cc)
+add_library(PyClassifiers SHARED ${PyClassifiers_SOURCES})
 #target_link_libraries(PyClassifiers ${Python3_LIBRARIES} "${TORCH_LIBRARIES}" ${LIBTORCH_PYTHON} Boost::boost Boost::python Boost::numpy xgboost::xgboost)
-target_link_libraries(PyClassifiers ${Python3_LIBRARIES} "${TORCH_LIBRARIES}" ${LIBTORCH_PYTHON} Boost::boost Boost::python Boost::numpy)
+target_link_libraries(PyClassifiers BayesNet ${Python3_LIBRARIES} "${TORCH_LIBRARIES}" ${LIBTORCH_PYTHON} Boost::boost Boost::python Boost::numpy)

src/PyClassifiers/XGBoost.cc

@@ -3,7 +3,7 @@
 
 
 
-See https ://stackoverflow.com/questions/36071672/using-xgboost-in-c
+//See https ://stackoverflow.com/questions/36071672/using-xgboost-in-c
 
 
 

tests/CMakeLists.txt

@@ -12,6 +12,6 @@ if(ENABLE_TESTING)
     )
     set(TEST_SOURCES_PYCLASSIFIERS TestPythonClassifiers.cc TestUtils.cc ${PyClassifiers_SOURCES})
     add_executable(${TEST_PYCLASSIFIERS} ${TEST_SOURCES_PYCLASSIFIERS})
-    target_link_libraries(${TEST_PYCLASSIFIERS} PUBLIC "${TORCH_LIBRARIES}" PyClassifiers ArffFiles mdlp Catch2::Catch2WithMain)
+    target_link_libraries(${TEST_PYCLASSIFIERS} PUBLIC "${TORCH_LIBRARIES}" ${Python3_LIBRARIES} ${LIBTORCH_PYTHON} Boost::boost Boost::python Boost::numpy ArffFiles mdlp Catch2::Catch2WithMain)
     add_test(NAME ${TEST_PYCLASSIFIERS} COMMAND ${TEST_PYCLASSIFIERS})
 endif(ENABLE_TESTING)