Add mdlp as submodule

.gitmodules

@@ -16,3 +16,6 @@
 [submodule "tests/lib/Files"]
 	path = tests/lib/Files
 	url = https://github.com/rmontanana/ArffFiles
+[submodule "lib/mdlp"]
+	path = lib/mdlp
+	url = https://github.com/rmontanana/mdlp

.vscode/launch.json

@@ -16,7 +16,7 @@
             "name": "test",
             "program": "${workspaceFolder}/build_Debug/tests/TestBayesNet",
             "args": [
-                "[Network]"
+                "Test Node computeCPT"
             ],
             "cwd": "${workspaceFolder}/build_Debug/tests"
         },

CHANGELOG.md

@@ -7,6 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Fixed
+
+- Prevent existing edges to be added to the network in the `add_edge` method.
+- Don't allow to add nodes or edges on already fiited networks.
+- Number of threads spawned
+- Network class tests
+
 ### Added
 
 - Library logo generated with <https://openart.ai> to README.md
@@ -19,12 +26,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add tests to check the correct version of the mdlp, folding and json libraries.
 - Library documentation generated with Doxygen.
 - Link to documentation in the README.md.
-- Three types of smoothing the Bayesian Network OLD_LAPLACE, LAPLACE and CESTNIK.
+- Three types of smoothing the Bayesian Network ORIGINAL, LAPLACE and CESTNIK.
 
 ### Internal
 
+- Fixed doxygen optional dependency
+- Add env parallel variable to Makefile
+- Add CountingSemaphore class to manage the number of threads spawned.
 - Ignore CUDA language in CMake CodeCoverage module.
-- Remove mdlp library from submodules and add it as a dependency.
+- Update mdlp library as a git submodule.
 - Create library ShuffleArffFile to limit the number of samples with a parameter and shuffle them.
 - Refactor catch2 library location to test/lib
 - Refactor loadDataset function in tests.

CMakeLists.txt

@@ -65,15 +65,9 @@ endif (ENABLE_CLANG_TIDY)
 # External libraries - dependencies of BayesNet
 # ---------------------------------------------
 
-find_library(FImdlp NAMES libfimdlp.a REQUIRED)
-find_path(FImdlp_INCLUDE_DIRS REQUIRED NAMES fimdlp)
-
-message(STATUS "FImdlp=${FImdlp}")
-message(STATUS "FImdlp_INCLUDE_DIRS=${FImdlp_INCLUDE_DIRS}")
-
-
 # include(FetchContent)
 add_git_submodule("lib/json")
+add_git_submodule("lib/mdlp")
 
 # Subdirectories
 # --------------

Makefile

@@ -43,7 +43,7 @@ setup: ## Install dependencies for tests and coverage
 	fi
 	@echo "* You should install plantuml & graphviz for the diagrams"
 
-diagrams: ## Create an UML class diagram & depnendency of the project (diagrams/BayesNet.png)
+diagrams: ## Create an UML class diagram & dependency of the project (diagrams/BayesNet.png)
 	@which $(plantuml) || (echo ">>> Please install plantuml"; exit 1)
 	@which $(dot) || (echo ">>> Please install graphviz"; exit 1)
 	@which $(clang-uml) || (echo ">>> Please install clang-uml"; exit 1)

README.md

@@ -7,7 +7,7 @@
 [![Security Rating](https://sonarcloud.io/api/project_badges/measure?project=rmontanana_BayesNet&metric=security_rating)](https://sonarcloud.io/summary/new_code?id=rmontanana_BayesNet)
 [![Reliability Rating](https://sonarcloud.io/api/project_badges/measure?project=rmontanana_BayesNet&metric=reliability_rating)](https://sonarcloud.io/summary/new_code?id=rmontanana_BayesNet)
 ![Gitea Last Commit](https://img.shields.io/gitea/last-commit/rmontanana/bayesnet?gitea_url=https://gitea.rmontanana.es:3000&logo=gitea)
-[![Coverage Badge](https://img.shields.io/badge/Coverage-97,1%25-green)](html/index.html)
+[![Coverage Badge](https://img.shields.io/badge/Coverage-96,8%25-green)](html/index.html)
 
 Bayesian Network Classifiers using libtorch from scratch
 

bayesnet/CMakeLists.txt

@@ -4,10 +4,9 @@ include_directories(
     ${BayesNet_SOURCE_DIR}/lib/json/include
     ${BayesNet_SOURCE_DIR}
     ${CMAKE_BINARY_DIR}/configured_files/include
-    ${FImdlp_INCLUDE_DIRS}
 )
 
 file(GLOB_RECURSE Sources "*.cc")
 
 add_library(BayesNet ${Sources})
-target_link_libraries(BayesNet ${FImdlp} "${TORCH_LIBRARIES}")
+target_link_libraries(BayesNet fimdlp "${TORCH_LIBRARIES}")

bayesnet/classifiers/Proposal.h

@@ -9,7 +9,7 @@
 #include <string>
 #include <map>
 #include <torch/torch.h>
-#include <fimdlp/CPPFImdlp.h>
+#include <CPPFImdlp.h>
 #include "bayesnet/network/Network.h"
 #include "Classifier.h"
 

sample/CMakeLists.txt

@@ -8,7 +8,6 @@ find_package(Torch REQUIRED)
 find_library(BayesNet NAMES libBayesNet BayesNet libBayesNet.a  REQUIRED)
 find_path(Bayesnet_INCLUDE_DIRS REQUIRED NAMES bayesnet)
 find_library(FImdlp NAMES libfimdlp.a  PATHS REQUIRED)
-find_path(FImdlp_INCLUDE_DIRS REQUIRED NAMES fimdlp)
 
 message(STATUS "FImdlp=${FImdlp}")
 message(STATUS "FImdlp_INCLUDE_DIRS=${FImdlp_INCLUDE_DIRS}")
@@ -23,4 +22,4 @@ include_directories(
 )
 
 add_executable(bayesnet_sample sample.cc) 
-target_link_libraries(bayesnet_sample ${FImdlp} "${TORCH_LIBRARIES}" "${BayesNet}")
+target_link_libraries(bayesnet_sample fimdlp "${TORCH_LIBRARIES}" "${BayesNet}")

sample/sample.cc

@@ -5,7 +5,7 @@
 // ***************************************************************
 
 #include <ArffFiles.hpp>
-#include <fimdlp/CPPFImdlp.h>
+#include <CPPFImdlp.h>
 #include <bayesnet/ensembles/BoostAODE.h>
 
 std::vector<mdlp::labels_t> discretizeDataset(std::vector<mdlp::samples_t>& X, mdlp::labels_t& y)

tests/CMakeLists.txt

@@ -6,13 +6,12 @@ if(ENABLE_TESTING)
         ${BayesNet_SOURCE_DIR}/lib/json/include
         ${BayesNet_SOURCE_DIR}
         ${CMAKE_BINARY_DIR}/configured_files/include
-        ${FImdlp_INCLUDE_DIRS}
     )
     file(GLOB_RECURSE BayesNet_SOURCES "${BayesNet_SOURCE_DIR}/bayesnet/*.cc")
     add_executable(TestBayesNet TestBayesNetwork.cc TestBayesNode.cc TestBayesClassifier.cc 
         TestBayesModels.cc TestBayesMetrics.cc TestFeatureSelection.cc TestBoostAODE.cc TestA2DE.cc 
         TestUtils.cc TestBayesEnsemble.cc TestModulesVersions.cc TestBoostA2DE.cc ${BayesNet_SOURCES})
-    target_link_libraries(TestBayesNet PUBLIC "${TORCH_LIBRARIES}" mdlp PRIVATE Catch2::Catch2WithMain)
+    target_link_libraries(TestBayesNet PUBLIC "${TORCH_LIBRARIES}" fimdlp PRIVATE Catch2::Catch2WithMain)
     add_test(NAME BayesNetworkTest COMMAND TestBayesNet)
     add_test(NAME A2DE COMMAND TestBayesNet "[A2DE]")
     add_test(NAME BoostA2DE COMMAND TestBayesNet "[BoostA2DE]")

tests/TestModulesVersions.cc

@@ -7,7 +7,7 @@
 #include <catch2/catch_test_macros.hpp>
 #include <catch2/matchers/catch_matchers.hpp>
 #include <string>
-#include <fimdlp/CPPFImdlp.h>
+#include <CPPFImdlp.h>
 #include <folding.hpp>
 #include <nlohmann/json.hpp>
 #define TO_STR2(x) #x

tests/TestUtils.h

@@ -12,7 +12,7 @@
 #include <map>
 #include <tuple>
 #include <ArffFiles.hpp>
-#include <fimdlp/CPPFImdlp.h>
+#include <CPPFImdlp.h>
 #include <folding.hpp>
 #include <bayesnet/network/Network.h>