Refactor to accept new Library structure

config/config.h.in

@@ -3,12 +3,8 @@
 #include <string>
 #include <string_view>
 
-#define PROJECT_VERSION_MAJOR @PROJECT_VERSION_MAJOR @
-#define PROJECT_VERSION_MINOR @PROJECT_VERSION_MINOR @
-#define PROJECT_VERSION_PATCH @PROJECT_VERSION_PATCH @
-
-static constexpr std::string_view project_name = "@PROJECT_NAME@";
-static constexpr std::string_view project_version = "@PROJECT_VERSION@";
-static constexpr std::string_view project_description = "@PROJECT_DESCRIPTION@";
-static constexpr std::string_view git_sha = "@GIT_SHA@";
-static constexpr std::string_view data_path = "@Platform_SOURCE_DIR@/tests/data/";
+static constexpr std::string_view platform_project_name = "@PROJECT_NAME@";
+static constexpr std::string_view platform_project_version = "@PROJECT_VERSION@";
+static constexpr std::string_view platform_project_description = "@PROJECT_DESCRIPTION@";
+static constexpr std::string_view platform_git_sha = "@GIT_SHA@";
+static constexpr std::string_view platform_data_path = "@Platform_SOURCE_DIR@/tests/data/";

gcovr.cfg

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

sample/CMakeLists.txt

@@ -7,9 +7,8 @@ include_directories(
     ${Platform_SOURCE_DIR}/lib/argparse/include
     ${Platform_SOURCE_DIR}/lib/folding
     ${Platform_SOURCE_DIR}/lib/json/include
-    /usr/local/include/bayesnet
-    /usr/local/include/pyclassifiers
+    ${CMAKE_BINARY_DIR}/configured_files/include
+    /usr/local/include
 )
 add_executable(PlatformSample sample.cc ${Platform_SOURCE_DIR}/src/main/Models.cc) 
-# target_link_libraries(PlatformSample "${PyClassifiers}" "${BayesNet}" ArffFiles mdlp "${TORCH_LIBRARIES}")
 target_link_libraries(PlatformSample "${PyClassifiers}" "${BayesNet}" ArffFiles mdlp ${Python3_LIBRARIES} "${TORCH_LIBRARIES}" ${LIBTORCH_PYTHON} Boost::python Boost::numpy)

sample/sample.cc

@@ -1,19 +1,19 @@
 #include <iostream>
-#include <torch/torch.h>
 #include <string>
 #include <map>
 #include <fstream>
+#include <torch/torch.h>
 #include <argparse/argparse.hpp>
 #include <nlohmann/json.hpp>
 #include <ArffFiles.h>
-#include <utils/BayesMetrics.h>
 #include <CPPFImdlp.h>
 #include <folding.hpp>
+#include <bayesnet/utils/BayesMetrics.h>
 #include "Models.h"
 #include "modelRegister.h"
 #include "config.h"
 
-const std::string PATH = { data_path.begin(), data_path.end() };
+const std::string PATH = { platform_data_path.begin(), platform_data_path.end() };
 
 pair<std::vector<mdlp::labels_t>, map<std::string, int>> discretize(std::vector<mdlp::samples_t>& X, mdlp::labels_t& y, std::vector<std::string> features)
 {

src/CMakeLists.txt

@@ -10,15 +10,9 @@ include_directories(
     ${MPI_CXX_INCLUDE_DIRS}
     ${TORCH_INCLUDE_DIRS}
     ${CMAKE_BINARY_DIR}/configured_files/include
-    /usr/local/include/bayesnet
-    /usr/local/include/pyclassifiers
+    /usr/local/include
     ## Platform
-    ${Platform_SOURCE_DIR}/src/common
-    ${Platform_SOURCE_DIR}/src/best
-    ${Platform_SOURCE_DIR}/src/grid
-    ${Platform_SOURCE_DIR}/src/main
-    ${Platform_SOURCE_DIR}/src/manage
-    ${Platform_SOURCE_DIR}/src/reports
+    ${Platform_SOURCE_DIR}/src
 )
 
 # b_best

src/best/BestResults.cc

@@ -4,12 +4,12 @@
 #include <iostream>
 #include <sstream>
 #include <algorithm>
-#include "BestResults.h"
-#include "Result.h"
-#include "Colors.h"
-#include "Statistics.h"
+#include "common/Colors.h"
+#include "common/CLocale.h"
+#include "main/Result.h"
 #include "BestResultsExcel.h"
-#include "CLocale.h"
+#include "Statistics.h"
+#include "BestResults.h"
 
 
 namespace fs = std::filesystem;

src/best/BestResultsExcel.cc

@@ -1,10 +1,10 @@
 #include <sstream>
-#include "BestResultsExcel.h"
-#include "Paths.h"
 #include <map>
 #include <nlohmann/json.hpp>
+#include "common/Paths.h"
+#include "reports/ReportExcel.h"
 #include "Statistics.h"
-#include "ReportExcel.h"
+#include "BestResultsExcel.h"
 
 namespace platform {
     json loadResultData(const std::string& fileName)

src/best/BestResultsExcel.h

@@ -1,9 +1,9 @@
 #ifndef BESTRESULTS_EXCEL_H
 #define BESTRESULTS_EXCEL_H
-#include "ExcelFile.h"
 #include <vector>
 #include <map>
 #include <nlohmann/json.hpp>
+#include "reports/ExcelFile.h"
 
 using json = nlohmann::json;
 

src/best/BestScore.h

@@ -3,7 +3,7 @@
 #include <string>
 #include <map>
 #include <utility>
-#include "DotEnv.h"
+#include "common/DotEnv.h"
 namespace platform {
     class BestScore {
     public:

src/best/Statistics.cc

@@ -1,10 +1,10 @@
 #include <sstream>
-#include "Statistics.h"
-#include "Colors.h"
-#include "Symbols.h"
 #include <boost/math/distributions/chi_squared.hpp>
 #include <boost/math/distributions/normal.hpp>
-#include "CLocale.h"
+#include "common/Colors.h"
+#include "common/Symbols.h"
+#include "common/CLocale.h"
+#include "Statistics.h"
 
 
 namespace platform {

src/best/b_best.cc

@@ -1,8 +1,8 @@
 #include <iostream>
 #include <argparse/argparse.hpp>
-#include "Paths.h"
+#include "common/Paths.h"
+#include "common/Colors.h"
 #include "BestResults.h"
-#include "Colors.h"
 #include "config.h"
 
 void manageArguments(argparse::ArgumentParser& program)
@@ -29,7 +29,7 @@ void manageArguments(argparse::ArgumentParser& program)
 
 int main(int argc, char** argv)
 {
-    argparse::ArgumentParser program("b_best", { project_version.begin(), project_version.end() });
+    argparse::ArgumentParser program("b_best", { platform_project_version.begin(), platform_project_version.end() });
     manageArguments(program);
     std::string model, score;
     bool build, report, friedman, excel;

src/common/Colors.h

@@ -1,5 +1,6 @@
 #ifndef COLORS_H
 #define COLORS_H
+#include <string>
 class Colors {
 public:
     static std::string MAGENTA() { return "\033[1;35m"; }

src/common/Dataset.cc

@@ -1,6 +1,6 @@
-#include "Dataset.h"
-#include "ArffFiles.h"
+#include <ArffFiles.h>
 #include <fstream>
+#include "Dataset.h"
 namespace platform {
     Dataset::Dataset(const Dataset& dataset) : path(dataset.path), name(dataset.name), className(dataset.className), n_samples(dataset.n_samples), n_features(dataset.n_features), features(dataset.features), states(dataset.states), loaded(dataset.loaded), discretize(dataset.discretize), X(dataset.X), y(dataset.y), Xv(dataset.Xv), Xd(dataset.Xd), yv(dataset.yv), fileType(dataset.fileType)
     {

src/common/Dataset.h

@@ -4,7 +4,7 @@
 #include <map>
 #include <vector>
 #include <string>
-#include "CPPFImdlp.h"
+#include <CPPFImdlp.h>
 #include "Utils.h"
 namespace platform {
     enum fileType_t { CSV, ARFF, RDATA };

src/common/Datasets.cc

@@ -1,5 +1,5 @@
-#include "Datasets.h"
 #include <fstream>
+#include "Datasets.h"
 namespace platform {
     void Datasets::load()
     {

src/grid/GridData.cc

@@ -1,5 +1,5 @@
-#include "GridData.h"
 #include <fstream>
+#include "GridData.h"
 
 namespace platform {
     GridData::GridData(const std::string& fileName)

src/grid/GridSearch.cc

@@ -1,11 +1,11 @@
 #include <iostream>
 #include <cstddef>
 #include <torch/torch.h>
+#include <folding.hpp>
+#include "main/Models.h"
+#include "common/Paths.h"
+#include "common/Colors.h"
 #include "GridSearch.h"
-#include "Models.h"
-#include "Paths.h"
-#include "folding.hpp"
-#include "Colors.h"
 
 namespace platform {
     std::string get_date()

src/grid/GridSearch.h

@@ -4,10 +4,10 @@
 #include <map>
 #include <mpi.h>
 #include <nlohmann/json.hpp>
-#include "Datasets.h"
-#include "HyperParameters.h"
+#include "common/Datasets.h"
+#include "common/Timer.h"
+#include "main/HyperParameters.h"
 #include "GridData.h"
-#include "Timer.h"
 
 namespace platform {
     using json = nlohmann::json;

src/grid/b_grid.cc

@@ -4,13 +4,13 @@
 #include <tuple>
 #include <nlohmann/json.hpp>
 #include <mpi.h>
-#include "DotEnv.h"
-#include "Models.h"
-#include "modelRegister.h"
+#include "main/Models.h"
+#include "main/modelRegister.h"
+#include "common/Paths.h"
+#include "common/Timer.h"
+#include "common/Colors.h"
+#include "common/DotEnv.h"
 #include "GridSearch.h"
-#include "Paths.h"
-#include "Timer.h"
-#include "Colors.h"
 #include "config.h"
 
 using json = nlohmann::json;
@@ -223,7 +223,7 @@ int main(int argc, char** argv)
     //
     // Manage arguments
     //
-    argparse::ArgumentParser program("b_grid", { project_version.begin(), project_version.end() });
+    argparse::ArgumentParser program("b_grid", { platform_project_version.begin(), platform_project_version.end() });
     // grid dump subparser
     argparse::ArgumentParser dump_command("dump");
     dump_command.add_description("Dump the combinations of hyperparameters of a model.");

src/list/DatasetsExcel.cc

@@ -1,6 +1,6 @@
 #include <sstream>
+#include "common/Paths.h"
 #include "DatasetsExcel.h"
-#include "Paths.h"
 
 
 namespace platform {

src/list/DatasetsExcel.h

@@ -1,9 +1,9 @@
 #ifndef DATASETS_EXCEL_H
 #define DATASETS_EXCEL_H
-#include "ExcelFile.h"
 #include <vector>
 #include <map>
 #include <nlohmann/json.hpp>
+#include "reports/ExcelFile.h"
 
 using json = nlohmann::json;
 

src/list/b_list.cc

@@ -2,9 +2,9 @@
 #include <locale>
 #include <argparse/argparse.hpp>
 #include <nlohmann/json.hpp>
-#include "Paths.h"
-#include "Colors.h"
-#include "Datasets.h"
+#include "common/Paths.h"
+#include "common/Colors.h"
+#include "common/Datasets.h"
 #include "DatasetsExcel.h"
 #include "config.h"
 
@@ -31,7 +31,7 @@ std::string outputBalance(const std::string& balance)
 int main(int argc, char** argv)
 {
     auto datasets = platform::Datasets(false, platform::Paths::datasets());
-    argparse::ArgumentParser program("b_list", { project_version.begin(), project_version.end() });
+    argparse::ArgumentParser program("b_list", { platform_project_version.begin(), platform_project_version.end() });
     program.add_argument("--excel")
         .help("Output in Excel format")
         .default_value(false)

src/main/Experiment.cc

@@ -1,8 +1,8 @@
-#include "Experiment.h"
-#include "Datasets.h"
+#include "common/Datasets.h"
+#include "reports/ReportConsole.h"
+#include "common/Paths.h"
 #include "Models.h"
-#include "ReportConsole.h"
-#include "Paths.h"
+#include "Experiment.h"
 namespace platform {
     using json = nlohmann::json;
 

src/main/Experiment.h

@@ -3,8 +3,8 @@
 #include <torch/torch.h>
 #include <nlohmann/json.hpp>
 #include <string>
-#include "folding.hpp"
-#include "BaseClassifier.h"
+#include <folding.hpp>
+#include "bayesnet/BaseClassifier.h"
 #include "HyperParameters.h"
 #include "Result.h"
 

src/main/HyperParameters.cc

@@ -1,7 +1,7 @@
-#include "HyperParameters.h"
 #include <fstream>
 #include <sstream>
 #include <iostream>
+#include "HyperParameters.h"
 
 namespace platform {
     HyperParameters::HyperParameters(const std::vector<std::string>& datasets, const json& hyperparameters_)

src/main/Models.h

@@ -1,21 +1,21 @@
 #ifndef MODELS_H
 #define MODELS_H
 #include <map>
-#include "BaseClassifier.h"
-#include "ensembles/AODE.h"
-#include "ensembles/AODELd.h"
-#include "ensembles/BoostAODE.h"
-#include "classifiers/TAN.h"
-#include "classifiers/KDB.h"
-#include "classifiers/SPODE.h"
-#include "classifiers/TANLd.h"
-#include "classifiers/KDBLd.h"
-#include "classifiers/SPODELd.h"
-#include "STree.h"
-#include "ODTE.h"
-#include "SVC.h"
-#include "XGBoost.h"
-#include "RandomForest.h"
+#include <bayesnet/BaseClassifier.h>
+#include <bayesnet/ensembles/AODE.h>
+#include <bayesnet/ensembles/AODELd.h>
+#include <bayesnet/ensembles/BoostAODE.h>
+#include <bayesnet/classifiers/TAN.h>
+#include <bayesnet/classifiers/KDB.h>
+#include <bayesnet/classifiers/SPODE.h>
+#include <bayesnet/classifiers/TANLd.h>
+#include <bayesnet/classifiers/KDBLd.h>
+#include <bayesnet/classifiers/SPODELd.h>
+#include <pyclassifiers/STree.h>
+#include <pyclassifiers/ODTE.h>
+#include <pyclassifiers/SVC.h>
+#include <pyclassifiers/XGBoost.h>
+#include <pyclassifiers/RandomForest.h>
 namespace platform {
     class Models {
     private:

src/main/Result.cc

@@ -1,12 +1,12 @@
-#include "Result.h"
 #include <filesystem>
 #include <fstream>
 #include <sstream>
-#include "BestScore.h"
-#include "Colors.h"
-#include "DotEnv.h"
-#include "CLocale.h"
-#include "Paths.h"
+#include "best/BestScore.h"
+#include "common/Colors.h"
+#include "common/DotEnv.h"
+#include "common/CLocale.h"
+#include "common/Paths.h"
+#include "Result.h"
 
 namespace platform {
     std::string get_actual_date()

src/main/Result.h

@@ -4,9 +4,9 @@
 #include <vector>
 #include <string>
 #include <nlohmann/json.hpp>
-#include "HyperParameters.h"
-#include "PartialResult.h"
-#include "Timer.h"
+#include "common/Timer.h"
+#include "main/HyperParameters.h"
+#include "main/PartialResult.h"
 
 namespace platform {
     using json = nlohmann::json;

src/main/b_main.cc

@@ -2,11 +2,11 @@
 #include <argparse/argparse.hpp>
 #include <nlohmann/json.hpp>
 #include "Experiment.h"
-#include "Datasets.h"
-#include "DotEnv.h"
+#include "common/Datasets.h"
+#include "common/DotEnv.h"
+#include "common/Paths.h"
 #include "Models.h"
 #include "modelRegister.h"
-#include "Paths.h"
 #include "config.h"
 
 
@@ -55,7 +55,7 @@ void manageArguments(argparse::ArgumentParser& program)
 
 int main(int argc, char** argv)
 {
-    argparse::ArgumentParser program("b_main", { project_version.begin(), project_version.end() });
+    argparse::ArgumentParser program("b_main", { platform_project_version.begin(), platform_project_version.end() });
     manageArguments(program);
     std::string file_name, model_name, title, hyperparameters_file;
     json hyperparameters_json;

src/manage/CommandParser.cc

@@ -2,8 +2,8 @@
 #include <iostream>
 #include <sstream>
 #include <algorithm>
-#include "Colors.h"
-#include "Utils.h"
+#include "common/Colors.h"
+#include "common/Utils.h"
 
 namespace platform {
     void CommandParser::messageError(const std::string& message)

src/manage/ManageResults.cc

@@ -1,13 +1,13 @@
-#include "ManageResults.h"
-#include "CommandParser.h"
 #include <filesystem>
 #include <tuple>
-#include "Colors.h"
-#include "CLocale.h"
-#include "Paths.h"
-#include "ReportConsole.h"
-#include "ReportExcel.h"
-#include "ReportExcelCompared.h"
+#include "common/Colors.h"
+#include "common/CLocale.h"
+#include "common/Paths.h"
+#include "reports/ReportConsole.h"
+#include "reports/ReportExcel.h"
+#include "reports/ReportExcelCompared.h"
+#include "CommandParser.h"
+#include "ManageResults.h"
 
 namespace platform {
 

src/manage/ManageResults.h

@@ -1,7 +1,7 @@
 #ifndef MANAGE_RESULTS_H
 #define MANAGE_RESULTS_H
+#include <xlsxwriter.h>
 #include "Results.h"
-#include "xlsxwriter.h"
 
 namespace platform {
     class ManageResults {

src/manage/Results.cc

@@ -1,5 +1,5 @@
-#include "Results.h"
 #include <algorithm>
+#include "Results.h"
 
 namespace platform {
     Results::Results(const std::string& path, const std::string& model, const std::string& score, bool complete, bool partial) :

src/manage/Results.h

@@ -4,7 +4,7 @@
 #include <vector>
 #include <string>
 #include <nlohmann/json.hpp>
-#include "Result.h"
+#include "main/Result.h"
 namespace platform {
     using json = nlohmann::json;
     class Results {

src/manage/b_manage.cc

@@ -33,7 +33,7 @@ void manageArguments(argparse::ArgumentParser& program, int argc, char** argv)
 
 int main(int argc, char** argv)
 {
-    auto program = argparse::ArgumentParser("b_manage", { project_version.begin(), project_version.end() });
+    auto program = argparse::ArgumentParser("b_manage", { platform_project_version.begin(), platform_project_version.end() });
     manageArguments(program, argc, argv);
     int number = program.get<int>("number");
     std::string model = program.get<std::string>("model");

src/reports/ExcelFile.cc

@@ -1,5 +1,5 @@
+#include "common/Paths.h"
 #include "ExcelFile.h"
-#include "Paths.h"
 
 namespace platform {
     ExcelFile::ExcelFile()

src/reports/ExcelFile.h

@@ -3,7 +3,7 @@
 #include <locale>
 #include <string>
 #include <map>
-#include "xlsxwriter.h"
+#include <xlsxwriter.h>
 
 namespace platform {
     struct separated : std::numpunct<char> {

src/reports/ReportBase.cc

@@ -1,8 +1,8 @@
 #include <sstream>
 #include <locale>
-#include "Datasets.h"
+#include "common/Datasets.h"
+#include "common/DotEnv.h"
 #include "ReportBase.h"
-#include "DotEnv.h"
 
 namespace platform {
     ReportBase::ReportBase(json data_, bool compare) : data(data_), compare(compare), margin(0.1)

src/reports/ReportBase.h

@@ -2,9 +2,9 @@
 #define REPORTBASE_H
 #include <string>
 #include <iostream>
-#include "Paths.h"
-#include "Symbols.h"
 #include <nlohmann/json.hpp>
+#include "common/Paths.h"
+#include "common/Symbols.h"
 
 using json = nlohmann::json;
 namespace platform {

src/reports/ReportConsole.cc

@@ -1,9 +1,9 @@
 #include <iostream>
 #include <sstream>
 #include <locale>
+#include "best/BestScore.h"
+#include "common/CLocale.h"
 #include "ReportConsole.h"
-#include "BestScore.h"
-#include "CLocale.h"
 
 namespace platform {
     std::string ReportConsole::headerLine(const std::string& text, int utf = 0)

src/reports/ReportConsole.h

@@ -1,8 +1,8 @@
 #ifndef REPORTCONSOLE_H
 #define REPORTCONSOLE_H
 #include <string>
+#include "common/Colors.h"
 #include "ReportBase.h"
-#include "Colors.h"
 
 namespace platform {
     const int MAXL = 133;

src/reports/ReportExcel.cc

@@ -1,7 +1,7 @@
 #include <sstream>
 #include <locale>
+#include "best/BestScore.h"
 #include "ReportExcel.h"
-#include "BestScore.h"
 
 
 namespace platform {

src/reports/ReportExcel.h

@@ -1,10 +1,10 @@
 #ifndef REPORTEXCEL_H
 #define REPORTEXCEL_H
-#include<map>
-#include "xlsxwriter.h"
+#include <map>
+#include <xlsxwriter.h>
+#include "common/Colors.h"
 #include "ReportBase.h"
 #include "ExcelFile.h"
-#include "Colors.h"
 namespace platform {
     class ReportExcel : public ReportBase, public ExcelFile {
     public:

tests/CMakeLists.txt

@@ -5,8 +5,8 @@ if(ENABLE_TESTING)
         ${Platform_SOURCE_DIR}/lib/argparse/include
         ${Platform_SOURCE_DIR}/lib/mdlp
         ${Platform_SOURCE_DIR}/lib/Files
-        /usr/local/include/bayesnet
-        /usr/local/include/pyclassifiers
+        ${CMAKE_BINARY_DIR}/configured_files/include
+        /usr/local/include
     )
     set(TEST_SOURCES_PLATFORM TestUtils.cc TestPlatform.cc)
     add_executable(${TEST_PLATFORM} ${TEST_SOURCES_PLATFORM})

tests/TestPlatform.cc

@@ -11,6 +11,6 @@
 
 TEST_CASE("Test Python Classifiers score", "[PyClassifiers]")
 {
-    std::string version = { project_version.begin(), project_version.end() };
+    std::string version = { platform_project_version.begin(), platform_project_version.end() };
     REQUIRE(version == "1.0.4");
 }

tests/TestUtils.cc

@@ -5,7 +5,7 @@ class Paths {
 public:
     static std::string datasets()
     {
-        return { data_path.begin(), data_path.end() };
+        return { platform_data_path.begin(), platform_data_path.end() };
     }
 };