Move tests library to tests/lib

Add PBC4cip classifier

.gitmodules

@@ -3,8 +3,11 @@
 	path = lib/json
 	url = https://github.com/nlohmann/json.git
 [submodule "lib/catch2"]
-	path = lib/catch2
+	path = tests/lib/catch2
 	url = https://github.com/catchorg/Catch2.git
 [submodule "lib/mdlp"]
-	path = lib/mdlp
+	path = tests/lib/mdlp
 	url = https://github.com/rmontanana/mdlp
+[submodule "tests/lib/Files"]
+	path = tests/lib/Files
+	url = https://github.com/rmontanana/ArffFiles

CMakeLists.txt

@@ -78,9 +78,9 @@ add_subdirectory(pyclfs)
 # -------
 if (ENABLE_TESTING)
   MESSAGE("Testing enabled")
-  add_git_submodule(lib/catch2)
+  add_git_submodule(tests/lib/catch2)
-  add_git_submodule(lib/mdlp)
+  add_git_submodule(tests/lib/mdlp)
-  add_subdirectory(lib/Files)
+  add_subdirectory(tests/lib/Files)
   include(CTest)
   add_subdirectory(tests)
 endif (ENABLE_TESTING)

cmake/modules/CodeCoverage.cmake

@@ -137,7 +137,7 @@
 
 include(CMakeParseArguments)
 
-option(CODE_COVERAGE_VERBOSE "Verbose information" FALSE)
+option(CODE_COVERAGE_VERBOSE "Verbose information" TRUE)
 
 # Check prereqs
 find_program( GCOV_PATH gcov )
@@ -160,8 +160,12 @@ foreach(LANG ${LANGUAGES})
     endif()
   elseif(NOT "${CMAKE_${LANG}_COMPILER_ID}" MATCHES "GNU"
          AND NOT "${CMAKE_${LANG}_COMPILER_ID}" MATCHES "(LLVM)?[Ff]lang")
+         if ("${LANG}" MATCHES "CUDA")
+             message(STATUS "Ignoring CUDA")
+        else()
             message(FATAL_ERROR "Compiler is not GNU or Flang! Aborting...")
         endif()
+  endif()
 endforeach()
 
 set(COVERAGE_COMPILER_FLAGS "-g --coverage"

lib/Files/ArffFiles.cc

@@ -1,168 +0,0 @@
-#include "ArffFiles.h"
-#include <fstream>
-#include <sstream>
-#include <map>
-#include <iostream>
-
-ArffFiles::ArffFiles() = default;
-
-std::vector<std::string> ArffFiles::getLines() const
-{
-    return lines;
-}
-
-unsigned long int ArffFiles::getSize() const
-{
-    return lines.size();
-}
-
-std::vector<std::pair<std::string, std::string>> ArffFiles::getAttributes() const
-{
-    return attributes;
-}
-
-std::string ArffFiles::getClassName() const
-{
-    return className;
-}
-
-std::string ArffFiles::getClassType() const
-{
-    return classType;
-}
-
-std::vector<std::vector<float>>& ArffFiles::getX()
-{
-    return X;
-}
-
-std::vector<int>& ArffFiles::getY()
-{
-    return y;
-}
-
-void ArffFiles::loadCommon(std::string fileName)
-{
-    std::ifstream file(fileName);
-    if (!file.is_open()) {
-        throw std::invalid_argument("Unable to open file");
-    }
-    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") != std::string::npos || line.find("@ATTRIBUTE") != std::string::npos) {
-            std::stringstream ss(line);
-            ss >> keyword >> attribute;
-            type = "";
-            while (ss >> type_w)
-                type += type_w + " ";
-            attributes.emplace_back(trim(attribute), trim(type));
-            continue;
-        }
-        if (line[0] == '@') {
-            continue;
-        }
-        lines.push_back(line);
-    }
-    file.close();
-    if (attributes.empty())
-        throw std::invalid_argument("No attributes found");
-}
-
-void ArffFiles::load(const std::string& fileName, bool classLast)
-{
-    int labelIndex;
-    loadCommon(fileName);
-    if (classLast) {
-        className = std::get<0>(attributes.back());
-        classType = std::get<1>(attributes.back());
-        attributes.pop_back();
-        labelIndex = static_cast<int>(attributes.size());
-    } else {
-        className = std::get<0>(attributes.front());
-        classType = std::get<1>(attributes.front());
-        attributes.erase(attributes.begin());
-        labelIndex = 0;
-    }
-    generateDataset(labelIndex);
-}
-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 = std::get<0>(attributes[i]);
-            classType = std::get<1>(attributes[i]);
-            attributes.erase(attributes.begin() + i);
-            labelIndex = i;
-            found = true;
-            break;
-        }
-    }
-    if (!found) {
-        throw std::invalid_argument("Class name not found");
-    }
-    generateDataset(labelIndex);
-}
-
-void ArffFiles::generateDataset(int labelIndex)
-{
-    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++) {
-        std::stringstream ss(lines[i]);
-        std::string value;
-        int pos = 0;
-        int xIndex = 0;
-        while (getline(ss, value, ',')) {
-            if (pos++ == labelIndex) {
-                yy[i] = value;
-            } else {
-                if (value == "?") {
-                    X[xIndex++][i] = -1;
-                    removeLines.push_back(i);
-                } else
-                    X[xIndex++][i] = stof(value);
-            }
-        }
-    }
-    for (auto i : removeLines) {
-        yy.erase(yy.begin() + i);
-        for (auto& x : X) {
-            x.erase(x.begin() + i);
-        }
-    }
-    y = factorize(yy);
-}
-
-std::string ArffFiles::trim(const std::string& 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;
-}
-
-std::vector<int> ArffFiles::factorize(const std::vector<std::string>& labels_t)
-{
-    std::vector<int> yy;
-    yy.reserve(labels_t.size());
-    std::map<std::string, int> labelMap;
-    int i = 0;
-    for (const std::string& label : labels_t) {
-        if (labelMap.find(label) == labelMap.end()) {
-            labelMap[label] = i++;
-        }
-        yy.push_back(labelMap[label]);
-    }
-    return yy;
-}

lib/Files/ArffFiles.h

@@ -1,32 +0,0 @@
-#ifndef ARFFFILES_H
-#define ARFFFILES_H
-
-#include <string>
-#include <vector>
-
-class ArffFiles {
-private:
-    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(std::string);
-public:
-    ArffFiles();
-    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;
-    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

lib/Files/CMakeLists.txt

@@ -1 +0,0 @@
-add_library(ArffFiles ArffFiles.cc)

pyclfs/CMakeLists.txt

@@ -4,5 +4,5 @@ include_directories(
     ${PyClassifiers_SOURCE_DIR}/lib/json/include
     ${Bayesnet_INCLUDE_DIRS}
 )
-add_library(PyClassifiers ODTE.cc STree.cc SVC.cc RandomForest.cc XGBoost.cc PyClassifier.cc PyWrap.cc)
+add_library(PyClassifiers ODTE.cc STree.cc SVC.cc RandomForest.cc XGBoost.cc PyClassifier.cc PyWrap.cc PBC4cip.cc)
 target_link_libraries(PyClassifiers ${Python3_LIBRARIES} "${TORCH_LIBRARIES}" ${LIBTORCH_PYTHON} Boost::boost Boost::python Boost::numpy)

pyclfs/PBC4cip.cc

@@ -0,0 +1,8 @@
+#include "PBC4cip.h"
+
+namespace pywrap {
+    PBC4cip::PBC4cip() : PyClassifier("core.PBC4cip", "PBC4cip", true)
+    {
+        validHyperparameters = { "random_state" };
+    }
+} /* namespace pywrap */

pyclfs/PBC4cip.h

@@ -0,0 +1,13 @@
+#ifndef PBC4CIP_H
+#define PBC4CIP_H
+#include "PyClassifier.h"
+
+namespace pywrap {
+    class PBC4cip : public PyClassifier {
+    public:
+        PBC4cip();
+        ~PBC4cip() = default;
+    };
+
+} /* namespace pywrap */
+#endif /* PBC4CIP_H */

tests/TestPythonClassifiers.cc

@@ -136,3 +136,13 @@ TEST_CASE("XGBoost", "[PyClassifiers]")
 //     }
 //     std::cout << predict << std::endl;
 // }
+TEST_CASE("PBC4cip", "[PyClassifiers]")
+{
+    auto raw = RawDatasets("iris", true);
+    auto clf = pywrap::PBC4cip();
+    clf.fit(raw.Xt, raw.yt, raw.featurest, raw.classNamet, raw.statest);
+    nlohmann::json hyperparameters = { };
+    clf.setHyperparameters(hyperparameters);
+    auto score = clf.score(raw.Xt, raw.yt);
+    REQUIRE(score == Catch::Approx(0.98).epsilon(raw.epsilon));
+}