Merge a2ba5ee7e0 into 7b0673fd4b

Fix coverage report
Add coverage badge to README

.github/workflows/build.yml

@@ -13,7 +13,7 @@ jobs:
     env:
       BUILD_WRAPPER_OUT_DIR: build_wrapper_output_directory # Directory where build-wrapper output will be placed
     steps:
-      - uses: actions/checkout@v4.1.6
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
       - name: Install sonar-scanner and build-wrapper
@@ -28,17 +28,16 @@ jobs:
           unzip libtorch-cxx11-abi-shared-with-deps-2.3.1+cpu.zip
       - name: Tests & build-wrapper
         run: |
-          cmake -S . -B build -Wno-dev -DCMAKE_PREFIX_PATH=$(pwd)/libtorch -DENABLE_TESTING=ON
-          build-wrapper-linux-x86-64 --out-dir ${{ env.BUILD_WRAPPER_OUT_DIR }} cmake --build build/ --config Release
+          cmake -S . -B build -Wno-dev -DCMAKE_PREFIX_PATH=$(pwd)/libtorch -DCMAKE_BUILD_TYPE=Debug -DENABLE_TESTING=ON
+          build-wrapper-linux-x86-64 --out-dir ${{ env.BUILD_WRAPPER_OUT_DIR }} cmake --build build/ --config Debug
+          cmake --build build -j 4
           cd build
-          make
-          ctest -C Release --output-on-failure --test-dir tests
-          cd ..
-          gcovr -f CPPFImdlp.cpp -f Metrics.cpp -f BinDisc.cpp -f Discretizer.cpp --txt --sonarqube=coverage.xml
+          ctest -C Debug --output-on-failure -j 4
+          gcovr -f ../CPPFImdlp.cpp -f ../Metrics.cpp -f ../BinDisc.cpp -f ../Discretizer.cpp --txt --sonarqube=coverage.xml
       - name: Run sonar-scanner
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         run: |
           sonar-scanner --define sonar.cfamily.build-wrapper-output="${{ env.BUILD_WRAPPER_OUT_DIR }}" \
-                        --define sonar.coverageReportPaths=coverage.xml
+                        --define sonar.coverageReportPaths=build/coverage.xml

BinDisc.cpp

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #include <algorithm>
 #include <cmath>
 #include "BinDisc.h"

BinDisc.h

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #ifndef BINDISC_H
 #define BINDISC_H
 

CMakeLists.txt

@@ -6,6 +6,15 @@ include_directories(${TORCH_INCLUDE_DIRS})
 add_library(mdlp CPPFImdlp.cpp Metrics.cpp BinDisc.cpp Discretizer.cpp)
 target_link_libraries(mdlp "${TORCH_LIBRARIES}")
 add_subdirectory(sample)
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG}  -fno-elide-constructors")
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3")
+if (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+    set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fno-default-inline")
+endif()
 if (ENABLE_TESTING)
+    MESSAGE("Debug mode")
+    enable_testing()
+    set(CODE_COVERAGE ON)
+    SET(GCC_COVERAGE_LINK_FLAGS " ${GCC_COVERAGE_LINK_FLAGS} -lgcov --coverage")
     add_subdirectory(tests)
-endif(ENABLE_TESTING)
+endif(ENABLE_TESTING)

CPPFImdlp.cpp

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #include <numeric>
 #include <algorithm>
 #include <set>

CPPFImdlp.h

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #ifndef CPPFIMDLP_H
 #define CPPFIMDLP_H
 

Discretizer.cpp

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #include "Discretizer.h"
 
 namespace mdlp {
@@ -14,11 +20,6 @@ namespace mdlp {
         for (const precision_t& item : data) {
             auto pos = bound(first, last, item);
             int number = pos - first;
-            /*
-            OJO
-            */
-            if (number < 0)
-                throw std::runtime_error("number is less than 0 in discretizer::transform");
             discretizedData.push_back(number);
         }
         return discretizedData;

Discretizer.h

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #ifndef DISCRETIZER_H
 #define DISCRETIZER_H
 
@@ -24,7 +30,6 @@ namespace mdlp {
         torch::Tensor fit_transform_t(torch::Tensor& X_, torch::Tensor& y_);
         static inline std::string version() { return "1.2.3"; };
     protected:
-        void normalize_cutpoints();
         labels_t discretizedData = labels_t();
         cutPoints_t cutPoints; // At least two cutpoints must be provided, the first and the last will be ignored in transform
         bound_dir_t direction; // used in transform

Makefile

@@ -1,13 +1,32 @@
 SHELL := /bin/bash
 .DEFAULT_GOAL := build
 .PHONY: build test
+lcov := lcov
 
 build: 
 	@if [ -d build_release ]; then rm -fr build_release; fi
 	@mkdir build_release
 	@cmake -B build_release -S . -DCMAKE_BUILD_TYPE=Release -DENABLE_TESTING=OFF
-	@cmake --build build_release
+	@cmake --build build_release -j 8
 
 test:
-	@echo "Testing..."
-	@cd tests && ./test
+	@if [ -d build_debug ]; then rm -fr build_debug; fi
+	@mkdir build_debug
+	@cmake -B build_debug -S . -DCMAKE_BUILD_TYPE=Debug -DENABLE_TESTING=ON
+	@cmake --build build_debug -j 8
+	@cd build_debug/tests && ctest --output-on-failure -j 8
+	@cd build_debug/tests && $(lcov) --capture --directory ../ --demangle-cpp --ignore-errors source,source --ignore-errors mismatch --output-file coverage.info >/dev/null 2>&1; \
+	$(lcov) --remove coverage.info '/usr/*' --output-file coverage.info >/dev/null 2>&1; \
+	$(lcov) --remove coverage.info 'lib/*' --output-file coverage.info >/dev/null 2>&1; \
+	$(lcov) --remove coverage.info 'libtorch/*' --output-file coverage.info >/dev/null 2>&1; \
+	$(lcov) --remove coverage.info 'tests/*' --output-file coverage.info >/dev/null 2>&1; \
+	$(lcov) --remove coverage.info 'gtest/*' --output-file coverage.info >/dev/null 2>&1;
+	@genhtml build_debug/tests/coverage.info --demangle-cpp --output-directory build_debug/tests/coverage --title "Discretizer mdlp Coverage Report" -s -k -f --legend
+	@echo "* Coverage report is generated at build_debug/tests/coverage/index.html"
+	@which python || (echo ">>> Please install python"; exit 1)
+	@if [ ! -f build_debug/tests/coverage.info ]; then \
+		echo ">>> No coverage.info file found!"; \
+		exit 1; \
+	fi
+	@echo ">>> Updating coverage badge..."
+	@env python update_coverage.py build_debug/tests

Metrics.cpp

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #include "Metrics.h"
 #include <set>
 #include <cmath>

Metrics.h

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #ifndef CCMETRICS_H
 #define CCMETRICS_H
 

README.md

@@ -1,6 +1,7 @@
 [![Build](https://github.com/rmontanana/mdlp/actions/workflows/build.yml/badge.svg)](https://github.com/rmontanana/mdlp/actions/workflows/build.yml)
 [![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=rmontanana_mdlp&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=rmontanana_mdlp)
 [![Reliability Rating](https://sonarcloud.io/api/project_badges/measure?project=rmontanana_mdlp&metric=reliability_rating)](https://sonarcloud.io/summary/new_code?id=rmontanana_mdlp)
+[![Coverage Badge](https://img.shields.io/badge/Coverage-100,0%25-green)](html/index.html)
 
 # <img src="logo.png" alt="logo" width="50"/> mdlp
 
@@ -31,15 +32,14 @@ Other features:
 To run the sample, just execute the following commands:
 
 ```bash
-cmake -B build -S .
-cmake --build build
-build/sample/sample -f iris -m 2
-build/sample/sample -h
+make build
+build_release/sample/sample -f iris -m 2
+build_release/sample/sample -h
 ```
 
 ## Test
 
-To run the tests and see coverage (llvm & gcovr have to be installed), execute the following commands:
+To run the tests and see coverage (llvm with lcov and genhtml have to be installed), execute the following commands:
 
 ```bash
 make test

sample/sample.cpp

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #include <iostream>
 #include <vector>
 #include <iomanip>

sonar-project.properties

@@ -3,7 +3,7 @@ sonar.organization=rmontanana
 
 # This is the name and version displayed in the SonarCloud UI.
 sonar.projectName=mdlp
-sonar.projectVersion=1.2.1
+sonar.projectVersion=2.0.0
 # sonar.test.exclusions=tests/**
 # sonar.tests=tests/
 # sonar.coverage.exclusions=tests/**,sample/**
@@ -12,3 +12,4 @@ sonar.projectVersion=1.2.1
 
 # Encoding of the source code. Default is default system encoding
 sonar.sourceEncoding=UTF-8
+sonar.cfamily.compile-commands

tests/ArffFiles.cpp

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #include "ArffFiles.h"
 #include <fstream>
 #include <sstream>

tests/ArffFiles.h

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #ifndef ARFFFILES_H
 #define ARFFFILES_H
 

tests/BinDisc_unittest.cpp

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #include <fstream>
 #include <string>
 #include <iostream>

tests/Discretizer_unittest.cpp

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #include <fstream>
 #include <string>
 #include <iostream>
@@ -20,7 +26,7 @@ namespace mdlp {
         return "../../tests/datasets/";
     }
     const std::string data_path = set_data_path();
-
+    const labels_t iris_quantile = { 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 2, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 3, 3, 3, 1, 3, 1, 2, 0, 3, 1, 0, 2, 2, 2, 1, 3, 1, 2, 2, 1, 2, 2, 2, 2, 3, 3, 3, 3, 2, 1, 1, 1, 2, 2, 1, 2, 3, 2, 1, 1, 1, 2, 2, 0, 1, 1, 1, 2, 1, 1, 2, 2, 3, 2, 3, 3, 0, 3, 3, 3, 3, 3, 3, 1, 2, 3, 3, 3, 3, 2, 3, 1, 3, 2, 3, 3, 2, 2, 3, 3, 3, 3, 3, 2, 2, 3, 2, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 3, 2, 2 };
     TEST(Discretizer, Version)
     {
         Discretizer* disc = new BinDisc(4, strategy_t::UNIFORM);
@@ -51,9 +57,42 @@ namespace mdlp {
         auto y = labels_t();
         disc->fit(X[0], y);
         auto Xt = disc->transform(X[0]);
-        labels_t expected = { 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 2, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 3, 3, 3, 1, 3, 1, 2, 0, 3, 1, 0, 2, 2, 2, 1, 3, 1, 2, 2, 1, 2, 2, 2, 2, 3, 3, 3, 3, 2, 1, 1, 1, 2, 2, 1, 2, 3, 2, 1, 1, 1, 2, 2, 0, 1, 1, 1, 2, 1, 1, 2, 2, 3, 2, 3, 3, 0, 3, 3, 3, 3, 3, 3, 1, 2, 3, 3, 3, 3, 2, 3, 1, 3, 2, 3, 3, 2, 2, 3, 3, 3, 3, 3, 2, 2, 3, 2, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 3, 2, 2 };
         delete disc;
-        EXPECT_EQ(expected, Xt);
+        EXPECT_EQ(iris_quantile, Xt);
+    }
+
+    TEST(Discretizer, BinIrisQuantileTorch)
+    {
+        ArffFiles file;
+        Discretizer* disc = new BinDisc(4, strategy_t::QUANTILE);
+        file.load(data_path + "iris.arff", true);
+        auto X = file.getX();
+        auto y = file.getY();
+        auto X_torch = torch::tensor(X[0], torch::kFloat32);
+        auto yt = torch::tensor(y, torch::kInt32);
+        disc->fit_t(X_torch, yt);
+        torch::Tensor Xt = disc->transform_t(X_torch);
+        delete disc;
+        EXPECT_EQ(iris_quantile.size(), Xt.size(0));
+        for (int i = 0; i < iris_quantile.size(); ++i) {
+            EXPECT_EQ(iris_quantile.at(i), Xt[i].item<int>());
+        }
+    }
+    TEST(Discretizer, BinIrisQuantileTorchFit_transform)
+    {
+        ArffFiles file;
+        Discretizer* disc = new BinDisc(4, strategy_t::QUANTILE);
+        file.load(data_path + "iris.arff", true);
+        auto X = file.getX();
+        auto y = file.getY();
+        auto X_torch = torch::tensor(X[0], torch::kFloat32);
+        auto yt = torch::tensor(y, torch::kInt32);
+        torch::Tensor Xt = disc->fit_transform_t(X_torch, yt);
+        delete disc;
+        EXPECT_EQ(iris_quantile.size(), Xt.size(0));
+        for (int i = 0; i < iris_quantile.size(); ++i) {
+            EXPECT_EQ(iris_quantile.at(i), Xt[i].item<int>());
+        }
     }
 
     TEST(Discretizer, FImdlpIris)

tests/Experiments.hpp

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #ifndef EXPERIMENTS_HPP
 #define EXPERIMENTS_HPP
 #include<sstream>

tests/FImdlp_unittest.cpp

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #include "gtest/gtest.h"
 #include "../Metrics.h"
 #include "../CPPFImdlp.h"

tests/Metrics_unittest.cpp

@@ -1,3 +1,9 @@
+// ****************************************************************
+// SPDX - FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+// SPDX - FileType: SOURCE
+// SPDX - License - Identifier: MIT
+// ****************************************************************
+
 #include "gtest/gtest.h"
 #include "../Metrics.h"
 

tests/Testing/Temporary/CTestCostData.txt

@@ -1 +0,0 @@
----

tests/Testing/Temporary/LastTest.log

@@ -1,3 +0,0 @@
-Start testing: Jul 03 18:09 CEST
-----------------------------------------------------------
-End testing: Jul 03 18:09 CEST

tests/test

@@ -1,15 +0,0 @@
-#!/bin/bash
-if [ -d build ] && [ "$1" != "run" ]; then
-	rm -fr build
-fi
-if [ -d gcovr-report ] ; then
-	rm -fr gcovr-report
-fi
-cmake -S . -B build -Wno-dev -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS="--coverage" -DCMAKE_C_FLAGS="--coverage"
-cmake --build build
-cd build
-ctest --output-on-failure -j 8
-cd ..
-mkdir gcovr-report
-cd ..
-gcovr  --gcov-filter "CPPFImdlp.cpp" --gcov-filter "Metrics.cpp" --gcov-filter "BinDisc.cpp" --gcov-filter "Discretizer.cpp" --txt --sonarqube=tests/gcovr-report/coverage.xml --exclude-noncode-lines

tests/tests_do.py

@@ -1,3 +1,9 @@
+# ***************************************************************
+# SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+# SPDX-FileType: SOURCE
+# SPDX-License-Identifier: MIT
+# ***************************************************************
+
 import json
 from sklearn.preprocessing import KBinsDiscretizer
 

update_coverage.py

@@ -0,0 +1,38 @@
+# ***************************************************************
+# SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
+# SPDX-FileType: SOURCE
+# SPDX-License-Identifier: MIT
+# ***************************************************************
+
+import subprocess
+import sys
+
+readme_file = "README.md"
+print("Updating coverage...")
+# Generate badge line
+output = subprocess.check_output(
+    "lcov --summary " + sys.argv[1] + "/coverage.info",
+    shell=True,
+)
+value = output.decode("utf-8").strip()
+percentage = 0
+for line in value.splitlines():
+    if "lines" in line:
+        percentage = float(line.split(":")[1].split("%")[0])
+        break
+print(f"Coverage: {percentage}%")
+if percentage < 90:
+    print("⛔Coverage is less than 90%. I won't update the badge.")
+    sys.exit(1)
+percentage_label = str(percentage).replace(".", ",")
+coverage_line = f"[![Coverage Badge](https://img.shields.io/badge/Coverage-{percentage_label}%25-green)](html/index.html)"
+# Update README.md
+with open(readme_file, "r") as f:
+    lines = f.readlines()
+with open(readme_file, "w") as f:
+    for line in lines:
+        if "img.shields.io/badge/Coverage" in line:
+            f.write(coverage_line + "\n")
+        else:
+            f.write(line)
+print(f"✅Coverage updated with value: {percentage}")