chore: remove Codecov configuration and integrate SonarQube for code analysis

- Deleted the Codecov configuration file as part of the transition to SonarQube for code quality and coverage analysis.
- Updated the  to align coverage exclusions with SonarQube settings, ensuring consistency in coverage reporting.
- Added a new  file to configure SonarQube project settings, including source encoding, exclusions, and test report paths.
- Modified the GitHub Actions workflow to replace Codecov upload steps with SonarQube analysis, enhancing CI/CD integration for code quality checks.
- Updated README.md to reflect the new SonarQube badges for quality and coverage metrics.

Author: LouisTier

.github/workflows/test.yml

@@ -18,8 +18,8 @@ jobs:
         pytorch-version: ["2.7.0+cu126"]
         exclude:
           # Exclude some combinations to reduce CI load: macos doesn't work with CUDA, and ubuntu 3.9 triggers Codecov not available
-          - os: ubuntu-latest
-            python-version: "3.9"
+          # - os: ubuntu-latest
+          #   python-version: "3.9"
           - os: macos-latest
             python-version: "3.9"
           - os: macos-latest
@@ -71,17 +71,13 @@ jobs:
       #     -n auto \
       #     -m "unit or gpu"
 
-    - name: Upload coverage to Codecov
+    - name: Analyze code with SonarQube
       if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9' && matrix.pytorch-version == '2.7.0+cu126'
-      uses: codecov/codecov-action@v5
+      uses: SonarSource/sonarqube-scan-action@v5
       with:
-        files: coverage.xml
-        flags: unittests
-        name: codecov-umbrella
-        fail_ci_if_error: true
-        verbose: true
-        token: ${{ secrets.CODECOV_TOKEN }}
-        slug: michelin/TorchSOM
+        token: ${{ secrets.SONAR_TOKEN }}
+        # organization: michelin
+        # projectKey: michelin_TorchSOM
 
     - name: Upload test results
       uses: actions/upload-artifact@v4

README.md

@@ -2,19 +2,31 @@
 
 <div align="center">
 
-[![PyPI version](https://img.shields.io/pypi/v/torchsom.svg)](https://pypi.org/project/torchsom/)
-[![Python versions](https://img.shields.io/pypi/pyversions/torchsom.svg)](https://pypi.org/project/torchsom/)
+<!-- Global Package information -->
+[![PyPI version](https://img.shields.io/pypi/v/torchsom.svg?color=blue)](https://pypi.org/project/torchsom/)
+[![Python versions](https://img.shields.io/pypi/pyversions/torchsom.svg?color=blue)](https://pypi.org/project/torchsom/)
 [![PyTorch versions](https://img.shields.io/badge/PyTorch-2.7-EE4C2C.svg)](https://pytorch.org/)
+[![License: Apache 2.0](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/license/apache-2-0)
 
+<!-- Sonar Qube badges -->
+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=michelin_TorchSOM&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=michelin_TorchSOM)
+[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=michelin_TorchSOM&metric=coverage)](https://sonarcloud.io/summary/new_code?id=michelin_TorchSOM)
+[![Reliability Rating](https://sonarcloud.io/api/project_badges/measure?project=michelin_TorchSOM&metric=reliability_rating)](https://sonarcloud.io/summary/new_code?id=michelin_TorchSOM)
+[![Security Rating](https://sonarcloud.io/api/project_badges/measure?project=michelin_TorchSOM&metric=security_rating)](https://sonarcloud.io/summary/new_code?id=michelin_TorchSOM)
+[![Maintainability Rating](https://sonarcloud.io/api/project_badges/measure?project=michelin_TorchSOM&metric=sqale_rating)](https://sonarcloud.io/summary/new_code?id=michelin_TorchSOM)
+
+<!-- [![SonarQube Cloud](https://sonarcloud.io/images/project_badges/sonarcloud-light.svg)](https://sonarcloud.io/summary/new_code?id=michelin_TorchSOM) -->
+
+<!-- GitHub Workflows -->
 [![Tests](https://github.com/michelin/TorchSOM/workflows/Tests/badge.svg)](https://github.com/michelin/TorchSOM/actions/workflows/test.yml)
 [![Code Quality](https://github.com/michelin/TorchSOM/workflows/Code%20Quality/badge.svg)](https://github.com/michelin/TorchSOM/actions/workflows/code-quality.yml)
-<!-- [![Security](https://github.com/michelin/TorchSOM/workflows/Security%20Scanning/badge.svg)](https://github.com/michelin/TorchSOM/actions/workflows/security.yml)
-[![codecov](https://codecov.io/gh/michelin/TorchSOM/branch/main/graph/badge.svg)](https://codecov.io/gh/michelin/TorchSOM) -->
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
-[![License: Apache 2.0](https://img.shields.io/badge/License-Apache%202.0-red.svg)](https://opensource.org/license/apache-2-0)
+[![Downloads](https://static.pepy.tech/badge/torchsom)](https://pepy.tech/project/torchsom)
+<!-- [![Security](https://github.com/michelin/TorchSOM/workflows/Security%20Scanning/badge.svg)](https://github.com/michelin/TorchSOM/actions/workflows/security.yml) -->
 
-<!-- [![Downloads](https://static.pepy.tech/badge/torchsom)](https://pepy.tech/project/torchsom) -->
+<!-- Code Style and Tools -->
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Imports: isort](https://img.shields.io/badge/imports-isort-6c757d.svg?color=blue)](https://pycqa.github.io/isort/)
+[![Ruff](https://img.shields.io/badge/linter-ruff-6c757d.svg?color=blue)](https://github.com/astral-sh/ruff)
 
 <p align="center">
     <img src="assets/logo.jpg" alt="TorchSOM_logo" width="400"/>
@@ -27,6 +39,8 @@
 | [📊 Examples](notebooks/)
 | [🤝 Contributing](CONTRIBUTING.md)
 
+**⭐ If you find [`torchsom`](https://github.com/michelin/TorchSOM) valuable, please consider starring this repository ⭐**
+
 </div>
 
 ---
@@ -39,8 +53,6 @@ Whether you are a researcher or practitioner, TorchSOM empowers you to efficient
 
 TorchSOM is the official implementation accompanying the paper: [TorchSOM: A Scalable PyTorch-Compatible Library for Self-Organizing Maps](update_link), presented at @CONFERENCE, @DATE.
 
-**⭐ If you find TorchSOM valuable, please consider starring this repository ⭐**
-
 ### ⚡ Key Advantages
 
 | Feature | [TorchSOM](https://github.com/michelin/TorchSOM) | [MiniSom](https://github.com/JustGlowing/minisom) | [SOMPY](https://github.com/sevamoo/SOMPY) | [SOMToolbox](https://github.com/ilarinieminen/SOM-Toolbox) |

codecov.yml

@@ -186,16 +186,18 @@ timeout = 300
 source = ["torchsom"]
 # Files to exclude from coverage stats
 omit = [
+    "tests/**",                            # Exclude all test files
+    "docs/**",                             # Exclude documentation
+    "notebooks/**",                        # Exclude Jupyter notebooks
     "torchsom/core/base_som.py",           # Exclude base SOM implementation
-    "torchsom/core/growing/*",             # Exclude growing SOM implementation
-    "torchsom/core/hierarchical/*",        # Exclude hierarchical SOM implementation
-    "torchsom/visualization/*",            # Exclude visualization utilities
+    "torchsom/core/growing/**",            # Exclude growing SOM implementation
+    "torchsom/core/hierarchical/**",       # Exclude hierarchical SOM implementation
+    "torchsom/visualization/**",           # Exclude visualization utilities
     "torchsom/logger.py",                  # Exclude logging utilities
     "torchsom/version.py",                 # Exclude version info file
-    "*/tests/*",                           # Exclude tests themselves
-    "*/conftest.py",                       # Exclude pytest config
-    "*/__init__.py",                       # Exclude package init files
-    "*/setup.py",                          # Exclude setup scripts
+    "**/conftest.py",                      # Exclude pytest config
+    "**/__init__.py",                      # Exclude package init files
+    "**/setup.py",                         # Exclude setup scripts
 ]
 # Measure branch coverage in addition to line coverage
 branch = true

pyproject.toml

@@ -0,0 +1,39 @@
+# Project identification
+sonar.organization=michelin
+sonar.projectKey=michelin_TorchSOM
+sonar.projectName=TorchSOM
+sonar.projectVersion=1.0
+
+# Source encoding
+sonar.sourceEncoding=UTF-8
+
+# Where the source code is
+sonar.sources=torchsom
+
+# Exclusions (aligned with pyproject.toml coverage omit patterns)
+sonar.exclusions=\
+  tests/**,\
+  docs/**,\
+  notebooks/**,\
+  torchsom/core/base_som.py,\
+  torchsom/core/growing/**,\
+  torchsom/core/hierarchical/**,\
+  torchsom/visualization/**,\
+  torchsom/logger.py,\
+  torchsom/version.py,\
+  **/conftest.py,\
+  **/__init__.py,\
+  **/setup.py
+
+# Test sources
+sonar.tests=tests
+
+# Coverage report path (generated by pytest --cov-report=xml)
+sonar.python.coverage.reportPaths=coverage.xml
+
+# Test execution report path (generated by pytest --junit-xml)
+sonar.testExecutionReportPaths=junit.xml
+
+# Optional: Limit analysis to Python only
+sonar.language=py
+sonar.python.version=3.9,3.10,3.11