Feature/refresh saes

.editorconfig

@@ -0,0 +1,53 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+trim_trailing_whitespace = true
+
+# Python files
+[*.py]
+indent_style = space
+indent_size = 4
+max_line_length = 120
+
+# Markdown files
+[*.md]
+trim_trailing_whitespace = false
+max_line_length = off
+
+# YAML files
+[*.{yml,yaml}]
+indent_style = space
+indent_size = 2
+
+# JSON files
+[*.json]
+indent_style = space
+indent_size = 2
+
+# TOML files
+[*.toml]
+indent_style = space
+indent_size = 4
+
+# reStructuredText files
+[*.rst]
+indent_style = space
+indent_size = 3
+max_line_length = off
+
+# Makefile
+[Makefile]
+indent_style = tab
+
+# Shell scripts
+[*.sh]
+indent_style = space
+indent_size = 2
+

.github/workflows/test.yml

@@ -21,14 +21,17 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+      with:
+        version: "latest"
     - name: Set up Python 3.10
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: "3.10"
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install -e .[test]
+        uv pip install --system -e .[test,html]
     - name: Test with unittest
       run: |
         coverage run -m unittest discover tests

.gitignore

@@ -134,12 +134,17 @@ celerybeat.pid
 # Environments
 .env
 .venv
+.venv/
 env/
 venv/
 ENV/
 env.bak/
 venv.bak/
 
+# uv
+uv.lock
+.python-version
+
 # Spyder project settings
 .spyderproject
 .spyproject

.pre-commit-config.yaml

@@ -0,0 +1,52 @@
+# Pre-commit hooks for SAES
+# Install with: pre-commit install
+# Run manually with: pre-commit run --all-files
+
+repos:
+  # General file checks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+      - id: check-added-large-files
+        args: ['--maxkb=1000']
+      - id: check-merge-conflict
+      - id: check-case-conflict
+      - id: mixed-line-ending
+        args: ['--fix=lf']
+
+  # Python code formatting
+  - repo: https://github.com/psf/black
+    rev: 24.1.1
+    hooks:
+      - id: black
+        language_version: python3.10
+        args: ['--line-length=120']
+
+  # Import sorting
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ['--profile=black', '--line-length=120']
+
+  # Linting
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        args: ['--max-line-length=120', '--extend-ignore=E203,W503']
+        additional_dependencies: [flake8-docstrings]
+
+  # Type checking (optional - may need adjustments)
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v1.8.0
+  #   hooks:
+  #     - id: mypy
+  #       additional_dependencies: [types-all]
+  #       args: ['--ignore-missing-imports']
+

CHANGELOG.md

@@ -2,10 +2,141 @@
 
 All notable changes to this project will be documented in this file.
 
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
+### Fixed
+- Corrected 'frtom' typo to 'from' in all plot module docstrings (23 instances across 5 files)
+
 ## [Released]
 
-## [RELEASE_VERSION] - Released on RELEASE_DATE by COMMIT_AUTHOR
+## [1.3.6] - 2025-03-18
+
+### Added
+- HistoPlot visualization for algorithm performance distribution
+- Violin plot for enhanced performance distribution visualization
+
+### Fixed
+- Various bug fixes and added code comments for better maintainability
+
+## [1.3.5] - 2025-03-13
+
+### Added
+- Anova and T-test tables for parametric statistical analysis
+- Extra Friedman test variations (aligned-rank, Quade) for non-parametric analysis
+- ML notebook example demonstrating library usage with machine learning algorithms
+- Comprehensive tests for new features
+
+### Changed
+- Mean/median now used as estimators of best and second-best performance in LaTeX tables
+- Improved documentation across the entire library
+- Updated Bayesian notebook with better examples
+
+### Fixed
+- Bug in MeanMedian table show() function
+
+## [1.3.4] - 2025-03-06
+
+### Added
+- Frequency graph to the Bayesian posterior plot (Pplot)
+- Article references for statistical test implementations
+
+### Fixed
+- Fixed dependency issues (v2)
+- Fixed tests to accommodate new changes
+
+## [1.3.2] - 2025-03-06
+
+### Changed
+- Updated internal dependencies and configurations
+
+## [1.3.1] - 2025-03-05
+
+### Fixed
+- Minor bug fixes and improvements
+
+## [1.3.0] - 2025-03-05
+
+### Added
+- Bayesian posterior plot (Pplot) for probabilistic algorithm comparison
+- HTML module for generating interactive analysis reports
+
+### Changed
+- Updated multi-objective fronts notebook
+- Updated sphinx documentation
+
+## [1.2.0] - 2025-03-04
+
+### Added
+- Reference fronts support in 2D and 3D for multi-objective optimization module
+- Parallel coordinates visualization for multi-objective analysis
+- Fronts notebook with comprehensive examples
+
+### Changed
+- Updated all SAES fstring documentation format
+
+### Fixed
+- Bug fixed in pareto_front.py
+
+## [1.1.0] - 2025-02-26
+
+### Changed
+- Updated Sphinx documentation to v1.1.0
+- Updated README.md with improved examples and instructions
+
+## [1.0.3] - 2025-02-07
+
+### Changed
+- Documentation improvements and README updates
+
+## [1.0.2] - 2025-02-06
+
+### Changed
+- Minor improvements and documentation updates
+
+## [1.0.1] - 2025-02-06
+
+### Fixed
+- Initial post-release bug fixes
+
+## [1.0.0] - 2025-02-05
+
+### Added
+- First stable release
+- Core statistical analysis features (Friedman test, Wilcoxon signed-rank test)
+- LaTeX table generation (Median, Friedman, Wilcoxon tables)
+- Visualization tools (Boxplot, Critical Distance plot)
+- Multi-objective optimization support (Pareto front visualization)
+- Command-line interface
+- Comprehensive documentation
+
+## [0.6.0] - 2025-02-03
+
+### Added
+- Pre-release version with core features
+- Initial multi-objective optimization module
+
+## [0.5.1] - 2025-01-21
+
+### Added
+- Initial beta release
+- Basic statistical testing framework
+- CSV data processing utilities
+
+[Unreleased]: https://github.com/jMetal/SAES/compare/v1.3.6...HEAD
+[1.3.6]: https://github.com/jMetal/SAES/compare/v1.3.5...v1.3.6
+[1.3.5]: https://github.com/jMetal/SAES/compare/v1.3.4...v1.3.5
+[1.3.4]: https://github.com/jMetal/SAES/compare/v1.3.2...v1.3.4
+[1.3.2]: https://github.com/jMetal/SAES/compare/v1.3.1...v1.3.2
+[1.3.1]: https://github.com/jMetal/SAES/compare/v1.3.0...v1.3.1
+[1.3.0]: https://github.com/jMetal/SAES/compare/v1.2.0...v1.3.0
+[1.2.0]: https://github.com/jMetal/SAES/compare/v1.1.0...v1.2.0
+[1.1.0]: https://github.com/jMetal/SAES/compare/v1.0.3...v1.1.0
+[1.0.3]: https://github.com/jMetal/SAES/compare/v1.0.2...v1.0.3
+[1.0.2]: https://github.com/jMetal/SAES/compare/v1.0.1...v1.0.2
+[1.0.1]: https://github.com/jMetal/SAES/compare/v1.0.0...v1.0.1
+[1.0.0]: https://github.com/jMetal/SAES/compare/v0.6.0...v1.0.0
+[0.6.0]: https://github.com/jMetal/SAES/compare/v0.5.1...v0.6.0
+[0.5.1]: https://github.com/jMetal/SAES/releases/tag/v0.5.1