Merge remote-tracking branch 'origin/master'

# Conflicts:
#	ChangeLog.md

CITATION.cff

@@ -5,7 +5,7 @@ authors:
     given-names: "Nguyen"
     orcid: "https://orcid.org/0000-0001-9994-8747"
 title: "Opfunu: An Open-source Python Library for Optimization Benchmark Functions"
-version: 1.0.1
+version: 1.0.4
 doi: 10.5281/zenodo.3620960
 date-released: 2022-07-13
 url: "https://github.com/thieu1995/opfunu"

CONTRIBUTING.md

@@ -0,0 +1,95 @@
+# Contributing to Opfunu
+
+We appreciate your interest in contributing to Opfunu! This guide details how to contribute in a way that is efficient 
+for everyone.
+
+## Table of Contents
+
+- [Code of Conduct](#code-of-conduct)
+- [Getting Started](#getting-started)
+- [How Can I Contribute?](#how-can-i-contribute)
+- [Pull Requests](#pull-requests)
+- [Issue Tracking](#issue-tracking)
+
+## Code of Conduct
+
+All contributors are expected to adhere to the project's [Code of Conduct](CODE_OF_CONDUCT.md). Please read the document before contributing. 
+
+## Getting Started
+
+1. Fork the project repository and clone your fork:
+
+    ```
+    git clone https://github.com/thieu1995/opfunu.git
+    ```
+
+2. Create a new branch for your changes:
+
+    ```
+    git checkout -b name-of-your-branch
+    ```
+
+3. Make your changes and commit them:
+
+    ```
+    git commit -m "Detailed commit message"
+    ```
+
+4. Push your changes to your fork:
+
+    ```
+    git push origin name-of-your-branch
+    ```
+
+5. Create a pull request from your branch to the Opfunu main branch.
+
+## How Can I Contribute?
+
+Here are some ways to contribute:
+
+- Improve documentation
+- Fix bugs or add new features
+- Write tutorials or blog posts
+- Review code submissions
+- Test the application and report issues
+
+However, before contributing, make sure that the unit tests pass and that new functionality is covered by unit tests. 
+The unit tests can be run using `pytest`. Change working directory to opfunu and then use:
+
+```python
+# Test CEC-based functions
+python -m pytest tests/cec_based
+
+# Test Name-based functions
+python -m pytest tests/name_based
+```
+
+Or you can test all files by:
+
+```python
+python -m pytest
+```
+
+
+## Pull Requests
+
+[Pull requests](https://github.com/thieu1995/opfunu/pulls) are the best way to propose changes to the codebase. We 
+actively welcome your pull requests:
+
+1. Fork the repo and create your branch from `main`.
+2. If you've added code that should be tested, add tests.
+3. If you've changed APIs, update the documentation.
+4. Ensure the test suite passes.
+5. Issue that pull request!
+
+## Issue Tracking
+
+We use [GitHub issues](https://github.com/thieu1995/opfunu/issues) to track public bugs and requests. Please ensure 
+your description is clear and has sufficient instructions to be able to reproduce the issue.
+
+## Any questions?
+
+Don't hesitate to contact us if you have any questions. Contact [@thieu1995](mailto:[email protected])
+or ask your question on issues.
+
+Thank you for your contributions!

ChangeLog.md

@@ -1,15 +1,30 @@
-# Version 1.0.4
+# Version 1.0.5
 
 + Fix schaffer_f7_func to match the cec implementation and reference document
 + Fix zakharov_func to match the cec implementation and reference document
 + Added a direct conversion of the lunacek_bi_rastrigin_cec_func
 + Added tests for cec functions comparing outputs to the reference implementations
 ---------------------------------------------------------------------
+# Version 1.0.4
+
++ Fix p value in F10 and F17 of CEC-2017
++ Add plot_latex to Benchmark class.
++ User can use draw_latex from opfunu to draw their latex equation.
++ Update examples for draw latex function
+
+---------------------------------------------------------------------
+
 # Version 1.0.3
 
 + Optimized katsuura_func performance, at 1M ndim > 80x speedup
++ Add plot_2d, plot_3d to Benchmark class.
++ User can use draw_2d, draw_3d from opfunu to draw their function.
++ Add tutorial on how to integrate with other optimization frameworks like Mealpy, Opytimizer, Niapy
++ Update examples and update documentations
++ Update citation and paper (Got published at Journal of Open Research Software)
 
 ---------------------------------------------------------------------
+
 # Version 1.0.2
 
 + Fix modified_schwefel_func() in operator.py

README.md

@@ -4,7 +4,7 @@
 ---
 
 
-[![GitHub release](https://img.shields.io/badge/release-1.0.2-yellow.svg)](https://github.com/thieu1995/opfunu/releases)
+[![GitHub release](https://img.shields.io/badge/release-1.0.4-yellow.svg)](https://github.com/thieu1995/opfunu/releases)
 [![Wheel](https://img.shields.io/pypi/wheel/gensim.svg)](https://pypi.python.org/pypi/opfunu) 
 [![PyPI version](https://badge.fury.io/py/opfunu.svg)](https://badge.fury.io/py/opfunu)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/opfunu.svg)
@@ -34,6 +34,28 @@ optimization benchmark functions. Contains all CEC competition functions from 20
 * **Dependencies:** numpy, matplotlib
 
 
+# Citation Request 
+
+Please include these citations if you plan to use this library:
+
+- LaTeX:
+
+```bibtex
+  @article{Van_Thieu_2024_Opfunu,
+      author = {Van Thieu, Nguyen},
+      title = {Opfunu: An Open-source Python Library for Optimization Benchmark Functions},
+      doi = {10.5334/jors.508},
+      journal = {Journal of Open Research Software},
+      month = {May},
+      year = {2024}
+  }
+```
+
+- APA:
+
+  Van Thieu, N. (2024). Opfunu: An Open-source Python Library for Optimization Benchmark Functions. <i>Journal of Open Research Software</i>, <i>12</i>(1), 8. https://doi.org/10.5334/jors.508
+
+
 # Installation and Usage
 
 ### Install with pip
@@ -57,44 +79,13 @@ $ python
 >>> opfunu.CEC_DATABASE       # List all cec_based functions
 >>> opfunu.ALL_DATABASE       # List all functions in this library
 
->>> opfunu.get_functions_by_classname("CEC2014")
+>>> opfunu.get_functions_by_classname("MiShra04")
 >>> opfunu.get_functions_based_classname("2015")
->>> opfunu.get_functions_by_ndim(30)
->>> opfunu.get_functions_based_ndim(2)
->>> opfunu.get_all_named_functions()
->>> opfunu.get_all_cec_functions()
->>> opfunu.get_functions()
->>> opfunu.get_cecs()
-```
+>>> opfunu.get_functions_by_ndim(2)
+>>> opfunu.get_functions_based_ndim(50)
 
-### Lib's structure
-
-```code
-
-docs
-examples
-opfunu
-    cec_based
-        cec.py
-        cec2005.py
-        cec2008.py
-        ...
-        cec2021.py
-        cec2022.py
-    name_based
-        a_func.py
-        b_func.py
-        ...
-        y_func.py
-        z_func.py
-    utils
-        operator.py
-        validator.py
-        visualize.py
-    __init__.py
-    benchmark.py
-README.md
-setup.py
+>>> opfunu.get_name_based_functions(ndim=10, continuous=True)
+>>> opfunu.get_cec_based_functions(ndim=2)
 ```
 
 Let's go through some examples.
@@ -124,7 +115,6 @@ func.evaluate(func.create_solution())
 #### 2nd way
 
 ```python
-
 import opfunu
 
 funcs = opfunu.get_functions_by_classname("F12014")
@@ -135,57 +125,91 @@ func.evaluate(func.create_solution())
 
 all_funcs_2014 = opfunu.get_functions_based_classname("2014")
 print(all_funcs_2014)
-
 ```
 
-For more usage examples please look at [examples](/examples) folder.
 
+### How to draw 2D, 3D 
+
+Two ways if you want to draw functions that available in Opfunu.
+
+```python
+from opfunu.cec_based import F12010
+f0 = F12010()
 
+# Visualize opfunu function using method in object
+f0.plot_2d(selected_dims=(2, 3), n_points=300, ct_cmap="viridis", ct_levels=30, ct_alpha=0.7,
+           fixed_strategy="mean", fixed_values=None, title="Contour map of the F1 CEC 2010 function",
+           x_label=None, y_label=None, figsize=(10, 8), filename="2d-f12010", exts=(".png", ".pdf"), verbose=True)
 
-# Get helps (questions, problems)
+f0.plot_3d(selected_dims=(1, 6), n_points=500, ct_cmap="viridis", ct_levels=30, ct_alpha=0.7,
+           fixed_strategy="mean", fixed_values=None, title="3D visualization of the F1 CEC 2010 function",
+           x_label=None, y_label=None, figsize=(10, 8), filename="3d-f12010", exts=(".png", ".pdf"), verbose=True)
 
-* Official source code repo: https://github.com/thieu1995/opfunu
-* Official document: https://opfunu.readthedocs.io/
-* Download releases: https://pypi.org/project/opfunu/
-* Issue tracker: https://github.com/thieu1995/opfunu/issues
-* Notable changes log: https://github.com/thieu1995/opfunu/blob/master/ChangeLog.md
-* Examples with different version: https://github.com/thieu1995/opfunu/blob/master/examples.md
-* Official chat group: https://t.me/+fRVCJGuGJg1mNDg1
+## Visualize opfunu function using utility function
+from opfunu import draw_2d, draw_3d
 
-* This project also related to our another projects which are optimization and machine learning. Check it here:
-    * https://github.com/thieu1995/metaheuristics
-    * https://github.com/thieu1995/mealpy
-    * https://github.com/thieu1995/mafese
-    * https://github.com/thieu1995/pfevaluator
-    * https://github.com/thieu1995/MetaCluster
-    * https://github.com/thieu1995/enoppy
-    * https://github.com/thieu1995/permetrics
-    * https://github.com/aiir-team
+draw_2d(f0.evaluate, f0.lb, f0.ub, selected_dims=(2, 3), n_points=300)
+draw_3d(f0.evaluate, f0.lb, f0.ub, selected_dims=(2, 3), n_points=300)
+```
 
+<table>
+  <tr>
+    <td style="text-align: center;">
+      <img src=".github/img/2d-f12010.png" alt="F1-2010 CEC 2D" style="width: 100%;">
+      <p style="text-align: center;">F1-2010 CEC 2D</p>
+    </td>
+    <td style="text-align: center;">
+      <img src=".github/img/3d-f12010.png" alt="F1-2010 CEC 3D" style="width: 100%;">
+    <p style="text-align: center;">F1-2010 CEC 3D</p>
+    </td>
+  </tr>
+</table>
 
-## Cite Us
 
-If you are using opfunu in your project, we would appreciate citations:
+### How to draw Latex
 
-```code
-@software{thieu_nguyen_2020_3711682,
-  author       = {Nguyen Van Thieu},
-  title        = {Opfunu: An Open-source Python Library for Optimization Benchmark Functions},
-  year         = 2020,
-  publisher    = {Zenodo},
-  doi          = {10.5281/zenodo.3620960},
-  url          = {https://doi.org/10.5281/zenodo.3620960.}
-}
-```
+Two ways if you want to draw latex equation. 
 
+```python
+from opfunu.cec_based import F12010
+from opfunu.name_based import Ackley02
+from opfunu.utils.visualize import draw_latex
 
-## References 
+f0 = F12010()
+f1 = Ackley02()
 
-```code
-1. http://benchmarkfcns.xyz/fcns
-2. https://en.wikipedia.org/wiki/Test_functions_for_optimization
-3. https://www.cs.unm.edu/~neal.holts/dga/benchmarkFunction/
-4. http://www.sfu.ca/~ssurjano/optimization.html
-5. A Literature Survey of Benchmark Functions For Global Optimization Problems (2013)
-6. Problem Definitions and Evaluation Criteria for the CEC 2014 Special Session and Competition on Single Objective Real-Parameter Numerical Optimization 
+## Plot using function inside the object
+f0.plot_latex(f0.latex_formula, figsize=(8, 3), dpi=500, title="Latex equation", exts=(".png", ".pdf"), verbose=True)
+f1.plot_latex(f1.latex_formula_global_optimum, figsize=(8, 3), dpi=500, title="Global optimum", verbose=True)
+
+## Plot using module
+draw_latex(f0.latex_formula_bounds, title="Boundary for Function")
+draw_latex(f1.latex_formula_dimension, title=None)
 ```
+
+
+
+For more usage examples please look at [examples](/examples) folder.
+
+
+
+# Contributing
+
+There are lots of ways how you can contribute to Permetrics's development, and you are welcome to join in! For example, 
+you can report problems or make feature requests on the [issues](/issues) pages. To facilitate contributions, 
+please check for the guidelines in the [CONTRIBUTING.md](/CONTRIBUTING.md) file.
+
+
+# Official channels 
+
+* [Official source code repository](https://github.com/thieu1995/opfunu)
+* [Official document](https://opfunu.readthedocs.io/)
+* [Download releases](https://pypi.org/project/opfunu/) 
+* [Issue tracker](https://github.com/thieu1995/opfunu/issues) 
+* [Notable changes log](/ChangeLog.md)
+* [Official discussion group](https://t.me/+fRVCJGuGJg1mNDg1)
+
+
+---
+
+Developed by: [Thieu](mailto:[email protected]?Subject=Opfunu_QUESTIONS) @ 2023

docs/source/conf.py

@@ -29,7 +29,7 @@
 author = 'Thieu'
 
 # The full version, including alpha/beta/rc tags
-release = '1.0.3'
+release = '1.0.4'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/index.rst

@@ -6,7 +6,7 @@
 Welcome to OPFUNU's documentation!
 ==================================
 
-.. image:: https://img.shields.io/badge/release-1.0.2-yellow.svg
+.. image:: https://img.shields.io/badge/release-1.0.4-yellow.svg
    :target: https://github.com/thieu1995/opfunu/releases
 
 .. image:: https://img.shields.io/pypi/wheel/gensim.svg
@@ -74,7 +74,9 @@ traditional functions with different dimensions are implemented.
    :caption: Introduction:
 
    pages/quick_start.rst
-   pages/notes.rst
+   pages/integrated.rst
+   pages/visualization.rst
+   pages/categories.rst
 
 
 .. toctree::