Merge pull request #25 from jMetal/develop

Major release 0.5.0

.gitignore

@@ -1,36 +1,110 @@
-*.class
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
 
-# Mobile Tools for Java (J2ME)
-.mtj.tmp/
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
 
-# Package Files #
-*.jar
-*.war
-*.ear
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
 
-# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
-hs_err_pid*
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
 
-venv
-env
-.idea
-*.pyc
+# Unit test / coverage reports
+htmlcov/
+.tox/
 .coverage
-__pycache__/
-build
-dist
-*.spec
-coverage.xml
-*.egg-info
+.coverage.*
 .cache
-pytest-env
-*.zip
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
 .ipynb_checkpoints
 
-# Avoid documentation
-auto-docs/build
-auto-docs/source/*.rst
-!auto-docs/source/index.rst
-.RData
-.Rhistory
-_pycache__
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# idea
+.idea
+
+# pypi
+.pypirc
+
+# Dask
+dask-worker-space

.readthedocs.yml

@@ -0,0 +1,8 @@
+build:
+  image: latest
+
+python:
+  version: 3.6
+  pip_install: true
+
+requirements_file: docs/requirements.txt

.travis.yml

@@ -7,11 +7,11 @@ branches:
   - master
   - /.*/
 deploy:
- provider: pypi
- skip_cleanup: true
- user: ajnebro
- distributions: sdist bdist_wheel
- password:
-   secure: "pJhh2ZwuDaMELZO7kmNGWa7sRaUi6s4By4GdBxf1hPjIBkB0GkOGHKxuivnWitAYLbmzpSoMcp2rHETcRiSqYTPlyovLA8A7YpY1HXIcNBrrmqnOpzc9bN3Ka90HMu0ySw2uYZgaQ2neFMm5CvD6W47IG0UUaFPYl68aZ8lEe8t7Tea7kFLU4UgXZxp3BXLTHF7xx7V29Ba5aKv2"
- on:
-   branch: master
+  provider: pypi
+  skip_cleanup: true
+  user: ajnebro
+  distributions: sdist bdist_wheel
+  password:
+    secure: "pJhh2ZwuDaMELZO7kmNGWa7sRaUi6s4By4GdBxf1hPjIBkB0GkOGHKxuivnWitAYLbmzpSoMcp2rHETcRiSqYTPlyovLA8A7YpY1HXIcNBrrmqnOpzc9bN3Ka90HMu0ySw2uYZgaQ2neFMm5CvD6W47IG0UUaFPYl68aZ8lEe8t7Tea7kFLU4UgXZxp3BXLTHF7xx7V29Ba5aKv2"
+  on:
+    branch: master

CONTRIBUTING.md

@@ -8,4 +8,20 @@ Contributions to the jMetalPy project are welcome. Please, take into account the
 - [Incorporate the new features of Python 3.5](resources/pages/features_python3.md)
 - [Respect the initial structure](resources/pages/project_structure.md)
 - [How to create auto documentation using compatible code](resources/pages/auto_doc.md)
-- [Performance analysis of Python](resources/pages/profiling.md)
+- [Performance analysis of Python](resources/pages/profiling.md)
+
+# Documentation
+
+To generate the documentation, install [Sphinx](http://www.sphinx-doc.org/en/master/) by running:
+
+```bash
+$ pip install sphinx
+$ pip install sphinx_rtd_theme
+```
+
+And then `cd` to `/docs` and run:
+
+```bash
+$ sphinx-apidoc -f -o source/ ../jmetal/
+$ make html
+```

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Antonio J. Nebro
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,47 +1,50 @@
-# jMetalPy: Python version of the jMetal framework
-[![Build Status](https://travis-ci.org/jMetal/jMetalPy.svg?branch=master)](https://travis-ci.org/jMetal/jMetalPy)
-[![PyPI](https://img.shields.io/pypi/l/jMetalPy.svg)]()
-[![PyPI](https://img.shields.io/pypi/v/jMetalPy.svg)]()
-
-> jMetalPy is currently under heavy development!  
-
-I started a new project called jMetalPy in February 2017. The initial idea was not to write the whole jMetal proyect in Python but to use it as a practical study to learn that programming language, although due to the interest of some researchers the goal of an usable jMetal version in Python is an ongoing work.
+<p align="center">
+  <br/>
+  <img src=docs/source/jmetalpy.png alt="jMetalPy">
+  <br/>
+</p>
 
-Any ideas about how the structure the project, coding style, useful tools (I'm using PyCharm), or links to related projects are welcome (see [CONTRIBUTING](https://github.com/jMetal/jMetalPy/blob/master/CONTRIBUTING.md)). The starting point is the jMetal architecture:
-
-![jMetal architecture](resources/jMetal5UML.png)
-
----
+# jMetalPy: Python version of the jMetal framework
+[![Build Status](https://img.shields.io/travis/jMetal/jMetalPy.svg?style=flat-square)](https://travis-ci.org/jMetal/jMetalPy)
+[![Read the Docs](https://img.shields.io/readthedocs/jmetalpy.svg?style=flat-square)](https://readthedocs.org/projects/jmetalpy/)
+[![PyPI License](https://img.shields.io/pypi/l/jMetalPy.svg?style=flat-square)]()
+[![PyPI Python version](https://img.shields.io/pypi/pyversions/jMetalPy.svg?style=flat-square)]()
 
-# Table of Contents
+## Table of Contents
+- [Installation](#installation)
 - [Usage](#usage)
-	- [Dependencies](#dependencies)
-- [History](#history)
-	- [Last changes (December 18th 2017)](#last-changes-december-18th-2017)
+- [Features](#features)
 - [Contributing](#contributing)
 - [License](#license)
 
-
-# Usage
-Examples of configuring and running all the included algorithms are located in the [jmetal.runner](https://github.com/jMetal/jMetalPy/tree/master/jmetal/runner) folder.
-
-## Dependencies
-With Python 3.6 installed, run:
-```Bash
+## Installation
+To download jMetalPy just clone the Git repository hosted in GitHub:
+```bash
 $ git clone https://github.com/jMetal/jMetalPy.git
-$ pip install -r requirements.txt
+$ python setup.py install
 ```
 
-# History
-See [CHANGELOG](CHANGELOG.md) for full version history.
+Alternatively, you can install it with `pip`:
+```bash
+$ pip install jmetalpy
+```
+
+## Usage
+Examples of configuring and running all the included algorithms are located [in the docs](https://jmetalpy.readthedocs.io/en/latest/examples.html).
+
+## Features
+The current release of jMetalPy (v0.5.0) contains the following components:
 
-## Last changes (January 18th 2018)
-* (Fix) Search solution in `ScatterPlot()` now return only one solution object (as intended).
-* Added class `ParallelEvaluator` (Contribution of Michael Cipold)
-* Fixed a bug in class `DominanceComparator`
+* Algorithms: random search, NSGA-II, SMPSO, SMPSO/RP
+* Problems: ZDT1-6, DTLZ1-2, unconstrained (Kursawe, Fonseca, Schaffer, Viennet2), constrained (Srinivas, Tanaka).
+* Encodings: real, binary
+* Operators: selection (binary tournament, ranking and crowding distance, random, nary random, best solution), crossover (single-point, SBX), mutation (bit-blip, polynomial, uniform, random)
+* Quality indicators: hypervolume
+* Density estimator: crowding distance
+* Graphics: 2D/3D plotting in real-time
 
-# Contributing
+## Contributing
 Please read [CONTRIBUTING](CONTRIBUTING.md) for details on how to contribute to the project.
 
-# License
+## License
 This project is licensed under the terms of the MIT - see the [LICENSE](LICENSE) file for details.