Merge branch 'dev'

.github/workflows/pythonapp_push.yml

@@ -6,13 +6,16 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.6', '3.7', '3.8', '3.9']
 
     steps:
     - uses: actions/checkout@master
-    - name: Set up Python 3.7
-      uses: actions/setup-python@master
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.gitignore

@@ -9,3 +9,11 @@ build/
 moead_framework.egg-info/
 
 dist/
+
+.coverage
+
+coverage.xml
+
+docs/doctrees/
+docs/.buildinfo
+docs/.DS_Store

README.md

@@ -2,33 +2,34 @@
 
 [![status](https://joss.theoj.org/papers/a81ea21d0358e013000b0b3b926bd4ba/status.svg)](https://joss.theoj.org/papers/a81ea21d0358e013000b0b3b926bd4ba)
 [![Python application](https://github.com/moead-framework/framework/workflows/Python%20application/badge.svg?branch=master)](https://github.com/moead-framework/framework/actions?query=workflow%3A%22Python+application%22)
+[![codecov](https://codecov.io/gh/moead-framework/framework/branch/master/graph/badge.svg?token=J7MAU5E6BB)](https://codecov.io/gh/moead-framework/framework)
 [![PyPI](https://img.shields.io/pypi/v/moead-framework)](https://pypi.org/project/moead-framework/)
 [![GitHub](https://img.shields.io/github/license/moead-framework/framework?style=flat)](https://github.com/moead-framework/framework/blob/master/LICENCE)
 
 This python package *moead-framework* is a modular framework for multi-objective evolutionary algorithms by decomposition. 
 The goal  is to provide a modular framework for scientists and researchers interested in 
 experimenting with MOEA/D and its numerous variants.
 
-The documentation is available here: [https://moead-framework.github.io/documentation/](https://moead-framework.github.io/documentation/html/index.html) and can be edited on this repository: [https://github.com/moead-framework/documentation](https://github.com/moead-framework/documentation).
+The documentation is available here: [https://moead-framework.github.io/framework/](https://moead-framework.github.io/framework/html/index.html) and can be edited in the folder docs of this repository.
 
 # Installation instructions
 
 Create a virtual environment with [conda](https://docs.conda.io/en/latest/miniconda.html) or [virtualenv](https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/#creating-a-virtual-environment)
 
-The package is available in pypi, you can install it with:
+The package is available in pypi with a linux environment for python 3.6, 3.7, 3.8 and 3.9, you can install it with:
 
     pip install moead-framework
 
 # Example
 
-    from moead_framework.aggregation.tchebycheff import Tchebycheff
-    from moead_framework.algorithm.combinatorial.moead import Moead
-    from moead_framework.problem.combinatorial.rmnk import Rmnk
+    from moead_framework.aggregation import Tchebycheff
+    from moead_framework.algorithm.combinatorial import Moead
+    from moead_framework.problem.combinatorial import Rmnk
     from moead_framework.tool.result import save_population
 
 
     ###############################
-    #      Init the problem       #
+    #   Initialize the problem    #
     ###############################
     # The file is available here : https://github.com/moead-framework/data/blob/master/problem/RMNK/Instances/rmnk_0_2_100_1_0.dat
     # Others instances are available here : https://github.com/moead-framework/data/tree/master/problem/RMNK/Instances

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = .
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/custom_theme.css

@@ -0,0 +1,15 @@
+/* This file intentionally left blank. */
+.wy-nav-content {
+    max-width: inherit;
+}
+
+.wy-menu-vertical li.toctree-l3 span.toctree-expand, .wy-menu-vertical li.current > a span.toctree-expand{
+    display: none;
+}
+
+.wy-menu-vertical li.toctree-l4{
+    display: none;
+}
+.wy-body-for-nav .wy-nav-content-wrap a:visited {
+    color: #2980B9;
+}

docs/api.rst

@@ -0,0 +1,10 @@
+.. _components:
+
+Library Reference
+===========================================
+
+.. toctree::
+	:maxdepth: 2
+
+	main_components
+	other_components

docs/conf.py

@@ -0,0 +1,72 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'The Moead Framework'
+copyright = '2021, Geoffrey Pruvost'
+author = 'Geoffrey Pruvost'
+
+# The full version, including alpha/beta/rc tags
+release = '1.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinxcontrib.bibtex',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.coverage',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.coverage',
+    'sphinx.ext.intersphinx',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+autosummary_generate = True
+autodoc_default_flags = ['class', 'members', 'inherited-members', 'show-inheritance']
+autodoc_member_order = 'groupwise'
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+#html_theme = 'alabaster'
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+html_css_files = [
+    'custom_theme.css',
+]

docs/contributing.rst

@@ -0,0 +1,25 @@
+
+Contributing
+===========================================
+
+When contributing to this project, please first discuss the change you wish to make via issue,
+email, or any other method with the owners of this repository before making a change. 
+
+Please note we have a code of conduct, please follow it in all your interactions with the project.
+
+Pull Request Process
+________________________________
+
+1. Ensure any install or build dependencies are removed before the end of the layer when doing a 
+   build.
+2. Update the README.md with details of changes to the interface, this includes new environment 
+   variables, exposed ports, useful file locations and container parameters.
+3. Update the documentation with a new Pull Request on the repository https://github.com/moead-framework/documentation.
+4. Don't forget to add unit tests.
+5. Create a new branch and a Pull Request to merge your work on the **dev** branch of the project.
+
+
+Code of Conduct
+________________________________
+
+The code of conduct is available here: https://github.com/moead-framework/framework/blob/master/CODE_OF_CONDUCT.md.