started to add docs using sphinx for readthedocs (ongoing)

.gitignore

@@ -65,6 +65,8 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/build/
+docs/source/docstring/
 
 # PyBuilder
 target/

docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# 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/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/make_docs.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash 
+
+# . venv/bin/activate 
+
+rm -Rf build
+rm -Rf source/docstring
+
+sphinx-apidoc -f -o source/docstring/ ../pyrobolearn
+make html
+

docs/source/conf.py

@@ -0,0 +1,187 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- 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 = u'PyRoboLearn'
+copyright = u'2019, Brian Delhaisse'
+author = u'Brian Delhaisse'
+
+# The short X.Y version
+version = u''
+# The full version, including alpha/beta/rc tags
+release = u'0.0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# 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 = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- 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 = 'sphinx_rtd_theme' # 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'PyRoboLearndoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'PyRoboLearn.tex', u'PyRoboLearn Documentation',
+     u'Brian Delhaisse', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'pyrobolearn', u'PyRoboLearn Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'PyRoboLearn', u'PyRoboLearn Documentation',
+     author, 'PyRoboLearn', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}

docs/source/examples.rst

@@ -0,0 +1,2 @@
+.. include:: ../../examples/README.rst
+

docs/source/index.rst

@@ -0,0 +1,38 @@
+.. PyRoboLearn documentation master file, created by
+   sphinx-quickstart on Thu Jun 20 20:28:11 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root toctree directive.
+
+Welcome to PyRoboLearn's documentation!
+=======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: PyRoboLearn
+
+   readme
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Installation
+
+   installation
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Examples
+
+   examples
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Package Reference
+
+   docstring/modules
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Index
+
+   indices
+

docs/source/indices.rst

@@ -0,0 +1,6 @@
+Indices and tables
+==================
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

docs/source/installation.rst

@@ -0,0 +1,145 @@
+Installation
+============
+
+There are 2 ways to install the PyRoboLearn framework.
+
+1. via :ref:`Docker`
+2. using a :ref:`Virtual Environment`
+
+
+.. _Docker:
+
+Docker
+-------
+
+At the moment the docker is a self contained Ubuntu image with all the libraries installed. When launched we have access to a Python3.6 interpreter and we can import pyrobolearn directly.
+In the future, ROS may be splitted in another container and linked to this one.
+
+1. Install Docker and nvidia-docker
+
+.. code-block:: bash
+
+    sudo apt-get update
+    sudo apt install apt-transport-https ca-certificates curl software-properties-common
+    curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
+    sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu bionic stable # you should replace bionic by your version
+    sudo apt update
+    sudo apt install docker-ce
+    sudo systemctl status docker # check that docker is active
+
+2. Build the image
+
+.. code-block:: bash
+
+    docker build -t pyrobolearn .
+
+3. You can now start the python interpreter with every library already installed
+
+.. code-block:: bash
+    
+    docker run -p 11311:11311 -v catkin_ws:/pyrobolearn/catkin_ws/ -ti pyrobolearn python3
+
+
+To open an interactive terminal in the docker image use:
+
+.. code-block:: bash
+
+    docker run -p 11311:11311 -v catkin_ws:/pyrobolearn/catkin_ws/ -ti pyrobolearn /bin/bash
+
+
+4. If the GPU is not recognized in the interpreter, you can install ``nvidia-docker``
+
+.. code-block:: bash
+    
+    curl -sL https://nvidia.github.io/nvidia-docker/gpgkey | sudo apt-key add -
+    distribution=$(. /etc/os-release;echo $ID$VERSION_ID)
+    curl -sL https://nvidia.github.io/nvidia-docker/$distribution/nvidia-docker.list | sudo tee /etc/apt/sources.list.d/nvidia-docker.list
+    sudo apt-get update
+    sudo apt-get install nvidia-docker2
+    sudo pkill -SIGHUP dockerd
+
+And use:
+
+.. code-block:: bash
+    
+    nvidia-docker run -p 11311:11311 -v catkin_ws:/pyrobolearn/catkin_ws/ -ti pyrobolearn
+
+
+.. _Virtual Environment:
+
+Virtual Environment
+-------------------
+
+0. Prerequisites: install the following packages on your Ubuntu system
+
+.. code-block:: bash
+
+    sudo apt-get install cmake gfortran
+
+
+1. First download the ``pip`` Python package manager and create a virtual environment for Python as described in the following link: https://packaging.python.org/guides/installing-using-pip-and-virtualenv/
+
+On Ubuntu, you can install ``pip`` and ``virtualenv`` by typing in the terminal: 
+
+- In Python 2.7:
+
+.. code-block:: bash
+
+    sudo apt install python-pip
+    sudo pip install virtualenv
+
+- In Python 3.5:
+
+.. code-block:: bash
+
+    sudo apt install python3-pip
+    sudo pip install virtualenv
+
+
+You can then create the virtual environment by typing:
+
+.. code-block:: bash
+
+    virtualenv -p /usr/bin/python<version> <virtualenv_name>
+    # activate the virtual environment
+    source <virtualenv_name>/bin/activate
+
+where ``<version>`` is the python version you want to use (select between ``2.7`` or ``3.5``), and ``<virtualenv_name>`` is a name of your choice for the virtual environment. For instance, it can be ``py2.7`` or ``py3.5``.
+
+To deactivate the virtual environment, just type:
+
+.. code-block:: bash
+
+    deactivate
+
+
+2. clone this repository and install the requirements by executing the ``setup.py``
+
+In Python 2.7:
+
+.. code-block:: bash
+
+    git clone https://github.com/robotlearn/pyrobolearn
+    cd pyrobolearn
+    pip install numpy cython
+    pip install http://github.com/cornellius-gp/gpytorch/archive/alpha.zip  # this is for Python 2.7
+    pip install -e .  # this will install pyrobolearn as well as the required packages (so no need for: pip install -r requirements.txt)
+
+In Python 3.5:
+
+.. code-block:: bash
+
+    git clone https://github.com/robotlearn/pyrobolearn
+    cd pyrobolearn
+    pip install numpy cython
+    pip install gpytorch  # this is for Python 3.5
+    pip install -e .  # this will install pyrobolearn as well as the required packages (so no need for: pip install -r requirements.txt)
+
+
+Depending on your computer configuration and the python version you use, you might need to install also the following packages through ``apt-get``:
+
+.. code-block:: bash
+
+    sudo apt install python-tk  # if python 2.7
+    sudo apt install python3-tk  # if python 3.5
+

docs/source/readme.rst

@@ -0,0 +1,22 @@
+PyRoboLearn
+===========
+
+.. include:: ../../README.md
+
+Design Decisions
+================
+
+.. image:: ../UML/pyrobolearn_uml.png
+
+Citation
+========
+
+.. code-block:: latex
+
+   @misc{delhaisse2019pyrobolearn,
+    author = {Delhaisse, Brian and Xin, Songyan and Rozo, Leonel, and Caldwell, Darwin},
+    title = {PyRoboLearn: A Python Framework for Robot Learning Practitioners},
+    howpublished = {\url{https://github.com/robotlearn/pyrobolearn}},
+    year=2019,
+   }
+

examples/README.md

@@ -1,21 +0,0 @@
-## Examples
-
-In this folder, you will find different examples on how to use the framework.
-
-Warning: this folder is currently being updated; few files might still have some bugs or not 
-implemented completely. Some other folders will be added in the upcoming days.
-
-You can check the following folders:
-- `worlds`: how to create a world in the simulator, load various objects inside and interact with 
-them, use the camera, and load or generate terrains.
-- `robots`: check how to load a specific robot (biped, quadruped, wheeled, etc) into the world.
-- `interfaces`: the various interfaces (game controllers, webcam, etc) and bridges that you can use.
-- `kinematics`: check how to use forward and inverse kinematics as well as position and velocity control.
-- `manipulability`: check how to use the velocity and dynamic manipulability ellipsoids.
-
-- `states`: how to query the states / observations.
-- `models`: the different learning models that you can use.
-
-- `imitation`: how to use imitation learning with the framework.
-- `gym/cartpole`: policies are trained with different algorithms on the gym Cartpole environment.
-

examples/README.rst

@@ -0,0 +1,20 @@
+Examples
+========
+
+In this folder, you will find different examples on how to use the framework.
+
+Warning: this folder is currently being updated; few files might still have some bugs or not 
+implemented completely. Some other folders will be added in the upcoming days.
+
+You can check the following folders:
+
+- ``worlds``: how to create a world in the simulator, load various objects inside and interact with them, use the camera, and load or generate terrains.
+- ``robots``: check how to load a specific robot (biped, quadruped, wheeled, etc) into the world.
+- ``interfaces``: the various interfaces (game controllers, webcam, etc) and bridges that you can use.
+- ``kinematics``: check how to use forward and inverse kinematics as well as position and velocity control.
+- ``manipulability``: check how to use the velocity and dynamic manipulability ellipsoids.
+- ``states``: how to query the states / observations.
+- ``models``: the different learning models that you can use.
+- ``imitation``: how to use imitation learning with the framework.
+- ``gym/cartpole``: policies are trained with different algorithms on the gym Cartpole environment.
+