updating links to agrum.org + WIP for doc

parent f86adff7
......@@ -8,6 +8,6 @@ It is written to provide the basic building blocks to perform the following task
Homepage
========
[aGrUM/pyAgrum on gitlab.io](http://agrum.gitlab.io)
[aGrUM/pyAgrum on gitlab.io](http://agrum.org)
......@@ -3,7 +3,7 @@ Entity Contributor Non-Exclusive License Agreement including the Traditional Pat
Thank you for your interest in contributing to aGrUM ("We" or “Us").
The purpose of this contributor agreement ("Agreement") is to clarify and document the rights granted by contributors to Us. To make this document effective, please follow the instructions at http://agrum.gitlab.io/pages/contribution-licence-agreement.html.
The purpose of this contributor agreement ("Agreement") is to clarify and document the rights granted by contributors to Us. To make this document effective, please follow the instructions at http://agrum.org/pages/contribution-licence-agreement.html.
1. DEFINITIONS
"You" means any Legal Entity on behalf of whom a Contribution has been made to Us.
......
......@@ -3,7 +3,7 @@ Individual Contributor Non-Exclusive License Agreement including the Traditional
Thank you for your interest in contributing to aGrUM ("We" or “Us").
The purpose of this contributor agreement ("Agreement") is to clarify and document the rights granted by contributors to Us. To make this document effective, please follow the instructions at http://agrum.gitlab.io/pages/contribution-licence-agreement.html.
The purpose of this contributor agreement ("Agreement") is to clarify and document the rights granted by contributors to Us. To make this document effective, please follow the instructions at http://agrum.org/pages/contribution-licence-agreement.html.
1. DEFINITIONS
"You" means the Individual Copyright owner who submits a Contribution to Us. If You are an employee and submit the Contribution as part of your employment, You have had Your employer approve this Agreement or sign the Entity version of this document.
......
# -*- coding: utf-8 -*-
"""
`pyAgrum <http://agrum.gitlab.io>`_ is a Python wrapper for the C++ `aGrUM <https://agrum.lip6.fr>`_ library.
`pyAgrum <http://agrum.org>`_ is a Python wrapper for the C++ `aGrUM <https://agrum.lip6.fr>`_ library.
It provides a high-level interface to the part of aGrUM allowing to create, handle and make computations into Bayesian Networks.
The module is generated using the `SWIG <https://www.swig.org>`_ interface generator. Custom-written code was added to make the interface more friendly.
......@@ -8,7 +8,7 @@ The module is generated using the `SWIG <https://www.swig.org>`_ interface gener
pyAgrum includes :
* API documentation <http://www-desir.lip6.fr/~phw/aGrUM/docs/last/pyAgrum/>,
* examples as `notebooks <http://www-desir.lip6.fr/~phw/aGrUM/docs/last/notebooks/01-tutorial.ipynb.html>`_,
* a `website <http://agrum.gitlab.io>`_.
* a `website <http://agrum.org>`_.
"""
# aGrum Licence (GPL)
......@@ -30,7 +30,7 @@ pyAgrum includes :
__version__ = '@PYAGRUM_VERSION@'
__license__ = __doc__
__project_url__ = 'http://agrum.gitlab.io'
__project_url__ = 'http://agrum.org'
import numpy as np
from .functions import *
......
......@@ -2,17 +2,18 @@ Metadata-Version: 1.1
Name: pyAgrum
Version: @PYAGRUM_VERSION@
Summary: Bayesian Networks in python
Home-page: http://agrum.gitlab.io
Home-page: http://agrum.org
Author: Pierre-Henri WUILLEMIN
Author-email: pierre-henri.wuillemin@lip6.fr
License: GPL
Download-URL: http://agrum.gitlab.io
Download-URL: http://agrum.org
Description:pyAgrum is a Python wrapper for the C++ aGrUM library.
It provides a high-level interface to the part of aGrUM allowing to create, handle and make computations into Bayesian Networks.
The module is a straightforward application of the SWIG interface generator. Custom-written code was added to make the interface more similar to OpenBayes, a free Bayesian Network library for Python.
Platform: any
Classifier: License :: OSI Approved :: GPL License
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
......@@ -23,4 +24,18 @@ Classifier: Programming Language :: Python :: @PYTHON_VERSION@
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers and Researchers
Classifier: Topic :: Scientific/Engineering
Natural Language :: English
Intended Audience :: Science/Research
Framework :: IPython
Framework :: Jupyter
Programming Language :: C++
Programming Language :: Python :: 2.7
Programming Language :: Python :: 3
Topic :: Scientific/Engineering
Topic :: Scientific/Engineering :: Artificial Intelligence
Requires: numpy
......@@ -35,13 +35,16 @@ import os
# ones.
import sys
import matplotlib
matplotlib.use('agg') # work around for tkinter.file_dialog not found
sys.path.insert(0, os.path.abspath('.'))
sys.path.insert(0, os.path.abspath('../../../build/release/wrappers/'))
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.todo',
'sphinx.ext.viewcode',
#'sphinx.ext.todo',
#'sphinx.ext.viewcode',
'sphinx.ext.coverage',
'sphinx.ext.napoleon'
] # Napoleon settings
......@@ -82,6 +85,7 @@ author = 'Pierre-henri Wuillemin'
# built documents.
#
import pyAgrum as gum
import gumDoc
print("GUM VERSION =" + gum.__version__)
# The short X.Y version.
......@@ -223,8 +227,7 @@ html_static_path = ['_static']
# html_split_index = False
# If true, links to the reST sources are added to the pages.
#
# html_show_sourcelink = True
html_show_sourcelink = False
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#
......@@ -238,7 +241,7 @@ html_show_copyright = True
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#
# html_use_opensearch = ''
html_use_opensearch = ''
# This is the file name suffix for HTML files (e.g. ".xhtml").
# html_file_suffix = None
......@@ -248,7 +251,7 @@ html_show_copyright = True
# 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
# 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr', 'zh'
#
# html_search_language = 'en'
html_search_language = 'en'
# A dictionary with options for the search language support, empty by default.
# 'ja' uses this config value.
......@@ -459,10 +462,12 @@ autoclass_content = 'both'
import re
gumReplaceList = [
('pyAgrum.pyAgrum','pyAgrum'),
('gum::Idx', 'int'),
('gum::Size', 'int'),
('gum::NodeId', 'int'),
('std::string', 'str'),
('str &', 'str'),
('gum::', 'pyAgrum.'),
('_double ', ' '),
('< double > *', ' '),
......@@ -517,8 +522,11 @@ def skip(app, what, name, obj, skip, options):
return True
return None
autodoc_default_flags = ['members', 'private-members', 'special-members',
#'undoc-members','show-inheritance'
autodoc_default_flags = ['members',
#'private-members',
#'special-members',
#'undoc-members',
#'show-inheritance',
]
def setup(app):
app.connect('autodoc-process-docstring', process_docstring)
......
import pyAgrum
pyAgrum.DiscreteVariable.__doc__ = """
Discrete Variable cannot be instantiated but declare a common API for all discrete variables.
Discrete Variable cannot be instantiated but declares a common API for all discrete variables.
"""
pyAgrum.DiscreteVariable.__init__.__doc__ = None
import pyAgrum
pyAgrum.LabelizedVariable.__doc__ = """
LabelizedVariable is a discrete random variable with a customizable sequence of labels.
Available constructors:
`LabelizedVariable(aName, aDesc="", nbrLabel=2) -> LabelizedVariable`
`LabelizedVariable(aLDRV) -> LabelizedVariable`
Parameters
----------
aName: str
The name of the variable
aDesc: str
The (optional) description of the variable
nbrLabel: int
The number of labels to create. By default , the value start from "0" to "nbrLabel-1"
aLDRV: pyAgrum.LabelizedVariable
Another `LabelizedVariable` that will be copied
Examples
--------
>>> import pyAgrum as gum
>>> v=gum.LabelizedVariable("v")
>>> print(v)
v<0,1>
>>> w=gum.LabelizedVariable("w","",4)
>>> print(w)
w<0,1,2,3>
"""
pyAgrum.LabelizedVariable.__init__.__doc__ = None
......@@ -10,9 +10,9 @@ Introduction to pyAgrum
.. figure:: _static/agrum.png
:align: right
:alt: aGrUM
:target: http://agrum.gitlab.io
:target: http://agrum.org
pyAgrum is a Python wrapper for the C++ `aGrUM <http://agrum.gitlab.io>`_ library.
pyAgrum is a Python wrapper for the C++ `aGrUM <http://agrum.org>`_ library.
It provides a high-level interface to the part of aGrUM allowing to create, handle and make computations into Bayesian Networks.
.. warning:: For now, this documentation is mainly automatically produced by `SWIG <https://www.swig.org>`_.
......@@ -27,7 +27,7 @@ pyAgrum aims to allow to easily use (as well as to prototype new algorithms on)
pyAgrum contains
* a `comprehensive API documentation <http://www-desir.lip6.fr/~phw/aGrUM/docs/last/pyAgrum/index.html>`_,
* `examples as jupyter notebooks <http://www-desir.lip6.fr/~phw/aGrUM/docs/last/notebooks/01-tutorial.ipynb.html>`_,
* and a `website <http://agrum.gitlab.io>`_.
* and a `website <http://agrum.org>`_.
pyAgrum library
......@@ -38,7 +38,8 @@ pyAgrum library
functions
graph
randomVariablesAndPotentials
randomVariables
potential
bayesianNetwork
PRM
credalNetwork
......
Potentials and Instantiation
============================
Instantiation
-------------
.. autoclass:: pyAgrum.Instantiation
:members:
Potential
---------
.. autoclass:: pyAgrum.Potential
:members:
Random Variables and Potentials
===============================
Random Variables
================
aGrUM/pyAgrum is dedicated for discrete probability distribution.
There are 3 types of discrete random variables in aGrUM/pyAgrum : LabelizedVariable, DiscretizedVariable and RangeVariable. The 3 types are mainly provided in order to ease the modelisation. Derived from DiscreteVariable, they share a common API. They essentially differ by the means to create, name and access to their modalities.
Common API for Random Discrete Variables
----------------
----------------------------------------
.. autoclass:: pyAgrum.DiscreteVariable
:members:
Concrete classes for Random Discrete Variables
----------------
----------------------------------------------
.. autoclass:: pyAgrum.LabelizedVariable
:members:
......@@ -20,11 +20,3 @@ Concrete classes for Random Discrete Variables
.. autoclass:: pyAgrum.RangeVariable
:members:
Instantiation and Potential
---------------------------
.. autoclass:: pyAgrum.Instantiation
:members:
.. autoclass:: pyAgrum.Potential
:members:
ipython
tkinter
numpy
pydotplus
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