[pyAgrum] trying a new framework for pyAgrum documentation

parent 14a76840
DESTDIR=$(shell python -c "import os;import pyAgrum;print(os.path.dirname(pyAgrum.__file__))")
run:
swig -c++ -python -outdir $(DESTDIR) -py3 -I..\..\swig -I..\..\..\src -I..\..\..\build\Release -I.. pyAgrum.i
cd sphinx && make -f Makefile.win html
For Windows
===========
- install conda
- conda install sphinx swig cmake
- git clone [aGrUM@gitlab]
- git checkout documentation/swigDoc
-
%feature("docstring") gum::BayesNet
"
C'est un fameux 3 mats
Parameters
==========
problem : :class:`~openturns.OptimizationProblem`
Optimization problem to solve.
tau : float
Multiplicative decrease of linear step.
omega : float
Armijo factor.
smooth : float
Growing factor in penalization term.
"
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS = -c . -a -E -w sphinx_warnings.txt
SPHINXBUILD = python3 `which sphinx-build`
PAPER =
BUILDDIR = ../../../build/release/wrappers/pyAgrum/docs
AGRUMBUILDDIR = "{agrum}/build/release/wrappers/pyAgrum/docs"
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
.PHONY: help
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html to make standalone HTML files"
@echo " dirhtml to make HTML files named index.html in directories"
@echo " singlehtml to make a single large HTML file"
@echo " pickle to make pickle files"
@echo " json to make JSON files"
@echo " htmlhelp to make HTML files and a HTML help project"
@echo " qthelp to make HTML files and a qthelp project"
@echo " applehelp to make an Apple Help Book"
@echo " devhelp to make HTML files and a Devhelp project"
@echo " epub to make an epub"
@echo " epub3 to make an epub3"
@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
@echo " latexpdf to make LaTeX files and run them through pdflatex"
@echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
@echo " text to make text files"
@echo " man to make manual pages"
@echo " texinfo to make Texinfo files"
@echo " info to make Texinfo files and run them through makeinfo"
@echo " gettext to make PO message catalogs"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " xml to make Docutils-native XML files"
@echo " pseudoxml to make pseudoxml-XML files for display purposes"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
@echo " coverage to run coverage check of the documentation (if enabled)"
@echo " dummy to check syntax errors of document sources"
.PHONY: clean
clean:
rm -rf $(BUILDDIR)/*
.PHONY: html
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(AGRUMBUILDDIR)/html."
.PHONY: dirhtml
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
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.PHONY: singlehtml
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@echo
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.PHONY: pickle
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@echo "Running LaTeX files through pdflatex..."
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.PHONY: latexpdfja
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@echo "Running LaTeX files through platex and dvipdfmx..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
@echo "pdflatex finished; the PDF files are in $(AGRUMBUILDDIR)/latex."
.PHONY: text
text:
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
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.PHONY: man
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@echo
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.PHONY: texinfo
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"or in $(BUILDDIR)/linkcheck/output.txt."
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@echo "Testing of doctests in the sources finished, look at the " \
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.PHONY: dummy
dummy:
$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
@echo
@echo "Build finished. Dummy builder generates no files."
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS = -c . -a -E -w sphinx_warnings.txt
SPHINXBUILD = sphinx-build.exe
PAPER =
BUILDDIR = outputs
AGRUMBUILDDIR = $(BUILDIR)
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)\doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
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@echo " htmlhelp to make HTML files and a HTML help project"
@echo " qthelp to make HTML files and a qthelp project"
@echo " applehelp to make an Apple Help Book"
@echo " devhelp to make HTML files and a Devhelp project"
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@echo " epub3 to make an epub3"
@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
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@echo " gettext to make PO message catalogs"
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@echo " xml to make Docutils-native XML files"
@echo " pseudoxml to make pseudoxml-XML files for display purposes"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
@echo " coverage to run coverage check of the documentation (if enabled)"
@echo " dummy to check syntax errors of document sources"
.PHONY: clean
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.PHONY: html
html:
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@echo
@echo "Build finished. The HTML pages are in $(AGRUMBUILDDIR)\html."
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@echo "Build finished; now you can run "qcollectiongenerator" with the" \
".qhcp project file in $(BUILDDIR)\qthelp, like this:"
@echo "# qcollectiongenerator $(BUILDDIR)\qthelp\pyAgrum.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)\qthelp\pyAgrum.qhc"
.PHONY: applehelp
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$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)\applehelp
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Probabilistic Relational Models
===============================
For now, pyAgrum only allows to explore Probabilistic Relational Models written with o3prm syntax.
.. autoclass:: pyAgrum.PRMexplorer
:members:
This diff is collapsed.
Bayesian Network
================
Model
-----
.. autoclass:: pyAgrum.BayesNet
.. autoclass:: pyAgrum.pyAgrum.BayesNet_double
:members:
:inherited-members:
Inference
---------
.. autoclass:: pyAgrum.LazyPropagation
.. autoclass:: pyAgrum.pyAgrum.LazyPropagation_double
:members:
:inherited-members:
.. autoclass:: pyAgrum.GibbsInference
.. autoclass:: pyAgrum.pyAgrum.GibbsInference_double
:members:
:herited-members:
Learning
--------
.. autoclass:: pyAgrum.BNLearner
.. autoclass:: pyAgrum.pyAgrum.BNLearner_double
:members:
This diff is collapsed.
Credal Networks
=================
Model
_____
.. autoclass:: pyAgrum.CredalNet
.. autoclass:: pyAgrum.pyAgrum.InfluenceDiagram_double
:members:
Inference
_________
.. autoclass:: pyAgrum.CNMonteCarloSampling
.. autoclass:: pyAgrum.pyAgrum.CNMonteCarloSampling_double
:members:
.. autoclass:: pyAgrum.CNLoopyPropagation
.. autoclass:: pyAgrum.pyAgrum.CNLoopyPropagation_double
:members:
Exceptions from aGrUM
=====================
.. autoexception:: pyAgrum.DefaultInLabel
.. autoexception:: pyAgrum.DuplicateElement
.. autoexception:: pyAgrum.DuplicateLabel
.. autoexception:: pyAgrum.EmptyBSTree
.. autoexception:: pyAgrum.EmptySet
.. autoexception:: pyAgrum.GumException
.. autoexception:: pyAgrum.FatalError
.. autoexception:: pyAgrum.FormatNotFound
.. autoexception:: pyAgrum.GraphError
.. autoexception:: pyAgrum.IOError
.. autoexception:: pyAgrum.IdError
.. autoexception:: pyAgrum.InvalidArc
.. autoexception:: pyAgrum.InvalidArgument
.. autoexception:: pyAgrum.InvalidArgumentsNumber
.. autoexception:: pyAgrum.InvalidDirectedCycle
.. autoexception:: pyAgrum.InvalidEdge
.. autoexception:: pyAgrum.InvalidNode
.. autoexception:: pyAgrum.NoChild
.. autoexception:: pyAgrum.NoNeighbour
.. autoexception:: pyAgrum.NoParent
.. autoexception:: pyAgrum.NotFound
.. autoexception:: pyAgrum.NullElement
.. autoexception:: pyAgrum.OperationNotAllowed
.. autoexception:: pyAgrum.OutOfBounds
.. autoexception:: pyAgrum.OutOfLowerBound
.. autoexception:: pyAgrum.OutOfUpperBound
.. autoexception:: pyAgrum.ReferenceError
.. autoexception:: pyAgrum.SizeError
.. autoexception:: pyAgrum.SyntaxError
.. autoexception:: pyAgrum.UndefinedElement
.. autoexception:: pyAgrum.UndefinedIteratorKey
.. autoexception:: pyAgrum.UndefinedIteratorValue
.. autoexception:: pyAgrum.UnknownLabelInDatabase
Functions from pyAgrum
======================
Useful functions in pyAgrum
.. autofunction:: pyAgrum.about
.. autofunction:: pyAgrum.fastBN
.. autofunction:: pyAgrum.getPosterior
Input/Output for bayesian networks
----------------------------------
.. autofunction:: pyAgrum.availableBNExts
.. autofunction:: pyAgrum.loadBN
.. autofunction:: pyAgrum.saveBN
Input for influence diagram
----------------------------------
.. autofunction:: pyAgrum.loadID
Graphs manipulation
===================
In aGrUM, graphs are undirected (with edges), directed (with arcs) or mixed. Some other types of graphs are described below. Edges and arcs are represented by pairs of int (nodeId).
For all types of graphs, nodes are int. If a graph of objects is needed (like :py:class:`pyAgrum.BayesNet`), the objects are mapped to nodeIds.
Edges and Arcs
--------------
.. autoclass:: pyAgrum.Arc
:members:
.. autoclass:: pyAgrum.Edge
:members:
Graphs
------
.. autoclass:: pyAgrum.DiGraph
:members:
.. autoclass:: pyAgrum.UndiGraph
:members:
.. autoclass:: pyAgrum.MixedGraph
:members:
.. autoclass:: pyAgrum.DAG
:members:
.. autoclass:: pyAgrum.CliqueGraph
:members:
.. pyAgrum documentation master file, created by
sphinx-quickstart on Mon Oct 17 16:59:01 2016.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Introduction to pyAgrum
=======================
.. figure:: _static/agrum.png
:align: right
:alt: aGrUM
:target: http://agrum.org
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>`_.
.. image:: _static/fastBNwithPyAgrum.png
The module is generated using the `SWIG <https://www.swig.org>`_ interface generator. Custom-written code was added to make
the interface more friendly.
pyAgrum aims to allow to easily use (as well as to prototype new algorithms on) Bayesian network and other graphical models.
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.org>`_.
pyAgrum library