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Commit a926af08 authored by Pierre-Henri Wuillemin's avatar Pierre-Henri Wuillemin
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[pyAgrum] trying a new framework for pyAgrum documentation

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wrappers/pyAgrum/doc/Makefile.win 0 → 100644
View file @ a926af08
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
wrappers/pyAgrum/doc/README_windows.rst 0 → 100644
View file @ a926af08
For Windows
===========
- install conda
- conda install sphinx swig cmake
- git clone [aGrUM@gitlab]
- git checkout documentation/swigDoc
-
wrappers/pyAgrum/doc/classes/BayesNet.i 0 → 100644
View file @ a926af08
%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.
"
wrappers/pyAgrum/doc/sphinx/Makefile 0 → 100644
View file @ a926af08
# 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
@echo "Build finished. The HTML pages are in $(AGRUMBUILDDIR)/dirhtml."
.PHONY: singlehtml
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
.PHONY: pickle
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
.PHONY: json
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
.PHONY: htmlhelp
htmlhelp:
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
@echo
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in $(BUILDDIR)/htmlhelp."
.PHONY: qthelp
qthelp:
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
@echo
@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
applehelp:
$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
@echo
@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
@echo "N.B. You won't be able to view it unless you put it in" \
"~/Library/Documentation/Help or install it in your application" \
"bundle."
.PHONY: devhelp
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/pyAgrum"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyAgrum"
@echo "# devhelp"
.PHONY: epub
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
.PHONY: epub3
epub3:
$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
@echo
@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
.PHONY: latex
latex:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo
@echo "Build finished; the LaTeX files are in $(AGRUMBUILDDIR)/latex."
@echo "Run \`make' in that directory to run these through (pdf)latex" \
"(use \`make latexpdf' here to do that automatically)."
.PHONY: latexpdf
latexpdf:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through pdflatex..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf
@echo "pdflatex finished; the PDF files are in $(AGRUMBUILDDIR)/latex."
.PHONY: latexpdfja
latexpdfja:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@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
@echo "Build finished. The text files are in $(AGRUMBUILDDIR)/text."
.PHONY: man
man:
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
@echo
@echo "Build finished. The manual pages are in $(AGRUMBUILDDIR)/man."
.PHONY: texinfo
texinfo:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo
@echo "Build finished. The Texinfo files are in $(AGRUMBUILDDIR)/texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
.PHONY: info
info:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)/texinfo info
@echo "makeinfo finished; the Info files are in $(AGRUMBUILDDIR)/texinfo."
.PHONY: gettext
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(AGRUMBUILDDIR)/locale."
.PHONY: changes
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
.PHONY: linkcheck
linkcheck:
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
@echo
@echo "Link check complete; look for any errors in the above output " \
"or in $(BUILDDIR)/linkcheck/output.txt."
.PHONY: doctest
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
.PHONY: coverage
coverage:
$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
@echo "Testing of coverage in the sources finished, look at the " \
"results in $(BUILDDIR)/coverage/python.txt."
.PHONY: xml
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(AGRUMBUILDDIR)/xml."
.PHONY: pseudoxml
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(AGRUMBUILDDIR)/pseudoxml."
.PHONY: dummy
dummy:
$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
@echo
@echo "Build finished. Dummy builder generates no files."
wrappers/pyAgrum/doc/sphinx/Makefile.win 0 → 100644
View file @ a926af08
# 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) .
.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
@echo "Build finished. The HTML pages are in $(AGRUMBUILDDIR)\dirhtml."
.PHONY: singlehtml
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)\singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)\singlehtml."
.PHONY: pickle
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)\pickle
@echo
@echo "Build finished; now you can process the pickle files."
.PHONY: json
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)\json
@echo
@echo "Build finished; now you can process the JSON files."
.PHONY: htmlhelp
htmlhelp:
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)\htmlhelp
@echo
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in $(BUILDDIR)\htmlhelp."
.PHONY: qthelp
qthelp:
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)\qthelp
@echo
@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
applehelp:
$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)\applehelp
@echo
@echo "Build finished. The help book is in $(BUILDDIR)\applehelp."
@echo "N.B. You won't be able to view it unless you put it in" \
"~\Library\Documentation\Help or install it in your application" \
"bundle."
.PHONY: devhelp
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)\devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME\.local\share\devhelp\pyAgrum"
@echo "# ln -s $(BUILDDIR)\devhelp $$HOME\.local\share\devhelp\pyAgrum"
@echo "# devhelp"
.PHONY: epub
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)\epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)\epub."
.PHONY: epub3
epub3:
$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)\epub3
@echo
@echo "Build finished. The epub3 file is in $(BUILDDIR)\epub3."
.PHONY: latex
latex:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)\latex
@echo
@echo "Build finished; the LaTeX files are in $(AGRUMBUILDDIR)\latex."
@echo "Run \`make' in that directory to run these through (pdf)latex" \
"(use \`make latexpdf' here to do that automatically)."
.PHONY: latexpdf
latexpdf:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)\latex
@echo "Running LaTeX files through pdflatex..."
$(MAKE) -C $(BUILDDIR)\latex all-pdf
@echo "pdflatex finished; the PDF files are in $(AGRUMBUILDDIR)\latex."
.PHONY: latexpdfja
latexpdfja:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)\latex
@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
@echo "Build finished. The text files are in $(AGRUMBUILDDIR)\text."
.PHONY: man
man:
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)\man
@echo
@echo "Build finished. The manual pages are in $(AGRUMBUILDDIR)\man."
.PHONY: texinfo
texinfo:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)\texinfo
@echo
@echo "Build finished. The Texinfo files are in $(AGRUMBUILDDIR)\texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
.PHONY: info
info:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)\texinfo
@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)\texinfo info
@echo "makeinfo finished; the Info files are in $(AGRUMBUILDDIR)\texinfo."
.PHONY: gettext
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)\locale
@echo
@echo "Build finished. The message catalogs are in $(AGRUMBUILDDIR)\locale."
.PHONY: changes
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)\changes
@echo
@echo "The overview file is in $(BUILDDIR)\changes."
.PHONY: linkcheck
linkcheck:
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)\linkcheck
@echo
@echo "Link check complete; look for any errors in the above output " \
"or in $(BUILDDIR)\linkcheck\output.txt."
.PHONY: doctest
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)\doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)\doctest\output.txt."
.PHONY: coverage
coverage:
$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)\coverage
@echo "Testing of coverage in the sources finished, look at the " \
"results in $(BUILDDIR)\coverage\python.txt."
.PHONY: xml
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)\xml
@echo
@echo "Build finished. The XML files are in $(AGRUMBUILDDIR)\xml."
.PHONY: pseudoxml
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)\pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(AGRUMBUILDDIR)\pseudoxml."
.PHONY: dummy
dummy:
$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)\dummy
@echo
@echo "Build finished. Dummy builder generates no files."
wrappers/pyAgrum/doc/sphinx/PRM.rst 0 → 100644
View file @ a926af08
Probabilistic Relational Models
===============================
For now, pyAgrum only allows to explore Probabilistic Relational Models written with o3prm syntax.
.. autoclass:: pyAgrum.PRMexplorer
:members:
wrappers/pyAgrum/doc/sphinx/_static/fastBNwithPyAgrum.ipynb 0 → 100644
View file @ a926af08
{
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true,
"deletable": true,
"editable": true
},
"outputs": [],
"source": [
"import pyAgrum as gum\n",
"import pyAgrum.lib.notebook as gnb"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
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"<polygon fill=\"black\" points=\"78.9904,-114.439 71.3043,-107.147 72.7654,-117.641 78.9904,-114.439\" stroke=\"black\"/>\n",
"</a>\n",
"</g>\n",
"</g>\n",
"</g>\n",
"</svg></div></td><td style=\"border-top:hidden;border-bottom:hidden;\"><div align=\"center\"><table>\n",
"<tr><th colspan='2'></th><th colspan='3' style='background-color:#AAAAAA'><center>b</center></th></tr>\n",