From 030b426c9ab2946252e9bf41b6c6beccca6cf4dd Mon Sep 17 00:00:00 2001 From: Sergey Lisitsyn Date: Wed, 15 Apr 2015 19:33:26 +0300 Subject: [PATCH] Merged prototype from karlnapf/shogun_manual --- doc/sphinx/LICENSE | 22 ++ doc/sphinx/Makefile | 180 ++++++++++++ doc/sphinx/README.md | 21 ++ doc/sphinx/TODO | 2 + doc/sphinx/make.bat | 242 ++++++++++++++++ doc/sphinx/sgexample.py | 144 ++++++++++ doc/sphinx/source/conf.py | 272 ++++++++++++++++++ .../source/examples/classifier/knn/knn.rst | 30 ++ .../source/examples/classifier/knn/knn.sg | 25 ++ .../source/examples/classifier/pca/pca.rst | 5 + .../source/examples/classifier/svm/svm.rst | 5 + doc/sphinx/source/index.rst | 21 ++ doc/sphinx/source/static/EMPTY.YET | 1 + doc/sphinx/source/templates/layout.html | 14 + doc/sphinx/source/templates/page.html | 32 +++ 15 files changed, 1016 insertions(+) create mode 100644 doc/sphinx/LICENSE create mode 100644 doc/sphinx/Makefile create mode 100644 doc/sphinx/README.md create mode 100644 doc/sphinx/TODO create mode 100644 doc/sphinx/make.bat create mode 100644 doc/sphinx/sgexample.py create mode 100644 doc/sphinx/source/conf.py create mode 100644 doc/sphinx/source/examples/classifier/knn/knn.rst create mode 100644 doc/sphinx/source/examples/classifier/knn/knn.sg create mode 100644 doc/sphinx/source/examples/classifier/pca/pca.rst create mode 100644 doc/sphinx/source/examples/classifier/svm/svm.rst create mode 100644 doc/sphinx/source/index.rst create mode 100644 doc/sphinx/source/static/EMPTY.YET create mode 100644 doc/sphinx/source/templates/layout.html create mode 100644 doc/sphinx/source/templates/page.html diff --git a/doc/sphinx/LICENSE b/doc/sphinx/LICENSE new file mode 100644 index 00000000000..004f1819cdd --- /dev/null +++ b/doc/sphinx/LICENSE @@ -0,0 +1,22 @@ +The MIT License (MIT) + +Copyright (c) 2015 Heiko Strathmann + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. + diff --git a/doc/sphinx/Makefile b/doc/sphinx/Makefile new file mode 100644 index 00000000000..45642188fb7 --- /dev/null +++ b/doc/sphinx/Makefile @@ -0,0 +1,180 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = build + +# User-friendly check for sphinx-build +ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) +$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) +endif + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +preview: html + cd build; cd html; python -m SimpleHTTPServer 8000 + +help: + @echo "Please use \`make ' where 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 " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @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)" + +clean: + rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +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." + +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/Shogun-manual.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Shogun-manual.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/Shogun-manual" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Shogun-manual" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +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 $(BUILDDIR)/latex." + +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 $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +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 $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +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." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." + +xml: + $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml + @echo + @echo "Build finished. The XML files are in $(BUILDDIR)/xml." + +pseudoxml: + $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml + @echo + @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/doc/sphinx/README.md b/doc/sphinx/README.md new file mode 100644 index 00000000000..a876e59b6e8 --- /dev/null +++ b/doc/sphinx/README.md @@ -0,0 +1,21 @@ +# A new Shogun web manual +## aka minimal examples 2.0 + +We attempt to get documentation such as [sckit's](http://scikit-learn.org/stable/user_guide.html). +We showcase our main strength via allowing users to switch the target language of the code snippets with one click. + + +# Prototype + +This is a system to replace our modular examples, while automatically generating a more pretty documentation around them. +We combine easy API examples with a pretty web-documentation where we showcase Shogun's main strength: multiple language bindings with the same syntax. + +The idea is to write a two files ```source/examples/classifier/knn.rst``` and ```source/examples/code/knn.sg```, where we describe a method (see 1st file), and can include snippets from a meta-language example (see 2nd file). We then use Sphinx with a custom plugin to generate a pretty page that shows these examples with one tab for each language. Everything automatic! + +Run + +``` +make preview +``` + +and then open your browser at ```localhost:8000``` to see the demo. diff --git a/doc/sphinx/TODO b/doc/sphinx/TODO new file mode 100644 index 00000000000..1938fb34aa2 --- /dev/null +++ b/doc/sphinx/TODO @@ -0,0 +1,2 @@ +-Add automatic links to Shogun class docs whenever we see CKNN, or CKNN::train +-Think about a way to uniformly add a set of references (wiki, bixtex, weblink), in a way that changing the layout can be done globally diff --git a/doc/sphinx/make.bat b/doc/sphinx/make.bat new file mode 100644 index 00000000000..e40520b3847 --- /dev/null +++ b/doc/sphinx/make.bat @@ -0,0 +1,242 @@ +@ECHO OFF + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set BUILDDIR=build +set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% source +set I18NSPHINXOPTS=%SPHINXOPTS% source +if NOT "%PAPER%" == "" ( + set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% + set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% +) + +if "%1" == "" goto help + +if "%1" == "help" ( + :help + echo.Please use `make ^` where ^ 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. devhelp to make HTML files and a Devhelp project + echo. epub to make an epub + echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter + echo. text to make text files + echo. man to make manual pages + echo. texinfo to make Texinfo files + echo. gettext to make PO message catalogs + echo. changes to make an overview over 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 + goto end +) + +if "%1" == "clean" ( + for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i + del /q /s %BUILDDIR%\* + goto end +) + + +%SPHINXBUILD% 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 +) + +if "%1" == "html" ( + %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/html. + goto end +) + +if "%1" == "dirhtml" ( + %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. + goto end +) + +if "%1" == "singlehtml" ( + %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. + goto end +) + +if "%1" == "pickle" ( + %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the pickle files. + goto end +) + +if "%1" == "json" ( + %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the JSON files. + goto end +) + +if "%1" == "htmlhelp" ( + %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run HTML Help Workshop with the ^ +.hhp project file in %BUILDDIR%/htmlhelp. + goto end +) + +if "%1" == "qthelp" ( + %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run "qcollectiongenerator" with the ^ +.qhcp project file in %BUILDDIR%/qthelp, like this: + echo.^> qcollectiongenerator %BUILDDIR%\qthelp\Shogun-manual.qhcp + echo.To view the help file: + echo.^> assistant -collectionFile %BUILDDIR%\qthelp\Shogun-manual.ghc + goto end +) + +if "%1" == "devhelp" ( + %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. + goto end +) + +if "%1" == "epub" ( + %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The epub file is in %BUILDDIR%/epub. + goto end +) + +if "%1" == "latex" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "latexpdf" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + cd %BUILDDIR%/latex + make all-pdf + cd %BUILDDIR%/.. + echo. + echo.Build finished; the PDF files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "latexpdfja" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + cd %BUILDDIR%/latex + make all-pdf-ja + cd %BUILDDIR%/.. + echo. + echo.Build finished; the PDF files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "text" ( + %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The text files are in %BUILDDIR%/text. + goto end +) + +if "%1" == "man" ( + %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The manual pages are in %BUILDDIR%/man. + goto end +) + +if "%1" == "texinfo" ( + %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. + goto end +) + +if "%1" == "gettext" ( + %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The message catalogs are in %BUILDDIR%/locale. + goto end +) + +if "%1" == "changes" ( + %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes + if errorlevel 1 exit /b 1 + echo. + echo.The overview file is in %BUILDDIR%/changes. + goto end +) + +if "%1" == "linkcheck" ( + %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck + if errorlevel 1 exit /b 1 + echo. + echo.Link check complete; look for any errors in the above output ^ +or in %BUILDDIR%/linkcheck/output.txt. + goto end +) + +if "%1" == "doctest" ( + %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest + if errorlevel 1 exit /b 1 + echo. + echo.Testing of doctests in the sources finished, look at the ^ +results in %BUILDDIR%/doctest/output.txt. + goto end +) + +if "%1" == "xml" ( + %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The XML files are in %BUILDDIR%/xml. + goto end +) + +if "%1" == "pseudoxml" ( + %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml. + goto end +) + +:end diff --git a/doc/sphinx/sgexample.py b/doc/sphinx/sgexample.py new file mode 100644 index 00000000000..067c29d23d0 --- /dev/null +++ b/doc/sphinx/sgexample.py @@ -0,0 +1,144 @@ +from sphinx.directives.code import LiteralInclude +from docutils import nodes +import os +import uuid +import sys + +PATH_TO_SHOGUN_META = "../../examples/example-generation/" +sys.path.insert(0, PATH_TO_SHOGUN_META) +import parse +import translate +import json + +def setup(app): + app.add_config_value('target_languages', None, True) + + # register functions called upon node-visiting + app.add_node(sgexample, + html=(visit_sgexample_node, depart_sgexample_node)) + app.add_node(tabpanel, + html=(visit_tabpanel_node, depart_tabpanel_node)) + app.add_node(navtabs, + html=(visit_navtabs_node, depart_navtabs_node)) + app.add_node(navtab, + html=(visit_navtab_node, depart_navtab_node)) + app.add_node(fluid_tab_content, + html=(visit_fluid_tab_content, depart_fluid_tab_content)) + + app.add_directive('sgexample', ShogunExample) + app.connect('builder-inited', setup_languages) + + return {'version': '0.1'} + +class LocalContext(object): + pass + +context = LocalContext() + +def setup_languages(app): + context.target_languages = app.config.target_languages + +class sgexample(nodes.Element): + pass +class fluid_tab_content(nodes.Element): + pass +class tabpanel(nodes.Element): + pass +class navtabs(nodes.Element): + pass +class navtab(nodes.Element): + pass + +def visit_tabpanel_node(self, node): + self.body.append('
') +def depart_tabpanel_node(self, node): + self.body.append('
') + +def visit_navtabs_node(self, node): + self.body.append('') + +def visit_navtab_node(self, node): + cls = "" + if node.index is 0: + cls = 'class="active"' + self.body.append('') + +def visit_fluid_tab_content(self, node): + self.body.append('
') +def depart_fluid_tab_content(self, node): + self.body.append('
') + +def visit_sgexample_node(self, node): + cls = "" + if node.index is 0: + cls = 'active' + self.body.append('
' % (cls, node.language)) +def depart_sgexample_node(self, node): + self.body.append('
') + +class ShogunExample(LiteralInclude): + def element_id(self, target, uid): + return '%s-code-%s' % (target, uid) + def resolve_path(self, name): + return self.state.document.settings.env.relfn2path(name) + def convert_example(self, fname, target, extension): + source_path = self.resolve_path(fname)[1] + target_path = "%s/targets/%s.json" % (PATH_TO_SHOGUN_META, target) + destination_path = self.resolve_path(fname+'.'+extension)[1] + + with open(source_path, 'r') as source, \ + open(target_path, 'r') as translator, \ + open(destination_path,'w') as destination: + ast = parse.parse(source.read(), source_path) + language = json.load(translator) + translated = translate.translate(ast, language) + destination.write(translated) + + def run(self): + + section = self.arguments[0].split(':')[1] + if section == 'begin': + self.options['end-before'] = section + elif section == 'end': + self.options['start-after'] = section + else: + self.options['start-after'] = section + self.options['end-before'] = section + uid = str(uuid.uuid1())[:6] + result = tabpanel() + nvtbs = navtabs() + nvtbs.uid = uid + for i, (target, _) in enumerate(context.target_languages): + nvtb = navtab() + nvtb.language = self.element_id(target, uid) + nvtb.index = i + nvtbs += nvtb + + result += nvtbs + + # save original node + fname = self.arguments[0].split(':')[0].strip() + + tbcntnt = fluid_tab_content() + + # create nodes with parsed listings + for i, (target, extension) in enumerate(context.target_languages): + self.convert_example(fname, target, extension) + self.arguments[0] = fname+'.'+extension + self.options['language'] = target + # call base class, returns list + include_container = sgexample() + include_container.language = self.element_id(target, uid) + include_container.index = i + include_container += LiteralInclude.run(self) + tbcntnt += include_container + result += tbcntnt + + return [result] + +def meta_convert(fname): + pass diff --git a/doc/sphinx/source/conf.py b/doc/sphinx/source/conf.py new file mode 100644 index 00000000000..2519d9dbef7 --- /dev/null +++ b/doc/sphinx/source/conf.py @@ -0,0 +1,272 @@ +# -*- coding: utf-8 -*- +# +# Shogun-manual documentation build configuration file, created by +# sphinx-quickstart on Fri Mar 20 22:34:40 2015. +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys +import os + +# 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. +#sys.path.insert(0, os.path.abspath('.')) + + +# 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.mathjax', + 'sgexample' +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'Shogun-manual' +copyright = u'2015, Heiko' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = '4.0' +# The full version, including alpha/beta/rc tags. +release = '4.0' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = [] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + +# If true, keep warnings as "system message" paragraphs in the built documents. +#keep_warnings = False + + +# -- 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 = 'classic' + +# 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 themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# 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'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +#html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +target_languages = ( + ('python', 'py'), + ('octave', 'm'), + ('r', 'r'), + ('java', 'java') + ) + +html_context = { + 'target_languages': + [x[0] for x in target_languages] +} + +# Output file base name for HTML help builder. +htmlhelp_basename = 'Shogun-manualdoc' + + +# -- 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': '', +} + +# 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 = [ + ('index', 'Shogun-manual.tex', u'Shogun-manual Documentation', + u'Heiko', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'shogun-manual', u'Shogun-manual Documentation', + [u'Heiko'], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- 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 = [ + ('index', 'Shogun-manual', u'Shogun-manual Documentation', + u'Heiko', 'Shogun-manual', 'One line description of project.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +#texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +#texinfo_no_detailmenu = False diff --git a/doc/sphinx/source/examples/classifier/knn/knn.rst b/doc/sphinx/source/examples/classifier/knn/knn.rst new file mode 100644 index 00000000000..c6560f50aa1 --- /dev/null +++ b/doc/sphinx/source/examples/classifier/knn/knn.rst @@ -0,0 +1,30 @@ +================== +Nearest neighbours +================== + +Since Pythagoras, we know that :math:`a^2 + b^2 = c^2`. Use that for KNN. + +------- +Example +------- + +Lets setup environment: + +.. sgexample:: knn.sg:begin + +Imagine you have some training and test data. + +.. sgexample:: knn.sg:load_data + +In order to run KNN, we need to choose a distance, for example CEuclideanDistance, or other sub-classes of CDistance. The distance needs the data we want to classify. + +.. sgexample:: knn.sg:choose_distance + +Once you have chosen a distance, create an instance of the CKNN classifier, passing it training data and labels + +.. sgexample:: knn.sg:create_instance + +Now we run the KNN algorithm and apply it to test data + +.. sgexample:: knn.sg:train_and_apply +.. sgexample:: knn.sg:end diff --git a/doc/sphinx/source/examples/classifier/knn/knn.sg b/doc/sphinx/source/examples/classifier/knn/knn.sg new file mode 100644 index 00000000000..617997dc785 --- /dev/null +++ b/doc/sphinx/source/examples/classifier/knn/knn.sg @@ -0,0 +1,25 @@ +#![begin] +#![load_data] +CSVFile trainf("../data/fm_train_real.dat") +RealFeatures feats_train(trainf) +CSVFile testf("../data/fm_test_real.dat") +RealFeatures feats_test(testf) +CSVFile train_labels("../data/label_train_multiclass.dat") +MulticlassLabels labels(train_labels) +#![load_data] + +#![choose_distance] +EuclideanDistance distance(feats_train, feats_test) +#![choose_distance] + +#![create_instance] +KNN knn(3, distance, labels) +#![create_instance] + +#![train_and_apply] +knn.train() +Labels test_labels = knn.apply(feats_test) +RealVector output = test_labels.get_values() +print output +#![train_and_apply] +#![end] diff --git a/doc/sphinx/source/examples/classifier/pca/pca.rst b/doc/sphinx/source/examples/classifier/pca/pca.rst new file mode 100644 index 00000000000..d2c2fdb5e2d --- /dev/null +++ b/doc/sphinx/source/examples/classifier/pca/pca.rst @@ -0,0 +1,5 @@ +============================ +Principal Component Analysis +============================ + +PCA ist gut. diff --git a/doc/sphinx/source/examples/classifier/svm/svm.rst b/doc/sphinx/source/examples/classifier/svm/svm.rst new file mode 100644 index 00000000000..a0d9914aed4 --- /dev/null +++ b/doc/sphinx/source/examples/classifier/svm/svm.rst @@ -0,0 +1,5 @@ +======================= +Support Vector Machines +======================= + +SVM ist gut. diff --git a/doc/sphinx/source/index.rst b/doc/sphinx/source/index.rst new file mode 100644 index 00000000000..ecb023e55f3 --- /dev/null +++ b/doc/sphinx/source/index.rst @@ -0,0 +1,21 @@ +Welcome to Shogun documentation! +========================================= + +You may find something interesting here + +Contents +======== + +.. toctree:: + :maxdepth: 1 + :glob: + + examples/**/* + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/doc/sphinx/source/static/EMPTY.YET b/doc/sphinx/source/static/EMPTY.YET new file mode 100644 index 00000000000..8d1c8b69c3f --- /dev/null +++ b/doc/sphinx/source/static/EMPTY.YET @@ -0,0 +1 @@ + diff --git a/doc/sphinx/source/templates/layout.html b/doc/sphinx/source/templates/layout.html new file mode 100644 index 00000000000..0d9076dd96a --- /dev/null +++ b/doc/sphinx/source/templates/layout.html @@ -0,0 +1,14 @@ +{% extends "!layout.html" %} + +{% block rootrellink %} +
  • Shogun »
    • + {{ super() }} +{% endblock %} + +{% block extrahead %} + + + + {{ super() }} +{% endblock %} + diff --git a/doc/sphinx/source/templates/page.html b/doc/sphinx/source/templates/page.html new file mode 100644 index 00000000000..f6ebafc336d --- /dev/null +++ b/doc/sphinx/source/templates/page.html @@ -0,0 +1,32 @@ +{%- extends "layout.html" %} +{% block body %} +{% if pagename[:"examples"|length] == "examples" %} +
    +
    + + +
      + {% for lang in target_languages %} +
    • + {{lang|title}} +
      • + {% endfor %} +
    + +
    +
    + +{{ body }} + + + +{% else %} +{{ body }} +{% endif %} +{% endblock %}