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jmchiltonjmchilton
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Initial sphinx documentation configuration.
1 parent 2e8d6e1 commit 2144767

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Lines changed: 717 additions & 3 deletions

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‎.hgignore‎

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syntax: glob
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docs/_build
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*.pyc
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.coverage
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coverage_html_report
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*.key
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.venv
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paster.log
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paster.pid
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paster.pid

‎README.rst‎

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@@ -9,6 +9,7 @@ file systems. Input files, scripts, and
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config files are transferred to the remote system, the job is
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executed, and the results are transferred back to the Galaxy server.
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------------------
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Configuring Galaxy
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------------------

‎docs/Makefile‎

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# Makefile for Sphinx documentation
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#
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# You can set these variables from the command line.
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SPHINXOPTS =
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SPHINXBUILD = sphinx-build
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PAPER =
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BUILDDIR = _build
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# Internal variables.
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PAPEROPT_a4 = -D latex_paper_size=a4
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PAPEROPT_letter = -D latex_paper_size=letter
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ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
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# the i18n builder cannot share the environment and doctrees with the others
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I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
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.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
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help:
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@echo "Please use \`make <target>' where <target> is one of"
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@echo " html to make standalone HTML files"
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@echo " dirhtml to make HTML files named index.html in directories"
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@echo " singlehtml to make a single large HTML file"
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@echo " pickle to make pickle files"
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@echo " json to make JSON files"
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@echo " htmlhelp to make HTML files and a HTML help project"
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@echo " qthelp to make HTML files and a qthelp project"
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@echo " devhelp to make HTML files and a Devhelp project"
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@echo " epub to make an epub"
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@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
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@echo " latexpdf to make LaTeX files and run them through pdflatex"
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@echo " text to make text files"
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@echo " man to make manual pages"
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@echo " texinfo to make Texinfo files"
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@echo " info to make Texinfo files and run them through makeinfo"
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@echo " gettext to make PO message catalogs"
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@echo " changes to make an overview of all changed/added/deprecated items"
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@echo " linkcheck to check all external links for integrity"
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@echo " doctest to run all doctests embedded in the documentation (if enabled)"
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clean:
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-rm -rf $(BUILDDIR)/*
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html:
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$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
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dirhtml:
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$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
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singlehtml:
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$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
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@echo
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@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
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pickle:
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$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
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@echo
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@echo "Build finished; now you can process the pickle files."
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json:
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$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
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@echo
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@echo "Build finished; now you can process the JSON files."
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htmlhelp:
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$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
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@echo
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@echo "Build finished; now you can run HTML Help Workshop with the" \
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".hhp project file in $(BUILDDIR)/htmlhelp."
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qthelp:
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$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
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@echo
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@echo "Build finished; now you can run "qcollectiongenerator" with the" \
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".qhcp project file in $(BUILDDIR)/qthelp, like this:"
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@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/LWR.qhcp"
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@echo "To view the help file:"
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@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/LWR.qhc"
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devhelp:
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$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
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@echo
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@echo "Build finished."
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@echo "To view the help file:"
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@echo "# mkdir -p $$HOME/.local/share/devhelp/LWR"
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@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/LWR"
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@echo "# devhelp"
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epub:
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$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
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@echo
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@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
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latex:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo
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@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
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@echo "Run \`make' in that directory to run these through (pdf)latex" \
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"(use \`make latexpdf' here to do that automatically)."
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latexpdf:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo "Running LaTeX files through pdflatex..."
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$(MAKE) -C $(BUILDDIR)/latex all-pdf
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@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
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text:
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$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
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@echo
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@echo "Build finished. The text files are in $(BUILDDIR)/text."
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man:
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$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
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@echo
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@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
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texinfo:
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$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
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@echo
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@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
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@echo "Run \`make' in that directory to run these through makeinfo" \
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"(use \`make info' here to do that automatically)."
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info:
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$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
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@echo "Running Texinfo files through makeinfo..."
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make -C $(BUILDDIR)/texinfo info
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@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
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gettext:
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$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
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@echo
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@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
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changes:
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$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
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@echo
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@echo "The overview file is in $(BUILDDIR)/changes."
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linkcheck:
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$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
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@echo
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@echo "Link check complete; look for any errors in the above output " \
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"or in $(BUILDDIR)/linkcheck/output.txt."
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doctest:
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$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
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@echo "Testing of doctests in the sources finished, look at the " \
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"results in $(BUILDDIR)/doctest/output.txt."

‎docs/make.bat‎

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@ECHO OFF
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set BUILDDIR=_build
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set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
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set I18NSPHINXOPTS=%SPHINXOPTS% .
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if NOT "%PAPER%" == "" (
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set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
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set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
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)
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if "%1" == "" goto help
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if "%1" == "help" (
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:help
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echo.Please use `make ^<target^>` where ^<target^> is one of
21+
echo. html to make standalone HTML files
22+
echo. dirhtml to make HTML files named index.html in directories
23+
echo. singlehtml to make a single large HTML file
24+
echo. pickle to make pickle files
25+
echo. json to make JSON files
26+
echo. htmlhelp to make HTML files and a HTML help project
27+
echo. qthelp to make HTML files and a qthelp project
28+
echo. devhelp to make HTML files and a Devhelp project
29+
echo. epub to make an epub
30+
echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
31+
echo. text to make text files
32+
echo. man to make manual pages
33+
echo. texinfo to make Texinfo files
34+
echo. gettext to make PO message catalogs
35+
echo. changes to make an overview over all changed/added/deprecated items
36+
echo. linkcheck to check all external links for integrity
37+
echo. doctest to run all doctests embedded in the documentation if enabled
38+
goto end
39+
)
40+
41+
if "%1" == "clean" (
42+
for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
43+
del /q /s %BUILDDIR%\*
44+
goto end
45+
)
46+
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if "%1" == "html" (
48+
%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
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if errorlevel 1 exit /b 1
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echo.
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echo.Build finished. The HTML pages are in %BUILDDIR%/html.
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goto end
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)
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if "%1" == "dirhtml" (
56+
%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
57+
if errorlevel 1 exit /b 1
58+
echo.
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echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
60+
goto end
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)
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63+
if "%1" == "singlehtml" (
64+
%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
65+
if errorlevel 1 exit /b 1
66+
echo.
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echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
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goto end
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)
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if "%1" == "pickle" (
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%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
73+
if errorlevel 1 exit /b 1
74+
echo.
75+
echo.Build finished; now you can process the pickle files.
76+
goto end
77+
)
78+
79+
if "%1" == "json" (
80+
%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
81+
if errorlevel 1 exit /b 1
82+
echo.
83+
echo.Build finished; now you can process the JSON files.
84+
goto end
85+
)
86+
87+
if "%1" == "htmlhelp" (
88+
%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
89+
if errorlevel 1 exit /b 1
90+
echo.
91+
echo.Build finished; now you can run HTML Help Workshop with the ^
92+
.hhp project file in %BUILDDIR%/htmlhelp.
93+
goto end
94+
)
95+
96+
if "%1" == "qthelp" (
97+
%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
98+
if errorlevel 1 exit /b 1
99+
echo.
100+
echo.Build finished; now you can run "qcollectiongenerator" with the ^
101+
.qhcp project file in %BUILDDIR%/qthelp, like this:
102+
echo.^> qcollectiongenerator %BUILDDIR%\qthelp\LWR.qhcp
103+
echo.To view the help file:
104+
echo.^> assistant -collectionFile %BUILDDIR%\qthelp\LWR.ghc
105+
goto end
106+
)
107+
108+
if "%1" == "devhelp" (
109+
%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
110+
if errorlevel 1 exit /b 1
111+
echo.
112+
echo.Build finished.
113+
goto end
114+
)
115+
116+
if "%1" == "epub" (
117+
%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
118+
if errorlevel 1 exit /b 1
119+
echo.
120+
echo.Build finished. The epub file is in %BUILDDIR%/epub.
121+
goto end
122+
)
123+
124+
if "%1" == "latex" (
125+
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
126+
if errorlevel 1 exit /b 1
127+
echo.
128+
echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
129+
goto end
130+
)
131+
132+
if "%1" == "text" (
133+
%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
134+
if errorlevel 1 exit /b 1
135+
echo.
136+
echo.Build finished. The text files are in %BUILDDIR%/text.
137+
goto end
138+
)
139+
140+
if "%1" == "man" (
141+
%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
142+
if errorlevel 1 exit /b 1
143+
echo.
144+
echo.Build finished. The manual pages are in %BUILDDIR%/man.
145+
goto end
146+
)
147+
148+
if "%1" == "texinfo" (
149+
%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
150+
if errorlevel 1 exit /b 1
151+
echo.
152+
echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
153+
goto end
154+
)
155+
156+
if "%1" == "gettext" (
157+
%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
158+
if errorlevel 1 exit /b 1
159+
echo.
160+
echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
161+
goto end
162+
)
163+
164+
if "%1" == "changes" (
165+
%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
166+
if errorlevel 1 exit /b 1
167+
echo.
168+
echo.The overview file is in %BUILDDIR%/changes.
169+
goto end
170+
)
171+
172+
if "%1" == "linkcheck" (
173+
%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
174+
if errorlevel 1 exit /b 1
175+
echo.
176+
echo.Link check complete; look for any errors in the above output ^
177+
or in %BUILDDIR%/linkcheck/output.txt.
178+
goto end
179+
)
180+
181+
if "%1" == "doctest" (
182+
%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
183+
if errorlevel 1 exit /b 1
184+
echo.
185+
echo.Testing of doctests in the sources finished, look at the ^
186+
results in %BUILDDIR%/doctest/output.txt.
187+
goto end
188+
)
189+
190+
:end

‎docs/source/_static/.keep‎

Whitespace-only changes.

‎docs/source/_templates/.keep‎

Whitespace-only changes.

‎docs/source/code.rst‎

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.. automodule:: lwr
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:members:
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:undoc-members:
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:show-inheritance:
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