From cbf4d61b001b1848fdc434a813bb0f1da24d15bd Mon Sep 17 00:00:00 2001 From: Nathan Franklin Date: Wed, 11 Mar 2015 11:19:42 +0100 Subject: [PATCH 1/6] setup initial sphinx documentation --- README.rst | 20 ++- doc/Makefile | 177 ++++++++++++++++++++++ doc/make.bat | 242 ++++++++++++++++++++++++++++++ doc/source/conf.py | 344 +++++++++++++++++++++++++++++++++++++++++++ doc/source/index.rst | 22 +++ 5 files changed, 804 insertions(+), 1 deletion(-) create mode 100644 doc/Makefile create mode 100644 doc/make.bat create mode 100644 doc/source/conf.py create mode 100644 doc/source/index.rst diff --git a/README.rst b/README.rst index c875ec6..866c8bb 100644 --- a/README.rst +++ b/README.rst @@ -21,7 +21,7 @@ Requirements - enum34 >= 1.0.4 - pyyaml >= 3.11 - - `simphony-common`_ >= 0.0.1 +- `simphony-common`_ >= 0.0.1 Installation @@ -60,11 +60,29 @@ To run the full test-suite run:: python -m unittest discover +Documentation +------------- + +To build the documentation in the doc/build directory run:: + + python setup.py build_sphinx + +.. note:: + + - One can use the --help option with a setup.py command + to see all available options. + - The documentation will be saved in the ``./build`` directory. + Directory structure ------------------- - simlammps -- hold the lammps-md wrapper implementation - examples -- holds different examples +- doc -- Documentation related files + + - source -- Sphinx rst source files + - build -- Documentation build directory, if documentation has been generated + using the ``make`` script in the ``doc`` directory. .. _simphony-common: https://github.com/simphony/simphony-common diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 0000000..1354424 --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,177 @@ +# 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 + +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/Simphony-Lammps.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Simphony-Lammps.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/Simphony-Lammps" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Simphony-Lammps" + @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/make.bat b/doc/make.bat new file mode 100644 index 0000000..60a7d2a --- /dev/null +++ b/doc/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\Simphony-Lammps.qhcp + echo.To view the help file: + echo.^> assistant -collectionFile %BUILDDIR%\qthelp\Simphony-Lammps.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/source/conf.py b/doc/source/conf.py new file mode 100644 index 0000000..2d3e4e1 --- /dev/null +++ b/doc/source/conf.py @@ -0,0 +1,344 @@ +# -*- coding: utf-8 -*- +# +# SimPhoNy-LAMMPS documentation build configuration file, created by +# sphinx-quickstart on Tue Mar 10 16:10:57 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. + + +# 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('.')) + +# -- General configuration ------------------------------------------------ + +# 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.autodoc', + 'sphinx.ext.doctest', + 'sphinx.ext.intersphinx', + 'sphinx.ext.todo', + 'sphinx.ext.coverage', + 'sphinx.ext.mathjax', + 'sphinx.ext.ifconfig', + 'sphinx.ext.viewcode', +] + +# 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'SimPhoNy-LAMMPS' +copyright = (u'2015, SimPhoNy, EU FP7 Project (Nr. 604005) ' + u'www.simphony-project.eu') + +# 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 = '0.1' +# The full version, including alpha/beta/rc tags. +release = '0.1.1.dev0' + +# 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 = 'default' + +# 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 + +# Output file base name for HTML help builder. +htmlhelp_basename = 'SimPhoNy-LAMMPSdoc' + + +# -- 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', 'SimPhoNy-LAMMPS.tex', u'SimPhoNy-LAMMPS Documentation', + u'SimPhoNy, EU FP7 Project (Nr. 604005) www.simphony-project.eu', + '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', 'SimPhoNy-LAMMPS', u'SimPhoNy-LAMMPS Documentation', + [u'SimPhoNy, EU FP7 Project (Nr. 604005) www.simphony-project.eu'], 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', 'SimPhoNy-LAMMPS', u'SimPhoNy-LAMMPS Documentation', + u'SimPhoNy, EU FP7 Project (Nr. 604005) www.simphony-project.eu', + 'SimPhoNy-LAMMPS', '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 + + +# -- Options for Epub output ---------------------------------------------- + +# Bibliographic Dublin Core info. +epub_title = u'SimPhoNy-LAMMPS' +epub_author = u'SimPhoNy, EU FP7 Project (Nr. 604005) www.simphony-project.eu' +epub_publisher = (u'SimPhoNy, EU FP7 Project (Nr. 604005)', + u' www.simphony-project.eu') +epub_copyright = (u'2015, SimPhoNy, EU FP7 Project (Nr. 604005)', + ' www.simphony-project.eu') + +# The basename for the epub file. It defaults to the project name. +# epub_basename = u'SimPhoNy-LAMMPS' + +# The HTML theme for the epub output. Since default themes are not optimized +# for small screen space, using the same theme for HTML and epub output is +# usually not wise. This defaults to 'epub', a theme designed to save visual +# space. +# epub_theme = 'epub' + +# The language of the text. It defaults to the language option +# or en if the language is not set. +# epub_language = '' + +# The scheme of the identifier. Typical schemes are ISBN or URL. +# epub_scheme = '' + +# The unique identifier of the text. This can be a ISBN number +# or the project homepage. +# epub_identifier = '' + +# A unique identification for the text. +# epub_uid = '' + +# A tuple containing the cover image and cover page html template filenames. +# epub_cover = () + +# A sequence of (type, uri, title) tuples for the guide element of content.opf. +# epub_guide = () + +# HTML files that should be inserted before the pages created by sphinx. +# The format is a list of tuples containing the path and title. +# epub_pre_files = [] + +# HTML files shat should be inserted after the pages created by sphinx. +# The format is a list of tuples containing the path and title. +# epub_post_files = [] + +# A list of files that should not be packed into the epub file. +epub_exclude_files = ['search.html'] + +# The depth of the table of contents in toc.ncx. +# epub_tocdepth = 3 + +# Allow duplicate toc entries. +# epub_tocdup = True + +# Choose between 'default' and 'includehidden'. +# epub_tocscope = 'default' + +# Fix unsupported image types using the PIL. +# epub_fix_images = False + +# Scale large images. +# epub_max_image_width = 0 + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# epub_show_urls = 'inline' + +# If false, no index is generated. +# epub_use_index = True + + +# Example configuration for intersphinx: refer to the Python standard library. +intersphinx_mapping = {'http://docs.python.org/': None} diff --git a/doc/source/index.rst b/doc/source/index.rst new file mode 100644 index 0000000..cf37ba6 --- /dev/null +++ b/doc/source/index.rst @@ -0,0 +1,22 @@ +.. Simphony-Lammps documentation master file, created by + sphinx-quickstart on Tue Mar 10 16:10:57 2015. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to Simphony-Lammps's documentation! +=========================================== + +Contents: + +.. toctree:: + :maxdepth: 2 + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + From cdb12d936cde6f50e23da299511b3307498587a5 Mon Sep 17 00:00:00 2001 From: Nathan Franklin Date: Wed, 11 Mar 2015 11:20:05 +0100 Subject: [PATCH 2/6] add readme to documentation --- doc/source/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/index.rst b/doc/source/index.rst index cf37ba6..9aaa6e8 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -6,7 +6,7 @@ Welcome to Simphony-Lammps's documentation! =========================================== -Contents: +.. include:: ../../README.rst .. toctree:: :maxdepth: 2 From 1a175f88866f9cce3a9c5b6eccb78308f7c18f73 Mon Sep 17 00:00:00 2001 From: Nathan Franklin Date: Wed, 11 Mar 2015 11:26:12 +0100 Subject: [PATCH 3/6] add sphinx build to CI --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 0fe49e3..785dabe 100644 --- a/.travis.yml +++ b/.travis.yml @@ -22,6 +22,7 @@ script: - flake8 --exclude=mylammps . - coverage run -m unittest discover - coverage report + - python setup.py build_sphinx after_success: - coveralls From 62df5ccbb3bc469b9bdaa3cdc31f910ee80e5d34 Mon Sep 17 00:00:00 2001 From: Nathan Franklin Date: Wed, 11 Mar 2015 11:26:58 +0100 Subject: [PATCH 4/6] remove coverage report (as we are using coveralls --- .travis.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 785dabe..c03124c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -21,7 +21,6 @@ install: script: - flake8 --exclude=mylammps . - coverage run -m unittest discover - - coverage report - python setup.py build_sphinx after_success: From 61a3837f0039a375ba430a6caa98e837b3237cba Mon Sep 17 00:00:00 2001 From: Nathan Franklin Date: Wed, 11 Mar 2015 13:13:59 +0100 Subject: [PATCH 5/6] add sphinx to doc-requirements and to Travis-CI --- .travis.yml | 1 + README.rst | 7 +++++++ doc_requirements.txt | 5 +++++ 3 files changed, 13 insertions(+) create mode 100644 doc_requirements.txt diff --git a/.travis.yml b/.travis.yml index c03124c..0797400 100644 --- a/.travis.yml +++ b/.travis.yml @@ -15,6 +15,7 @@ install: - chmod +x install_simphony_common.sh && ./install_simphony_common.sh - pip install -r dev_requirements.txt + - pip install -r doc_requirements.txt - pip install coveralls - python setup.py develop diff --git a/README.rst b/README.rst index 866c8bb..dbb0dd6 100644 --- a/README.rst +++ b/README.rst @@ -23,6 +23,13 @@ Requirements - pyyaml >= 3.11 - `simphony-common`_ >= 0.0.1 +Optional requirements +~~~~~~~~~~~~~~~~~~~~~ + +To support the documentation built you need the following packages: + +- sphinx >= 1.2.3 + Installation ------------ diff --git a/doc_requirements.txt b/doc_requirements.txt new file mode 100644 index 0000000..c897e4c --- /dev/null +++ b/doc_requirements.txt @@ -0,0 +1,5 @@ +sphinx >= 1.2.3 +sphinxcontrib-napoleon >= 0.2.10 +enum34 >= 1.0.4 +stevedore >= 1.2.0 +mock From 6e0aee0190b4242fb46dbb59ce680b22e6ab69a5 Mon Sep 17 00:00:00 2001 From: Nathan Franklin Date: Wed, 11 Mar 2015 14:21:20 +0100 Subject: [PATCH 6/6] add readthedocs to README --- README.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.rst b/README.rst index dbb0dd6..e0334b4 100644 --- a/README.rst +++ b/README.rst @@ -11,6 +11,11 @@ The LAMMPS engine-wrapper for the SimPhoNy framework (www.simphony-project.eu). :target: https://coveralls.io/r/simphony/simphony-lammps-md :alt: Test coverage +.. image:: https://readthedocs.org/projects/simphony-lammps-md/badge/?version=master + :target: https://readthedocs.org/projects/simphony-lammps-md/?badge=master + :alt: Documentation Status + + Repository ----------