ximenesuk/ome-documentation

Sphinx-based documentation for the Open Microscopy Environment

Documentation files to be linked under the docs/sphinx directory of http://github.com/openmicroscopy/openmicroscopy.

Getting started with Sphinx

Sphinx depends on the sphinx-build Python script. As such, it can be installed on any system with a working Python installation and PIP. On Windows, make sure that the Scripts directory under the Python installation directory (e.g. C:\Python26\Scripts) is configured in your PATH. On OS X/Linux, sphinx-build has to be accessible from the command line.

The Sphinx documentation system can be obtained by issuing:

pip install Sphinx

The structure of the documentation folder follows the Sphinx system guidelines. A quick overview:

• source *.txt files with reST markup live in the root of the folder and under subfolders,
• compiled output is placed in _build,
• compiled visual themes are automatically placed in _static,
• Sphinx configuration is held in conf.py,
• goals for make and make.bat are held in Makefile.

A reference of reStructuredText (reST) is available at http://thomas-cokelaer.info. It is recommended to familiarise oneself with the syntax outlined there.

A tutorial covering Sphinx, which enhances working with reST documents, can be found at http://sphinx.pocoo.org.

Building the documentation

To clean the build directory of any previous builds, use:

make clean

To build the documentation locally in the form of HTML pages, use:

make html

To check the links (internal and external) of the documentation, use:

make linkcheck

To list all targets of the sphinx builder, use:

make

The output should look something like:

Please use `make <target>' where <target> is one of
  html       to make standalone HTML files
  dirhtml    to make HTML files named index.html in directories
  singlehtml to make a single large HTML file
  pickle     to make pickle files
  json       to make JSON files
  htmlhelp   to make HTML files and a HTML help project
  qthelp     to make HTML files and a qthelp project
  devhelp    to make HTML files and a Devhelp project
  epub       to make an epub
  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter
  latexpdf   to make LaTeX files and run them through pdflatex
  text       to make text files
  man        to make manual pages
  texinfo    to make Texinfo files
  info       to make Texinfo files and run them through makeinfo
  gettext    to make PO message catalogs
  changes    to make an overview of all changed/added/deprecated items
  linkcheck  to check all external links for integrity
  doctest    to run all doctests embedded in the documentation (if
             enabled)

Conventions used

Part of the conventions used here is based on work by Benoît Bryon.

File names

reST source file names should carry the txt suffix and use lowercase alphanumeric characters and the - (minus) symbol.

Indentation

Most reST directives don't need indentation, unless contents or options have to be supplied. For consistency, please use 4 space indentation whenever needed. Do not use indentation for the start of directives (start them at the edge of the new line). Any content under a reST directive has to be indented the same way as the options.

Example:

.. toctree::
    :maxdepth: 2

    Some content here...

Line wrapping

reST source files should use 78 lines for wrapping text. Please consult the manual of your favourite text editor to see how to switch on text wrapping.

Blank lines

Two new lines should be put before top-lined, top-level section names, i.e. before H1 and H2. One new line in any other case.

Example:

###############
Part title (H1)
###############

Introduction text.
(blank)
(blank)
******************
Chapter title (H2)
******************

Title headings

Every reST source file should begin with an H2 (level two) title. H1 titles are reserved for the index files (index.txt).

Titles should be capitalised (see http://grammar.about.com for a discussion about capitalisation styles).

The following symbols should be used to create headings:

• # with top line for parts
• * with top line for chapters
• = for sections
• - for subsections
• ^ for subsubsections
• " for paragraphs

Example:

###############
Part title (H1)
###############

H1 only in indexes.


******************
Chapter title (H2)
******************

Sample file content.


********************
Another chapter (H2)
********************

Section title (H3)
==================

Subsection title (H4)
---------------------

Subsubsection title (H5)
^^^^^^^^^^^^^^^^^^^^^^^^

Paragraph title (H6)
""""""""""""""""""""

And some text.

Page labels and references

Every reST document should start with a label that matches the path and name of the document:

.. _path/name-of-the-page:

*****************
Title of the page
*****************

This label allows the page to be uniquely referenced in the rest of the documentation. To do so, use the following syntax :ref: `path/name-of-the-page` or :ref: `link to my page <path/name-of-the-page>`.

References to labels above tables and images are also encouraged. The :ref: Sphinx role is advised over standard reST links, as it works across files and reference names are automatically generated (e.g. from caption of an image).

Images vs. Figures

reST allows for two types of image embedding: using the image and figure directive. It is recommended to use the latter, as legends and captions can be added easier.

All images referenced in a reST document shall be placed in an images folder in the same directory as the reST file.

Substitutions, aliases and hyperlinks

reST allows for using substitutions in cases where a piece of markup is used more than once, e.g.:

Please visit Python.org_

...

.. _Python.org: http://python.org

If a hyperlink appears only once, please use anonymous, "one-off" hyperlinks (two underscores):

`RFC 2396 <http://www.rfc-editor.org/rfc/rfc2396.txt>`__ and `RFC
2732 <http://www.rfc-editor.org/rfc/rfc2732.txt>`__ together
define the syntax of URIs.

Finally, please avoid using here as the hyperlink name, as in:

(...) go `here <http://www.google.com>`_.

Common markups

• Notes should be formatted using the note directive: .. note::
• Definition lists can be created and cross-referenced using the glossary directive: .. glossary::
• References to external documentation can be formatted using: .. seealso::
• Menu selections should be marked using the appropriate role: :menuselection: `Start --> Programs`

Global substitution

Some substitutions have been implemented using rst_epilog in conf.py. They can be used in all pages of the documentation.

Name	Path
|OmeroPy|	developers/Omero/Python
|OmeroCpp|	developers/Omero/Cpp
|OmeroJava|	developers/Omero/Java
|OmeroMatlab|	developers/Omero/Matlab
|OmeroCli|	developers/Omero/CommandLine
|OmeroApi|	developers/Omero/Modules/Api
|OmeroWeb|	developers/Omero/Web
|OmeroClients|	developers/Omero/GettingStarted
|OmeroInsight|	developers/Omero/Insight
|OmeroGrid|	developers/Omero/Grid
|OmeroSessions|	developers/Omero/Server/Sessions
|OmeroModel|	developers/Omero/Model
|ExtendingOmero|	developers/Server/ExtendingOmero
|BlitzGateway|	developers/Omero/Python/Gateway

For the most up-to-date list, please consult conf.py (section rst_epilog).

Common URLs

Some URLs are widely used across the OME documentation. Using the Sphinx extlinks extension, a dictionary of aliases to base URLs has been defined for the following:

• Trac tickets: :ticket: `3442`, displayed as <a>#3442</a>
• Snapshots: :snapshot: `omero/myzip.zip`
• Plone pages: :plone: `Downloads <support/omero4/downloads>`
• DOIs: :doi: `Dantas, et al., JCB <10.1083/jcb.201012093>`
• Github source code, e.g. :source: `etc/omero.properties`
• OME Forums: :forum: `viewforum.php?f=3`

For the most up-to-date list, please consult conf.py (section extlinks).

Inclusion of content

When a specific type of content (e.g. code snippet) repeats itself among many pages, it is advised to store it in a seperate file without the default .txt extension. This file can then be later included using the literalinclude directive.