imunro/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

Initial setup

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

Most Linux distributions will also provide it in a python-sphinx package (or similar).

LaTeX

To build the PDF documentation, XeLaTeX is also required (the xelatex command must be available on the PATH). This is available via TeX Live) for Linux and MacOS X. Many Linux distributions also have it packaged; so long as it is version 2010 or greater, it should be fine. If you install by hand, note that you must run

ln -s $TEXMFSYSVAR/fonts/conf/texlive-fontconfig.conf /etc/fonts/conf.d/09-texlive.conf
fc-cache -rsvf

to add the TeX fonts to the system font configuration. TEXMFSYSVAR is the path to texmf-var, e.g. /usr/local/texlive/2013/texmf-var.

MacOS X users can also install MacTeX instead of TeXLive, but we have noticed that fonts do not work without extra configuration. See:

• Mail on macosx-tex
• TeX Gyre on Stack Exchange

To add the MacTeX fonts system-wide:

• Open Font Book.app
• Select File-->New Library; call the new library TeX Gyre
• Right-click on TeX Gyre and select Add Font…
• Navigate to /usr/local/texlive/2013/texmf-dist/fonts/opentype/public/tex-gyre and click Open. (Type /usr/local to get there initially.)

Graphviz

The Contributing documentation now requires you to install Graphviz to build the diagrams.

Structure and organization

The OME documentation is organized into multiple folders:

• the OMERO documentation is under the omero folder,
• the OME Model and Formats documentation is under the formats folder,
• the OME Contributing Developer documentation is under the contributing folder,
• the shared configuration and themes are under the common folder.

The structure of each 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,
• images/screenshots are placed under images,
• downloadable files are placed under downloads,
• 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

The documentation may be built with make or ant. Note that ant requires ant-contrib to be on the classpath.

Basic build commands

To build a set of documentation, first move to the documentation folder. To build the OMERO documentation:

cd omero/

or to build the OME Model and Formats documentation:

cd formats/

or to build the Contributing Developer documentation:

cd contributing/

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

make clean
ant clean

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

make html
ant html

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

make linkcheck
ant 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)

Top-level build command

The top-level directory Makefile also defines targets for building all the OMERO, Contributing, and Model and Formats sets of documentation at once.

To clean the build directories of any previous builds, use one of:

make clean
ant clean

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

make html
ant html

To build the sets of documentation locally in the form of a PDF file, use one of:

make latexpdf
ant latexpdf

Makefile options

Additional options for sphinx-build can be passed using the SPHINXOPTS variable. The -W option turns all warnings into errors:

SPHINXOPTS=-W make clean html
SPHINXOPTS=-W ant clean html

Release number

The release number of two sets of the documentation is UNKNOWN by default. To modify this value:

• for the OMERO documentation, set the environment variable OMERO_RELEASE, e.g.:

  cd omero && OMERO_RELEASE=4.4.6 make clean html
  cd omero && OMERO_RELEASE=4.4.6 ant clean html
  

• for the OME Model and Formats documentation, set the environment variable FORMATS_RELEASE, e.g.:

  cd formats && FORMATS_RELEASE=2012-06 make clean html
  cd formats && FORMATS_RELEASE=2012-06 ant clean html
  

The Contributing Developer documentation has the release version removed as the intention is to update these files as and when necessary, so that they always reflect our current practices.

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 do not 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).

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 page can be uniquely referenced using the sphinx doc directive. Like other directives, you can use the absolute file path, i.e. relative to the top-level directory: :doc: `/path/name-of-the-page` or :doc: `link to my page </path/name-of-the-page>`.

Only when a good reason exists, a document can also start with a label:

.. _page-label:


Title Of The Page
=================

Use of labels to refer to whole files is discouraged. References to labels above tables and images are 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 top-level directory of the documentation.

Please do not use relative (../../../images/foo.jpg) paths to refer to images. Sphinx does a good job at creating paths, so one can use /images/foo.jpg

Tables

Please do not use tables for collections of links and figures, and leave them solely for use as actual tables. While it can be used in HTML to shoehorn content into boxes, it does not work too well for other output, e.g. latex.

Big tables (typically wider than 50 characters) should be managed as external files using the comma-separated values (CSV) format. These tables can then be included in the documentation with the csv-table directive. If tables are saved using the tab-separated values (TSV) format use the delim option to set the table delimiter to tab e.g.:

.. csv-table::
    :widths: 20 80
    :header-rows: 1
    :file: searchfieldnames.tsv
    :delim: tab

To control the column width in the LaTeX output, precede the table directive with tabularcolumns, e.g.:

.. tabularcolumns:: |p{3.5cm}|p{12cm}|

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

Please try to follow the rules outlined in Inline Markup. This allows for improving the semantics of the document elements.

• Notes should be formatted using the note directive: .. note::
• Definition lists can be created and cross-referenced using the glossary directive: .. glossary::. Each definition can be referenced anywhere in the documentation using the :term: role and an entry will be added for every term in the generated index.
• References to external documentation can be formatted using: .. seealso::
• Menu selections should be marked using the appropriate role: :menuselection: `Start --> Programs`
• Environment variables should be formatted using the :envvar: role. This role will add an entry for the variable in the generated index.
• CLI Commands can be formatted using the following role: :omerocmd: `admin start` This role will render as omero admin start and add an entry for the command in the generated index.
• Other commands should be formatted using the literal markup: :literal: `command` or double back quoted markup
• Other useful inline markups include: :option: and :guilabel:
• Do not use inline highlighting or other markups in headings or subheadings

Global substitutions

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

Hyperlinks

The table below lists targets for common hyperlinks.

Target name	Link
Python	http://python.org
Matplotlib	http://matplotlib.org/
Pillow	http://pillow.readthedocs.org
Hibernate	http://www.hibernate.org
ZeroC	http://www.zeroc.com
Ice	http://www.zeroc.com
Jenkins	http://jenkins-ci.org
roadmap	https://trac.openmicroscopy.org.uk/ome/roadmap
Open Microscopy Environment	http://www.openmicroscopy.org/site
Glencoe Software, Inc.	http://www.glencoesoftware.com/

Abbreviations

The table below lists substitutions for common abbreviations. These substitutions use the :abbr: Sphinx role meaning they are shown as tool-tip in HTML and output only once in LaTeX.

Name	Abbreviation	Explanation
|SSH|	SSH	Secure Shell
|VM|	VM	Virtual Machine
|OS|	OS	Operating System
|SSL|	SSL	Secure Socket Layer
|HDD|	HDD	Hard Disk Drive
|CLI|	CLI	Command Line Interface

OMERO page references

The table below lists substitutions that can be used to create references to sections of the OMERO documentation.

Name	Path
|OmeroPy|	developers/Python
|OmeroCpp|	developers/Cpp
|OmeroJava|	developers/Java
|OmeroMatlab|	developers/Matlab
|OmeroApi|	developers/Modules/Api
|OmeroWeb|	developers/Web
|OmeroClients|	developers/GettingStarted
|OmeroGrid|	sysadmins/grid
|OmeroSessions|	developers/Server/Sessions
|OmeroModel|	developers/Model
|ExtendingOmero|	developers/ExtendingOmero
|BlitzGateway|	developers/Python

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: :omero_plone: `OME 5 <>`
• OME Forums: :forum: `viewforum.php?f=3`
• Downloads: :downloads: `OMERO downloads <>`

For the most up-to-date list, please consult conf.py (section extlinks). Note that there are separate conf.py files for each set of documentation, as well as a shared one under common/.

Source code links

Links to the OMERO source code hosted on Github can be created using the source alias for single files, e.g. :source: `etc/grid/default.xml` or the sourcedir alias for directories, e.g. :sourcedir: `etc`.

By default, these links will point at the code under the develop branch or https://github.com/openmicroscopy/openmicroscopy. To specify a specific fork and/or branch, set the SOURCE_USER and SOURCE_BRANCH environment variables, e.g.:

SOURCE_USER=sbesson SOURCE_BRANCH=my_branch make clean html
SOURCE_USER=sbesson SOURCE_BRANCH=my_branch ant clean html

Jenkins links

Links to the continuous integration server can be created using the jenkins alias for the main server, e.g. :jenkins: `Jenkins server <>`, the jenkinsjob alias for a given job, e.g. :jenkinsjob: `OMERO-4.4` or the jenkinsview alias for a given view, e.g. :jenkinsview: `4.4`.

Mailing-list links

Links to the OME mailing lists can be created using the mailinglist alias, e.g. :mailinglist:`ome-users/`. To point at specific discussion threads, two aliases have been defined ome-users and ome-devel, e.g. :ome-users:`ome-users thread <2009-June/001839.html>`.

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 separate file without the default .txt extension. This file can then be later included using the literalinclude directive.

Writing Conventions

• Do not use contractions (can't, isn't, I'll, etc.) or '&' in the documentation.
• All H1 and H2 level headings should have a capital letter at the start of each word.
• All sub-headings (H3 +) should begin with a capital letter for the first word and continue in lowercase, except where they refer to terms which are abbreviated in the text e.g. Virtual Machine.
• Use the full product name, e.g. OMERO.insight instead of Insight.
• Avoid using resp. in brackets to refer to alternative file names etc. Just use 'or'.
• Use full words rather than symbols in headings if possible.
• When giving instructions, address the user as 'you' and try to maintain a professional attitude - i.e. no random asides about making coffee or smilies!
• Bullet point lists should begin with a capital letter and end with a full stop if each point is a complete sentence, or more than one sentence. If not, no punctuation is necessary (see http://oxforddictionaries.com/words/bullet-points).
• Note that if you are giving an example link which is phrased like a hyperlink but not formatted as one because it does not actually exist, you need to prepend it with a '\' to escape the link and stop the link-checker from reporting it as broken (e.g. \http://your_host/webclient/login/), unless you use the literal mark-up.