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Singularity User Docs

IMPORTANT NOTE: Singularity has been renamed to Apptainer. This repository is now only for archiving the history. Submit all current issues and pull requests to https://github.com/apptainer/apptainer.

Setting up an environment to contribute

The Singularity user documentation is written in reStructured Text (RST) format and generated using Sphinx. The ReadTheDocs theme for Sphinx is used.

We use RST instead of markdown as it's better at handling large documents with many linked sections, and Sphinx makes it easy to produce online documentation as well as PDFs.

Sphinx is written in Python. To get setup to contribute:

  • Install Python 3.5 or newer, from your OS package manager or the Python download site
  • Use pip3to install Sphinx and the RTD theme package into your home directory:
pip3 install --user Sphinx sphinx-rtd-theme

If your version of python 3 does not come with pip / pip3, you may need to install a python3-pippackage with apt or yum, or you can install pip following the instructions here.

You're all set! After this you will only need to use your favorite editor to work with the RST files.

How to edit & write RST

A Sphinx documentation project has some structure that it's good to know before you dive in and start editing or writing content.

Structure of the project

This project maintains the following structure:

  1. index.rst : contains the front page of the online documentation and the initial table of contents tree. Every documentation section is referenced by a tag next to its name. (e.g. Quick Start <quick_start>)
  2. All other .rstfiles are sections named to match reference tags described before. So, for the <quick_start> reference in index.rst you'll find a quick_start.rst file with the content for that section.
  3. The configuration used to build the final documentations from the .rst files is set in the conf.py file.

The conf.py file

This file sets the themes, extensions, variables and naming scheme for output created when building the documentation with Sphinx. Some important elements include:

  • version : Describes the current version of Singularity that the documentation is for. We set version to the major.minor values, e.g. 3.5, as we are not creating separate documentation for each patch release.
  • release: Would be used to specify the current release of the software being documented, including patch number, alpha tags etc. We leave this the same as version as we only generate documentation for each major.minor version of singularity.
  • html_theme: Sets the theme to be used for HTML output. We are using the RTD or Read The Docs theme.
  • html_context: Options here control links back to our GitHub repository.
  • html_logo: The logo for the sidebar
  • html_favicon: The faviconfor the entire project

Cheatsheet to get started with reStructured (RST) Text

RST is similar to Markdown, but has enough differences that you are likely to be caught out a few times until you are familiar with it. Let's look at some of the common things you need to do when writing or editing RST.

1. Create a section/subsection/subsubsection title

Sections titles are defined by surrounding or underlining them with different characters. Each combination of overline/underline and character used represents a different level section.

  • To create a main section title: A main section title is surrounded (above and below) with = characters:
================
New Main Section
================
  • To create a sub-section: A sub section title is surrounded (above and below) with - characters:
---------------
New Sub section
---------------
  • To create a sub-sub-section: A sub-sub section title is underlined with = characters:
New sub-sub section
===================
  • If you need more levels you can keep going: A sub-sub-sub-section is underlined with - characters.
New sub-sub-sub section
-----------------------

RST doesn't actually set a specific order for the characters you use to underline and overline titles, as it will pick up the method used for the first title at each level. Following the convention above, though, will make it easy to see what level a section is wherever you are working in the documentation.

2. Reference sections

To reference a section in an RST file you need to first create the reference above the title you need to reference, and second to reference it where you need the link to the reference section. When you build HTML or PDF output with Sphinx it will create the links for you, so the reader can jump around the documentation easily.

Step 1: Create the reference

To create the reference on the section you need to link, you must specify a tag:

.. _build-docker:

-------------------------
Build from a Docker Image
-------------------------

This example will let you refer to the section titled "Build from a Docker Image" with the tag build-docker. Note that the tag here doesn't include the _ that you have to prefix it with when creating the reference.

Step 2: Reference it

To reference a section you need to use this syntax:

:ref:`read the section covering docker images <build-docker>`

:ref: tells Sphinx that this is a reference. In between the `you should provide text for the link, and then the tag you created above between < >.

Further Reading

These are some of the basics of RST. For a more complete introduction, see the Sphinx documentation

Building HTML documentation

To build the HTML documentation, make sure you are in the top level of the singularity-userdocs repository and run:

make html SKIPCLI=1

This will generate a folder called _build/html with the output. Open index.html to browse the documentation.

The SKIPCLI=1 option tells make not to generate the CLI reference, which is created automatically from the Singularity source code. You can generate the CLI documentation by running make html alone. This requires a Go build environment (see below).

Generating PDF files from RST

This is very similar to the previous step, you will need to run:

make latexpdf SKIPCLI=1

Output is written into _build/latex and the final PDF will be named singularity-userdocs.pdf

Generating EPUB from RST

Very similar to the previous command, you will just need to run:

make epub SKIPCLI=1

Output is written into _build/epub and the final EPUB will be named singularity-userdocs.epub

Generating CLI docs

The Singularity CLI docs are generated using the actual code from Singularity. To do this, we include Singularity as a git submodule, and whenever a Makefile target (like make html) is run, Singularity itself is compiled and used to generate the CLI docs.

However, you might not want to compile Singularity, either because you can't on your machine, or because you want to test out a quick change to the docs. If this is the case, you can skip the CLI doc generation using the SKIPCLI argument. For example, to rebuild the HTML docs without including the CLI docs, just run make html SKIPCLI=1.

If Singularity has been updated and you want to synchronize the CLI docs with the new version of Singularity, you'll have to update the submodule. To do this, just run:

git submodule update --remote --merge
git add vendor/src/github.com/apptainer/singularity
git commit

This will update the Singularity submodule to the latest version of the master branch.