About this site

These docs originally came from the Triton User Guide, but now serves as a general Aalto scientific computing guide. The intention is a good central resources for researchers, kept up to date by the whole community. We can’t do this only by ourselves - we invite everyone to help us. Even pointing out unclear parts sets us on the right path. You can and should join us.


This documentation is Open Source (CC-BY 4.0), and we welcome contributions from the Aalto community. The project is run on Github in the repository AaltoSciComp/scicomp-docs.

To contribute, you can always use the normal Github contribution mechanisms: make a pull request, issues, or comments. If you are at Aalto, you can also get direct write access. Make a github issue, then contact us in person/by email for us to confirm.

The worst contribution is one that isn’t made. Don’t worry about making things perfect: since this is in version control, we track all changes and will just fix anything that’s not perfect. This is also true for formatting errors - if you can’t do ReStructudedText perfectly, just do your best (and pretend it’s markdown because all the basics are similar).

When you submit a change, there is continuous testing that will notify you of errors, so that you can make changes with confidence.

Contributing gives agreement to use content under the licenses (CC-BY 4.0 or CC0 for examples).

Requirements and building

To build the docs, run make html. You can run make clean check to build it and report only the errors that would cause a failure.

There is a requirements.txt file, but the only real Python dependencies to do basic tests is sphinx and sphinx_rtd_theme (debian packages: python-sphinx and python-sphinx-rtd-theme).

HTML output is in _build/html/index.html, and other output formats are available as well.


Look at examples and copy. To add sections, add a new page in a subfolder. Link it from the main Table of Contents (toctree) in index.rst to have the document appear and be cross-referenced.

You can see a complete example from UiT: source and compiled HTML.

ReStructured text

ReStructured Text is similar to markdown for basics, but has a more strictly defined syntax and more higher level structure. This allows more semantic markup, more power to compile into different formats (since there isn’t embedded HTML), and advanced things like indexing, permanent references, etc.

Restructured text home and quick reference.

Note: Literal inline text uses `` instead of a single ` (second works but gives warning).

A very quick guide is below.

Inline code/monospace, emphasis, strong emphasis

``Inline code/monospace``, *emphasis*, **strong emphasis**

Block quote
Block quote

  Block quote
  Block quote

Block quotes can also start with paragraph ending in double colon, like this:

Block quote
Block quotes can also start with paragraph ending in double colon,
like this::

    Block quote

Inline link, or anonymous, or separate, or different text links. Trailing underscores indicate links. Note there should be two underscores for the raw links.

Inline `link <https://www.python.org>`_, or
anonymous__, or
separate_, or
`different text <separate_>`_ links.
Trailing underscores indicate links.

__ https://www.python.org

.. _separate: https://www.python.org

Linking internally. If possible use a permanent reference (next section), but you can also refer to specific files by name. Note, that for internal links there are no trailing underscores:


With different text:
:doc:`Text <../tut/interactive.rst>`

Internal links. Permanent references across files

Label things this way (note only one colon):

.. _label-name:

Reference them this way:

:ref:`label-name`     (recommended)
`label-name`          (short, no warning if link breaks)
`Text <label-name>`   (short, no warning if link breaks)

Notes, warnings, etc.


This is a note


This is a warning

.. note::

  This is a note

.. warning::

  This is a warning


.. index:: commit; amend

.. index::
   commit; message
   pair: commit; amend


:index:`loop variables <pair: commit; amend>`