Hands-on Scientific Computing

Hands-on SciComp is a practical scientific computing reference and course. The intention is not to make a new course, but to organize all the best material that is already available and provide better introductions and motivation.

Courses

See DESIGN.rst for the philosophy behind choosing the courses and levels.

Local customization

One primary design criteria is standard material with local customizations. Thus, we can share the work of finding the overall best material and still allow local customization - either as standalone or embedding within another Sphinx project. This is done using our custom-developed Sphinx extension sphinx_ext_substitution.

To make local customizations, see the sites/ directory for examples. Define a yaml file with the key site-name, and then any other substitutions you would like. Set the path to this file using SPHINX_EXT_SUBSTITUTION_PATH and you'll get your local version. See sites/aalto/aalto.yaml for an example.

Embedding in another Sphinx project

These docs are designed to be embedded within another Sphinx project with your site-specific customizations. It is not fully automatic yet, but here are some hints:

::

git clone <handsonscicomp-url> _handsonscicomp --recurse-submodules

# Link the source path to where you want it to appear, do what

you want. ln -s training _handsonscicomp/source/ # ensure that PyYAML is installed

If your conf.py::

sys.path.insert(0, '_handsonscicomp/source/') import conf as handsonscicomp_conf handsonscicomp_conf.embed(globals())

globals().setdefault('exclude_patterns',

[]).append('_handsonscicomp')

# Set substitute_path to your site's own config substitute_path = '_handsonscicomp/sites/aalto/'

def setup(app): handsonscicomp_conf.setup(app)

Technical development

Structure

source/: Sphinx project
courses/: YAML files defining the "global" courses
sites/: YAML files defining site-specific (local) course data, to fill out the "Local" column. Site-specific config does not have to be in this repository, it can be tracked separately and referenced with an environment variables.
_ext/: Sphinx extensions.

Building

Clone the repo, update the extension submodule.
make html
You can set the environment variable SPHINX_EXT_SUBSTITUTION_PATH to the path of your site-local YAML configuration.

Maintenance and contributing

This is currently an alpha-level project. Until there is enough critical mass for code review, minor changes are pushed directly to master and more significant changes are pull-requested.

Hands-On Scicomp is currently under the CodeRefinery umbrella, but currently led by Aalto University. However, the intention is that this is a cross-university project so contributions from all members are considered equally. Contact: Richard Darst

khaldi-med/handsonscicomp