virtool-core 0.1.1

core utilities for Virtool backend

virtool-core

Core utilities for Virtool and associated packages.

Install

pip install virtool-core

Or install from source;

git clone https://github.com/virtool/virtool-core.git
pip install .

#  Or

pip install git+https://github.com/virtool/virtool-core.git

Contribute

Running Tests

tox is used to run the tests in a fresh virtual environment with all of the test dependencies. To install it use;

pip install tox

Then from the repository root;

tox

MongoDB

Some tests require an instance of MongoDB to be running on the local machine.

If you do not have MongoDB installed you can use the run_mongo_with_tests.sh script to run mongo using docker. The docker container used to run mongo will be stopped and removed once the tests have completed.

Documentation

For docstrings, use the Sphinx docstring format.

The packages sphinx_rtd_theme and sphinx_autoapi are used in rendering the documentation.

pip install sphinx_rtd_theme sphinx_autoapi

Markdown for Sphinx

recommonmark is used so that Sphinx can render documentation from markdown files as well as rst files. It will need to be installed before running sphinx-build:

pip install recommonmark

To use sphinx rst directives in a markdown file use the eval_rst code block

Building the documentation

cd sphinx && make html

The rendered HTML files are found under sphinx/build/html