virtool-core 0.1.0

core utilities for Virtool backend

virtool-core

Core utilities for Virtool and associated packages.

Install

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

Contribute

Running Tests

The testing framework used is pytest. Install it using:

pip install pytest

Run the tests from the root directory:

pytest

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