virtool-core

Core utilities for Virtool and associated packages.

Install

Last Stable Release

pip install virtool-core

Latest Changes

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

Contribute

Unit Tests

Install Tox

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 tox-poetry

Run Tests

tox

Any arguments given to tox after a -- token will be supplied to pytest.

tox -- --log-cli-level=DEBUG

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