How to run augur:
- see the
README.mdfiles in the respective pathogen's folder (
Throughout we assume that the fauna, augur and auspice are sister directories.
# Install with pip. pip install --user pytest tox # Or install inside a conda environment. source activate janus_python2 conda install pytest virtualenv pip install tox
Run tests from the augur root directory.
Tox builds an empty virtual environment, installs augur's requirements and a package of augur built from the local directory, and runs tests with pytest. The
tox.ini file defines the test environment and the
pytest.ini file defines which tests to run. Tox reuses the virtual environment with subsequent runs. Use the
-r flag to force it to rebuild its environment.
Note that on OS X, matplotlib may throw errors during testing stating
from matplotlib.backends import _macosx E RuntimeError: Python is not installed as a framework.
This can be resolved by switching matplotlib backends. Create a file in the home directory
~/.matplotlib/matplotlibrc and include the following:
This should fix the error.