Testing arviz-stats

Testing arviz-stats#

How to run the test suite#

The recommended way to run the test suite is to do it via tox. Tox manages the environment, its env variables and the command to run to allow testing the library with different combinations of optional dependencies from the same development env.

To run the full test suite run:

tox -e py312  # or py313, should match your python version

To run only the parts of the test suite that use modules with NumPy and SciPy as dependencies run:

tox -e minimal  # should work for any python version

How to write tests#

Use importorskip helper function from tests/helpers for any import outside of the Python standard library plus NumPy and SciPy. For example:

import copy
import re

import numpy as np

from .helpers import importorskip

xr = importorskip("xarray")

#... in the code use xr.Dataset, xr.DataArray as usual

As importorskip will skip all tests in that file, tests should be divided into files with tests of the array_stats interface always being on their own file with no optional dependencies import and the rest in a second (or more) files.

About arviz-stats testing#

The recommended install is via arviz-stats[xarray] which provides functionality similar to the functions that used to be within arviz/stats module. However, it is also possible to install arviz-stats without the xarray or arviz-base dependencies in which case a minimal version of the library that depends only on NumPy and SciPy is installed.

To take this into account, tests use the importorskip helper function from tests/helpers.py when importing optional dependencies like xarray, arviz-base or pandas so that tests are skipped if a dependency is not available. In addition, the env variable ARVIZ_REQUIRE_ALL_DEPS can be set to disable this behaviour and ensure uninstalled dependencies raise an error.

When using tox -e pyXXX all optional dependencies are installed, and ARVIZ_REQUIRE_ALL_DEPS is set to ensure all tests in the test suite run. However, tox -e minimal only installs arviz-stats and doesn’t set the env variable which ensures that the minimal install is viable and works as expected.

Consequently, when writing tests we need to take this into account and separate the testing of the array functions and their results from the xarray interface/api built on top of that.

At the time of writing, on GitHub Actions we run the full test suite for all python versions and the minimal test suite for one python version. Which tests are executed is defined by the combination of tox.ini and .github/workflows/test.yml.

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