Real World Example

Real World Example#

Let’s look at the testing in a larger python package. We’ll use our group’s python hydrodynamics code, pyro, as a test:

python-hydro/pyro2

Installing#

We need to install the package first, via the setup.py:

python setup.py install --user

or alternately as

pip install .

Running the tests#

We can run the tests via:

pytest -v pyro

Using notebooks as tests#

Sometimes we want to use Jupyter notebooks as tests themselves—this is enabled via the nbval plugin. In this way, pytest will execute the cells in the notebook and compare the result to the result stored in the notebook. If they agree, then the test passes.

Sometimes there’s a particular cell that we don’t want to be part of the testing—we can disable these on a cell-by-cell basis by adding tags to a cell.

We can test notebooks as:

pytest -v --nbval pyro

Coverage report#

The pytest-cov plugin enables the generation of a coverage report. This will tell you what fraction of each python file was tested. We run this as:

pytest -v --cov=pyro --nbval pyro

We can also generate a more detailed interactive report with

coverage html

Other types of tests#

Unit tests are only one form of testing—they test a function in isolation of others. Sometimes we need to test everything working together. For scientific codes, regression testing is often used. The basic workflow is:

  • Start with the project working in a way you are happy with

  • Store the output of one (or more) runs as a benchmark.

  • Each time you make changes, run the code and compare the new output to the stored benchmark.

    • If there are no differences, then your changes are likely good (but there is always the case of some feature not being tested).

    • If there are differences, then either you introduced a bug, in which case you should fix it, or you fixed a bug, in which case you should update the benchmarks.

For our example code, pyro, the regression test runs simulations using all the different solvers and compares against the stored output, zone-by-zone for any differences. The comparison itself is built into the main driver of the code and can be invoked as:

./pyro/test.py
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