We are currently writing tests formatted for the pytest package, for testing pyani.


Some tests are still targeted at nosetests, which is in maintenance mode and, although we are still in transition, our plan is to change the test framework completely to use pytest.

Test directory structure

All tests, supporting input and target data, are to be found in the tests/ subdirectory of the pyani repository.

  • Input data for tests is located under the tests/test_input directory, in subdirectories named for the general operation that is being tested.
  • Target data (known correct values) for tests is located under the tests/test_targets directory, in subdirectories named for the general operation being tested.
  • Test output is written to the tests/test_output directory, in subdirectories named for the general operation being tested.


If you wish to write new tests for pyani, we ask that your test data and operations conform to this structure

The tests/test_failing_data directory contains data that is known to cause problems for pyani in that at least two of the input genomes have no appreciable sequence identity.

Running tests

To run tests with nosetests, change directory to the root of the pyani repository, and invoke a nosetests command.

Run all tests locally

To run all tests locally on your machine, issue the following command from the repository root:

nosetests -v

This will cause nose to run all tests under the tests/ subdirectory.

Run individual tests

Tests are grouped in files with filenames that match test_*.py. We aim to write tests as classes that subclass unittest.TestCase, as described in the nosetests documentation. An example of this style can be found in the tests/test_anim.py test file.

This style allows us to run tests at several levels of granularity, specifying all tests (see above), all tests within a module (e.g. test_anim.py), or all tests within a class in that test file.

For example, to run all ANIm-related tests, we can issue:

nosetests -v tests/test_anim.py

To run all tests of nucmer command line generation, we can specify a single class within that file using the command:

nosetests -v tests/test_anim.py:TestNUCmerCmdline

And to test only “multiple command generation” we can issue the following:

nosetests -v tests/test_anim.py:TestNUCmerCmdline.test_multi_cmd_generation