Nipy uses the the Pytest framework. If you plan to do development on nipy please have a look at the Pytest docs and read through the numpy testing guidelines.

Automated testing

We run the tests on every commit with travis-ci |--| see nipy on travis.

We also have a farm of machines set up to run the tests on every commit to the main branch at nipy buildbot.

Writing tests

Test files

We like test modules to import their testing functions and classes from the module in which they are defined. For example, we might want to use the assert_array_equal, assert_almost_equal functions defined by numpy, and the funcfile, anatfile variables from nipy:

from numpy.testing import assert_array_equal, assert_almost_equal
from nipy.testing import funcfile, anatfile

Please name your test file with the test_ prefix followed by the module name it tests. This makes it obvious for other developers which modules are tested, where to add tests, etc… An example test file and module pairing:


All tests go in a tests subdirectory for each package.

Temporary files

If you need to create a temporary file during your testing, you could use one of these three methods, in order of convenience:

  1. StringIO

    StringIO creates an in memory file-like object. The memory buffer is freed when the file is closed. This is the preferred method for temporary files in tests.

  2. in_tmp_path Pytest fixture.

    This is a convenient way of putting you into a temporary directory so you can save anything you like into the current directory, and feel fine about it after. Like this:

    def test_func(in_tmp_path):
        f = open('myfile', 'wt')
        f.write('Anything at all')

    One thing to be careful of is that you may need to delete objects holding onto the file before you exit the enclosing function, otherwise Windows may refuse to delete the file.

  3. tempfile.mkstemp

    This will create a temporary file which can be used during testing. There are parameters for specifying the filename prefix and suffix.


    The tempfile module includes a convenience function NamedTemporaryFile which deletes the file automatically when it is closed. However, whether the files can be opened a second time varies across platforms and there are problems using this function on Windows.


    from tempfile import mkstemp
        fd, name = mkstemp(suffix='.nii.gz')
        tmpfile = open(name)
        save_image(fake_image, tmpfile.name)
        os.unlink(name)  # This deletes the temp file

Please don’t just create a file in the test directory and then remove it with a call to os.remove. For various reasons, sometimes os.remove doesn’t get called and temp files get left around.

Many tests in one test function

To keep tests organized, it’s best to have one test function correspond to one class method or module-level function. Often though, you need many individual tests to thoroughly cover the method/function. For convenience, we often write many tests in a single test function. This has the disadvantage that if one test fails, the testing framework will not run any of the subsequent tests in the same function. This isn’t a big problem in practice, because we run the tests so often (Automated testing) that we can quickly pick up and fix the failures.

For axample, this test function executes four tests:

def test_index():
    cs = CoordinateSystem('ijk')
    assert_equal(cs.index('i'), 0)
    assert_equal(cs.index('j'), 1)
    assert_equal(cs.index('k'), 2)
    assert_raises(ValueError, cs.index, 'x')

Suppress warnings on test output

In order to reduce noise when running the tests, consider suppressing warnings in your test modules. See the pytest documentation for various ways to do that, or search our code for pytest.mark for examples.

Running tests

Running the full test suite

To run nipy’s tests, you will need to pytest installed. Then:

pytest nipy

You can run the full tests, including doctests with:

pip install pytest-doctestplus

pytest --doctest-plus nipy

Install optional data packages for testing

For our tests, we have collected a set of fmri imaging data which are required for the tests to run. To do this, download the latest example data and template package files from NIPY data packages. See Optional data packages.

Running individual tests

You can also run the tests from the command line with a variety of options.

To test an individual module:

pytest nipy/core/image/tests/test_image.py

To test an individual function:

pytest nipy/core/image/tests/test_image.py::test_maxmin_values

To test a class:

pytest nipy/algorithms/clustering/tests/test_clustering.py::TestClustering

To test a class method:

pytest nipy/algorithms/clustering/tests/test_clustering.py::TestClustering.testkmeans1

Verbose mode (-v option) will print out the function names as they are executed. Standard output is normally suppressed by Pytest, to see any print statements you must include the -s option. In order to get a “full verbose” output, call Pytest like this:

pytest -sv nipy

To include doctests in the tests:

pytest -sv --docest-plus nipy

Coverage Testing

Coverage testing is a technique used to see how much of the code is exercised by the unit tests. It is important to remember that a high level of coverage is a necessary but not sufficient condition for having effective tests. Coverage testing can be useful for identifying whole functions or classes which are not tested, or for finding certain conditions which are never tested.

This is an excellent task for pytest - the automated test runner we are using. Pytest can run the python coverage tester. First make sure you have the coverage test plugin installed on your system:

pip install pytest-cov

Run Pytest with coverage testing arguments:

pytest --cov=nipy --doctest-plus nipy

The coverage report will cover any python source module imported after the start of the test. This can be noisy and difficult to focus on the specific module for which you are writing tests. For instance, the default report also includes coverage of most of numpy. To focus the coverage report, you can provide Pytest with the specific package you would like output from using the --cov=nipy (the option above).