Testing

Brian uses the pytest package for its testing framework.

Running the test suite

The pytest tool automatically finds tests in the code. However, to deal with the different code generation targets, and correctly set up tests for standalone mode, it is recommended to use Brian’s builtin test function that calls pytest appropriately:

>>> import brian2
>>> brian2.test()  

By default, this runs the test suite for all available (runtime) code generation targets. If you only want to test a specific target, provide it as an argument:

>>> brian2.test('numpy')  

If you want to test several targets, use a list of targets:

>>> brian2.test(['cython'])  

In addition to the tests specific to a code generation target, the test suite will also run a set of independent tests (e.g. parsing of equations, unit system, utility functions, etc.). To exclude these tests, set the test_codegen_independent argument to False. Not all available tests are run by default, tests that take a long time are excluded. To include these, set long_tests to True.

To run the C++ standalone tests, you have to set the test_standalone argument to the name of a standalone device. If you provide an empty argument for the runtime code generation targets, you will only run the standalone tests:

>>> brian2.test([], test_standalone='cpp_standalone')  

Writing tests

Generally speaking, we aim for a 100% code coverage by the test suite. Less coverage means that some code paths are never executed so there’s no way of knowing whether a code change broke something in that path.

Unit tests

The most basic tests are unit tests, tests that test one kind of functionality or feature. To write a new unit test, add a function called test_... to one of the test_... files in the brian2.tests package. Test files should roughly correspond to packages, test functions should roughly correspond to tests for one function/method/feature. In the test functions, use assertions that will raise an AssertionError when they are violated, e.g.:

G = NeuronGroup(42, model='dv/dt = -v / (10*ms) : 1')
assert len(G) == 42

When comparing arrays, use the array_equal function from numpy.testing.utils which takes care of comparing types, shapes and content and gives a nicer error message in case the assertion fails. Never make tests depend on external factors like random numbers – tests should always give the same result when run on the same codebase. You should not only test the expected outcome for the correct use of functions and classes but also that errors are raised when expected. For that you can use pytest’s raises function with which you can define a block of code that should raise an exception of a certain type:

with pytest.raises(DimensionMismatchError):
    3*volt + 5*second

You can also check whether expected warnings are raised, see the documentation of the logging mechanism for details

For simple functions, doctests (see below) are a great alternative to writing classical unit tests.

By default, all tests are executed for all selected runtime code generation targets (see Running the test suite above). This is not useful for all tests, some basic tests that for example test equation syntax or the use of physical units do not depend on code generation and need therefore not to be repeated. To execute such tests only once, they can be annotated with a codegen_independent marker, using the mark decorator:

import pytest
from brian2 import NeuronGroup

@pytest.mark.codegen_independent
def test_simple():
    # Test that the length of a NeuronGroup is correct
    group = NeuronGroup(5, '')
    assert len(group) == 5

Tests that are not “codegen-independent” are by default only executed for the runtimes device, i.e. not for the cpp_standalone device, for example. However, many of those tests follow a common pattern that is compatible with standalone devices as well: they set up a network, run it, and check the state of the network afterwards. Such tests can be marked as standalone_compatible, using the mark decorator in the same way as for codegen_independent tests.:

import pytest
from numpy.testing.utils import assert_equal
from brian2 import *

@pytest.mark.standalone_compatible
def test_simple_run():
    # Check that parameter values of a neuron don't change after a run
    group = NeuronGroup(5, 'v : volt')
    group.v = 'i*mV'
    run(1*ms)
    assert_equal(group.v[:], np.arange(5)*mV)

Tests that have more than a single run function but are otherwise compatible with standalone mode (e.g. they don’t need access to the number of synapses or results of the simulation before the end of the simulation), can be marked as standalone_compatible and multiple_runs. They then have to use an explicit device.build(...) call of the form shown below:

import pytest
from numpy.testing.utils import assert_equal
from brian2 import *

@pytest.mark.standalone_compatible
@pytest.mark.multiple_runs
def test_multiple_runs():
    # Check that multiple runs advance the clock as expected
    group = NeuronGroup(5, 'v : volt')
    mon = StateMonitor(group, 'v', record=True)
    run(1 * ms)
    run(1 * ms)
    device.build(direct_call=False, **device.build_options)
    assert_equal(defaultclock.t, 2 * ms)
    assert_equal(mon.t[0], 0 * ms)
    assert_equal(mon.t[-1], 2 * ms - defaultclock.dt)

Tests can also be written specifically for a standalone device (they then have to include the set_device call and possibly the build call explicitly). In this case tests have to be annotated with the name of the device (e.g. 'cpp_standalone') and with 'standalone_only' to exclude this test from the runtime tests. Such code would look like this for a single run() call, i.e. using the automatic “build on run” feature:

import pytest
from brian2 import *

@pytest.mark.cpp_standalone
@pytest.mark.standalone_only
def test_cpp_standalone():
    set_device('cpp_standalone', directory=None)
    # set up simulation
    # run simulation
    run(...)
    # check simulation results

If the code uses more than one run() statement, it needs an explicit build call:

import pytest
from brian2 import *

@pytest.mark.cpp_standalone
@pytest.mark.standalone_only
def test_cpp_standalone():
    set_device('cpp_standalone', build_on_run=False)
    # set up simulation
    # run simulation
    run(...)
    # do something
    # run again
    run(...)
    device.build(directory=None)
    # check simulation results

Summary

`@pytest.mark` marker	Executed for devices	explicit use of `device`
`codegen_independent`	independent of devices	none
none	Runtime targets	none
`standalone_compatible`	Runtime and standalone	none
`standalone_compatible, multiple_runs`	Runtime and standalone	`device.build(direct_call=False, **device.build_options)`
`cpp_standalone, standalone_only`	C++ standalone device	`set_device('cpp_standalone')` `...` `device.build(directory=None)`
`my_device, standalone_only`	“My device”	`set_device('my_device')` `...` `device.build(directory=None)`

Doctests

Doctests are executable documentation. In the Examples block of a class or function documentation, simply write code copied from an interactive Python session (to do this from ipython, use %doctestmode), e.g.:

>>> from brian2.utils.stringtools import word_substitute
>>> expr = 'a*_b+c5+8+f(A)'
>>> print(word_substitute(expr, {'a':'banana', 'f':'func'}))
banana*_b+c5+8+func(A)

During testing, the actual output will be compared to the expected output and an error will be raised if they don’t match. Note that this comparison is strict, e.g. trailing whitespace is not ignored. There are various ways of working around some problems that arise because of this expected exactness (e.g. the stacktrace of a raised exception will never be identical because it contains file names), see the doctest documentation for details.

Doctests can (and should) not only be used in docstrings, but also in the hand-written documentation, making sure that the examples actually work. To turn a code example into a doc test, use the .. doctest:: directive, see Equations for examples written as doctests. For all doctests, everything that is available after from brian2 import * can be used directly. For everything else, add import statements to the doctest code or – if you do not want the import statements to appear in the document – add them in a .. testsetup:: block. See the documentation for Sphinx’s doctest extension for more details.

Doctests are a great way of testing things as they not only make sure that the code does what it is supposed to do but also that the documentation is up to date!

Correctness tests

[These do not exist yet for brian2]. Unit tests test a specific function or feature in isolation. In addition, we want to have tests where a complex piece of code (e.g. a complete simulation) is tested. Even if it is sometimes impossible to really check whether the result is correct (e.g. in the case of the spiking activity of a complex network), a useful check is also whether the result is consistent. For example, the spiking activity should be the same when using code generation for Python or C++. Or, a network could be pickled before running and then the result of the run could be compared to a second run that starts from the unpickled network.