Quick tutorial

You can read the SciUnit Basic before starting this tutorial for understanding the components of SciUnit.

Creating a Model and a Test instance from scratch

Let’s create a model that can output a constant number.

Importing sciunit at the beginning.

import sciunit

Creating a subclass of SciUnit Capability class. The Capability subclass contains one or more unimplemented methods. It can be included in a Test class as required_capabilities, and only the models which implements the methods in the Capability subclass can be tested by the Test instance.

Here we define a simple capability through which a model can return a single number.

class ProducesNumCapability(sciunit.Capability):
    """An example capability for producing some generic number."""

    def produce_number(self):
        """The implementation of this method should return a number."""
        raise NotImplementedError("Must implement produce_number.")

And creating a subclass of SciUnit Model. A model we want to test is always an instance (with specific model arguments) of a more generic model class.

class ConstModel(sciunit.Model, ProducesNumCapability):
    """A model that always produces a constant number as output."""

    def __init__(self, constant, name=None):
        self.constant = constant
        super(ConstModel, self).__init__(name=name, constant=constant)

    def produce_number(self):
        return self.constant

Now we have a model and a capability. Let’s create a Test class and include the capability in a subclass of Test. Note that a SciUnit test class must contain:

  1. the capabilities a model requires to take the test.
  2. the type of score that it will return.
  3. an implementation of generate_prediction, which will use the model’s capabilities to get some values out of the model.
  4. an implementaiton of compute_score, to use the provided observation and the generated prediction to compute a sciunit Score.
class EqualsTest(sciunit.Test):
    """Tests if the model predicts
    the same number as the observation."""

    # The one capability required for a model to take this test.
    required_capabilities = (ProducesNumCapability,)

    # Set the type of score returned by judge method in a Test instance
    score_type = sciunit.scores.BooleanScore

    def generate_prediction(self, model):
        return model.produce_number()

    def compute_score(self, observation, prediction):
        score = self.score_type(observation['value'] == prediction) # Returns a BooleanScore.
        score.description = 'Passing score if the prediction equals the observation'
        return score

After defining the subclass of SciUnit Model, we can create an instance of the model that always produce number 37.

const_model_37 = ConstModel(37, name="Constant Model 37")

Suppose we have a observation value, and we want to test if the value match the number predicted (produced) by the model instance defined above.

observation = {'value':37}
equals_37_test = EqualsTest(observation=observation, name='Equal 37 Test')

Simply call the judge method of the Test instance with the model instance as an argument.

score = equals_37_test.judge(model=const_model_37)

Now we got the score instance.

>>> print(score)
Pass

Printing out the score and we can see that the test was passed. We can also summarize the score in its entirety, printing information about the associated model and test.

>>> score.summarize()
=== Model Constant Model 37 achieved score Pass on test 'Equal 37 Test'. ===

How was that score computed again?

>>> score.describe()
Passing score if the prediction equals the observation

Next, let’s create some other test instances that suppose to fail.

observation = {'value':36}
equals_36_test = EqualsTest(observation, name='Equal 36 Test')
observation = {'value':35}
equals_35_test = EqualsTest(observation, name='Equal 35 Test')
score1 = equals_36_test.judge(model=const_model_37)
score2 = equals_36_test.judge(model=const_model_37)

>>> print(score1)
Fail

>>> print(score2)
Fail

We can also put these test instances together in a TestSuite instance. The TestSuite also contains a judge method that can run every Test instance’s judge methods.

tests = [equals_35_test, equals_36_test, equals_37_test]
equals_suite = sciunit.TestSuite(tests=tests, name="Equals test suite")
score_matrix = equals_suite.judge(const_model_37)

>>> print(score_matrix)
                  Equal 35 Test Equal 36 Test Equal 37 Test
Constant Model 37          Fail          Fail          Pass

In the result, we can see a 1*3 score matrix that shows the results of each test.

We can create more models and subject those to the test suite to get a more extensive score matrix.

const_model_36 = ConstModel(36, name='Constant Model 36')
const_model_35 = ConstModel(35, name='Constant Model 35')
score_matrix = equals_suite.judge([const_model_36, const_model_35, const_model_37])

>>> print(score_matrix)
                  Equal 35 Test Equal 36 Test Equal 37 Test
Constant Model 37          Fail          Fail          Pass
Constant Model 36          Fail          Pass          Fail
Constant Model 35          Pass          Fail          Fail

Now, we can see the result is a 3*3 matrix, and each model pass the corresponding test.

We can also examine the results only for one of the tests in the suite.

>>> print(score_matrix[equals_35_test])
Constant Model 37    Fail
Constant Model 36    Fail
Constant Model 35    Pass
Name: Equal 35 Test, dtype: object

Or examine the results only for one of the models.

>>> print(score_matrix[const_model_35])
Equal 35 Test    Pass
Equal 36 Test    Fail
Equal 37 Test    Fail
Name: Constant Model 35, dtype: object

In the next section we’ll see how to build slightly more sophisticated tests using objects built-in to SciUnit.

Testing with help from the SciUnit standard library

The ConstModel class we defined in the last section was included in SciUnit package as an example, and we can just import it.

import sciunit

from sciunit.models.examples import ConstModel
from sciunit.capabilities import ProducesNumber

from sciunit.scores import ZScore # One of many SciUnit score types.
from sciunit.errors import ObservationError # An exception class raised when a test

Let’s create the instance of ConstModel.

const_model_37 = ConstModel(37, name="Constant Model 37")

And a new subclass of SciUnit Test class.

class MeanTest(sciunit.Test):
    """Tests if the model predicts the same number as the observation."""

    # The one capability required for a model to take this test.
    required_capabilities = (ProducesNumber,)

    # This test's 'judge' method will return a BooleanScore.
    score_type = ZScore

    def validate_observation(self, observation):
        if type(observation) is not dict:
            raise ObservationError("Observation must be a python dictionary")
        if 'mean' not in observation:
            raise ObservationError("Observation must contain a 'mean' entry")

    def generate_prediction(self, model):
        return model.produce_number()

    def compute_score(self, observation, prediction):

        # Compute and return a ZScore object.
        score = ZScore.compute(observation,prediction)

        score.description = ("A z-score corresponding to the normalized location of the"
                            "observation relative to the predicted distribution.")
        return score

Compared with the sruff in last section, we’ve done two new things here:

  • The optional validate_observation method checks the observation to make sure that it is the right type, that it has the right attributes, etc. This can be used to ensures that the observation is exactly as the other core test methods expect. If we don’t provide the right kind of observation:
  • Instead of returning a BooleanScore, encoding a True/False value, we return a ZScore encoding a more quantitative summary of the relationship between the observation and the prediction.

Let’s create a observation and attach it to the MeanTest instance.

observation = {'mean':37.8, 'std':2.1}
mean_37_test = MeanTest(observation, name='Equal 37 Test')
score = mean_37_test.judge(const_model_37)

And let’s see what’s the result:

>>> score.summarize()
=== Model Constant Model 37 achieved score Z = -0.38 on test 'Equal 37 Test'. ===

>>> score.describe()
A z-score corresponding to the normalized location of theobservation relative to the predicted distribution.

Example of RunnableModel and Backend

Beside the usual model in previous sections, let’s create a model that run a Backend instance to simulate and obtain results.

Firstly, import necessary components from SciUnit package.

import sciunit, random
from sciunit import Test
from sciunit.capabilities import Runnable
from sciunit.scores import BooleanScore
from sciunit.models import RunnableModel
from sciunit.models.backends import register_backends, Backend

Let’s define subclasses of SciUnit Backend, Test, and Model.

Note that:

  1. A SciUnit Backend subclass should implement _backend_run method.
  2. A SciUnit Backend subclass should implement run method.
class RandomNumBackend(Backend):
    '''generate a random integer between min and max'''

    def set_run_params(self, **run_params):

        # get min from run_params, if not exist, then 0.
        self.min = run_params.get('min', 0)

        # get max from run_params, if not exist, then self.min + 100.
        self.max = run_params.get('max', self.min + 100)

    def _backend_run(self):
        # generate and return random integer between min and max.
        return random.randint(self.min, self.max)

class RandomNumModel(RunnableModel):
    """A model that always produces a constant number as output."""

    def run(self):
        self.results = self._backend.backend_run()


class RangeTest(Test):
    """Tests if the model predicts the same number as the observation."""

    # Default Runnable Capability for RunnableModel
    required_capabilities = (Runnable,)

    # This test's 'judge' method will return a BooleanScore.
    score_type = BooleanScore

    def generate_prediction(self, model):
        model.run()
        return model.results

    def compute_score(self, observation, prediction):
        score = BooleanScore(
            observation['min'] <= prediction and observation['max'] >= prediction
        )
        return score

Let’s define the model instance named model 1.

model = RandomNumModel("model 1")

We must register any backend isntance in order to use it in model instances.

set_backend and set_run_params methods can help us to set the run-parameters in the model and its backend.

register_backends({"Random Number": RandomNumBackend})
model.set_backend("Random Number")
model.set_run_params(min=1, max=10)

Next, create an observation that requires the generated random integer between 1 and 10 and a test instance that use the observation and against the model

observation = {'min': 1, 'max': 10}
oneToTenTest = RangeTest(observation, "test 1")
score = oneToTenTest.judge(model)

print the score, and we can see the result.

>>> print(score)
Pass

Real Example

For real example of using SciUnit, you can read Chapter 5 and 6 of the Jupyter notebook tutorial.

Tutorial Chapter 5

Tutorial Chapter 6