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Improved documentation of custom tests

Open sulheim opened this issue 5 years ago • 0 comments

Problem description

It is not obvious from the current documentation what the keys "data" and "metric" are used for and what the difference is in the current documentation.

I tried to add custom tests to the memote report, but they were displayed as "Error" without any obvious reason or error-messages.

This was discussed on GItter: image

I think it would be good ta add a couple of simple examples to the documentation. Maybe also a couple of lines explaining hot to debug any issues etc.

Example

Maybe this can be used?

@annotate(title="Test that the model can produce germicidinC", format_type="number")
def test_germicidinC_production(model):
    """
    Test that the model can produce germicidin C, and report how much
    """
    with model:
        model.reactions.DM_germicidinC_c.objective_coefficient = 1
        model.reactions.BIOMASS_SCO.objective_coefficient = 0
        solution = model.optimize()
    ann = test_germicidinC_production.annotation
    ann["data"] = solution.objective_value
    ann["metric"] = int(solution.objective_value > 1e-3)
    ann["message"] = "The production of germicidinC is {0}".format(solution.objective_value)
    assert solution.objective_value > 1e-3, ann["message"]

sulheim avatar Nov 08 '18 14:11 sulheim