[Review Needed]Pytest Style TestEncore #1609
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@kain88-de @jbarnoud @richardjgowers Review please. |
| min_bound = 1E5 | ||
| self.assertGreater(result_value, min_bound, | ||
| msg="Unexpected value for Harmonic Ensemble Similarity: {0:f}. Expected {1:f}.".format(result_value, min_bound)) | ||
| assert result_value >= min_bound, "Unexpected value for Harmonic " \ |
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this is equivalent with self.assertGreaterEqual and not a pure greater cheak
| upper_bound = 0.6 | ||
| self.assertLess(result_value, upper_bound, | ||
| msg="Unexpected value for Dim. reduction Ensemble Similarity: {0:f}. Expected {1:f}.".format(result_value, upper_bound)) | ||
| assert result_value <= upper_bound, "Unexpected value for Dim. " \ |
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this is not a self.assertLess remove the equal sign.
| np.copy(cls.ens2_template.trajectory.timeseries(format='fac')[::5, :, :]), | ||
| assert average <= average_upper_bound, "Unexpected average value for " \ | ||
| "bootstrapped samples in Dim. reduction Ensemble similarity" | ||
| assert stdev <= stdev_upper_bound, "Unexpected standard deviation for" \ |
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see comment above for both asserts
| distances += YY | ||
| np.maximum(distances, 0, out=distances) | ||
| distances.flat[::distances.shape[0] + 1] = 0.0 | ||
| dimension = len(distances) |
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these should be in a fixture since arrays are not necessarily constant.
| template = mda.Universe( | ||
| template.filename, | ||
| np.copy(template.trajectory.timeseries(format='fac')[::5, :, :]), | ||
| format=mda.coordinates.memory.MemoryReader) |
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I think transfer_to_memory has a step argument now that you can use instead of this trick.
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Why do you still not use the step argument of transfer_to_memory here?
| distances += XX | ||
| distances += YY | ||
| np.maximum(distances, 0, out=distances) | ||
| distances.flat[::distances.shape[0] + 1] = 0.0 |
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all this setup code should be in a fixture for distance_matrix. It's he only one that uses this. I also don't see the use for the fixture of dimensions
utkbansal
changed the title
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@kain88-de I've used |
| template = mda.Universe( | ||
| template.filename, | ||
| np.copy(template.trajectory.timeseries(format='fac')[::5, :, :]), | ||
| format=mda.coordinates.memory.MemoryReader) |
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Why do you still not use the step argument of transfer_to_memory here?
| template.transfer_to_memory(step=5) | ||
| template = mda.Universe( | ||
| template.filename, | ||
| np.copy(template.trajectory.timeseries(format='fac')), |
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Do you know what this statement is doing? After using transfer to memory this shouldn't be necessary anymore.
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I don't think I have a real understanding of that statement.
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