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# Copyright 2014-2016 Marco Galardini. All rights reserved.
# Adapted from test_Mymodule.py by Jeff Chang
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Tests for the Bio.phenotype module's fitting functionality."""
try:
import numpy
del numpy
except ImportError:
from Bio import MissingExternalDependencyError
raise MissingExternalDependencyError(
"Install NumPy if you want to use Bio.phenotype."
) from None
try:
import scipy
del scipy
from scipy.optimize import OptimizeWarning
except ImportError:
from Bio import MissingExternalDependencyError
raise MissingExternalDependencyError(
"Install SciPy if you want to use Bio.phenotype fit functionality."
) from None
import json
import unittest
from Bio import BiopythonExperimentalWarning
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore", BiopythonExperimentalWarning)
from Bio import phenotype
# Example plate files
JSON_PLATE = "phenotype/Plate.json"
class TestPhenoMicro(unittest.TestCase):
"""Tests for phenotype module."""
def test_WellRecord(self):
"""Test basic functionalities of WellRecord objects."""
with open(JSON_PLATE) as handle:
p = json.load(handle)
times = p["measurements"]["Hour"]
w = phenotype.phen_micro.WellRecord(
"A10",
signals={times[i]: p["measurements"]["A10"][i] for i in range(len(times))},
)
with warnings.catch_warnings():
warnings.simplefilter("ignore", OptimizeWarning)
w.fit()
self.assertAlmostEqual(w.area, 20879.5)
self.assertEqual(w.model, "gompertz")
self.assertAlmostEqual(w.lag, 6.0425868725090357, places=5)
self.assertAlmostEqual(w.plateau, 188.51404344898586, places=4)
self.assertAlmostEqual(w.slope, 48.190618284831132, places=4)
self.assertAlmostEqual(w.v, 0.10000000000000001, places=5)
self.assertAlmostEqual(w.y0, 45.879770069807989, places=5)
self.assertEqual(w.max, 313.0)
self.assertEqual(w.min, 29.0)
self.assertEqual(w.average_height, 217.82552083333334)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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