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Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597) #1183

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merged 15 commits into from
Feb 4, 2017
Merged

Added exception and unittest for dist_mat_to_vec of analysis/psa.py (Part of #597) #1183

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9a49244
Added exception and unittest for function dist_mat_to_vec of analysis…
vedantrathore Jan 22, 2017
ceb1618
Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in…
vedantrathore Jan 22, 2017
1b04205
Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in…
vedantrathore Jan 23, 2017
3af71be
Added exception and unittest for dist_mat_to_vec of analysis/psa.py (…
vedantrathore Jan 23, 2017
bf8765b
Added exception and unittest for dist_mat_to_vec of analysis/psa.py (…
vedantrathore Jan 23, 2017
cda6c57
Added exception and unittest for dist_mat_to_vec of analysis/psa.py (…
vedantrathore Jan 23, 2017
dcc6168
Adds validation for dist_mat_to_vec function inputs
vedantrathore Jan 28, 2017
cecc350
Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in…
vedantrathore Jan 28, 2017
3943ddc
Added exception and unittest for dist_mat_to_vec of analysis/psa.py (…
vedantrathore Jan 31, 2017
b706493
Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in…
vedantrathore Jan 31, 2017
f12458e
Added exception and unittest for dist_mat_to_vec of analysis/psa.py (…
vedantrathore Jan 31, 2017
ece534a
Added exception and unittest for dist_mat_to_vec of analysis/psa.py (…
vedantrathore Feb 2, 2017
36acf58
Added exception and unittest for dist_mat_to_vec of analysis/psa.py (…
vedantrathore Feb 3, 2017
376b0b1
Added exception and unittest for dist_mat_to_vec of analysis/psa.py (…
vedantrathore Feb 3, 2017
bd94007
Added exception and unittest for dist_mat_to_vec of analysis/psa.py (…
vedantrathore Feb 3, 2017
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17 changes: 9 additions & 8 deletions testsuite/MDAnalysisTests/analysis/test_psa.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@

from numpy.testing import (TestCase, dec, assert_array_less,
assert_array_almost_equal, assert_,
assert_almost_equal)
assert_almost_equal, assert_equal)
import numpy as np

from MDAnalysisTests.datafiles import PSF, DCD, DCD2
Expand Down Expand Up @@ -94,15 +94,14 @@ def test_dendrogram_produced(self):
assert_(type(self.plot_data[1]) is dict, err_msg)

def test_dist_mat_to_vec_i_less_j(self):
"""Test that distance is correct if i < j"""
"""Test the index of corresponding distance vector is correct if i < j"""
err_msg = "dist_mat_to_vec function returning wrong values"
assert_(PSA.dist_mat_to_vec(5, 3, 4) is 9, err_msg)
assert_equal(PSA.dist_mat_to_vec(5, 3, 4), 9, err_msg)

def test_dist_mat_to_vec_i_greater_j(self):
"""Test that distance is correct if i < j"""
"""Test the index of corresponding distance vector is correct if i > j"""
err_msg = "dist_mat_to_vec function returning wrong values"
assert_(PSA.dist_mat_to_vec(5, 4, 3) is 9, err_msg)

assert_equal(PSA.dist_mat_to_vec(5, 4, 3), 9, err_msg)

class TestPSAExceptions(TestCase):
'''Tests for exceptions that should be raised
Expand All @@ -126,10 +125,12 @@ def test_get_coord_axes_bad_dims(self):
PSA.get_coord_axes(np.zeros((5,5,5,5)))

def test_dist_mat_to_vec_func_out_of_bounds(self):
"""Test that ValueError is raised when i or j is
"""Test that ValueError is raised when i or j or both are
out of bounds of N"""

with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, 6, 4)
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Have each of these line in a different with block, or in a different test. The way it is now makes it difficult to now which one failed if there is a failure.

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Add a comment to tell what index is out of bonds. It is obvious when you are in the context of writing the test, but it makes you loose quite a lot of time when you have to figure it out latter on.

PSA.dist_mat_to_vec(5, 4, 6)
PSA.dist_mat_to_vec(5, 6, 6)
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Please, add cases with only i out of bonds, and with only j out of bonds.


def test_dist_mat_to_vec_func_bad_integers(self):
Expand All @@ -138,7 +139,7 @@ def test_dist_mat_to_vec_func_bad_integers(self):

with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, '6', '7')
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What if i, or j is a float?


PSA.dist_mat_to_vec(5, float(6), 7)
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Same as above: separate the assertions.


class _BaseHausdorffDistance(TestCase):
'''Base Class setup and unit tests
Expand Down