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Issue 1006: minor fixes and several new unit tests for PSA module #1508

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merged 13 commits into from
Dec 11, 2017
Merged

Issue 1006: minor fixes and several new unit tests for PSA module #1508

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b48275e
Changed test name(s) from test_asymmetric_weight() to test_asymmetric…
sseyler Jul 17, 2017
46448c9
New names for (w)avg_hausdorff tests + reverting back to old (same) t…
sseyler Jul 17, 2017
6bfbf1c
Added two tests for Hausdorff neighbors--only the distances
sseyler Jul 17, 2017
3e3ac06
New test for Hausdorff pair frames in pairs analysis; pairs analysis …
sseyler Jul 18, 2017
2ee4e65
Added fix, change, author sseyler to CHANGELOG; updated run_pairs_ana…
sseyler Jul 18, 2017
6b6fde1
Changed to old-style division in dist_mat_to_vec to ensure integer ou…
sseyler Jul 18, 2017
86273c6
Small fixes/changes:
sseyler Jul 19, 2017
7a5b9a7
Added docstring in PSAnalysis.cluster for dist_mat kwarg
sseyler Jul 19, 2017
3f87c79
get_path_metric_func now raises KeyError with error string; it's unit…
sseyler Jul 31, 2017
37881f4
Fixed up type checking in metric filename
richardjgowers Dec 9, 2017
251df4d
Updated error strings in analysis.psa
richardjgowers Dec 9, 2017
b7af4d7
Updated docstrings to numpy style in analysis.psa
richardjgowers Dec 9, 2017
3c75a00
Merge branch 'develop' into issue-1006-psatests
richardjgowers Dec 10, 2017
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9 changes: 3 additions & 6 deletions package/MDAnalysis/analysis/psa.py
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Original file line number Diff line number Diff line change
Expand Up @@ -252,12 +252,9 @@ def get_path_metric_func(name):
try:
return path_metrics[name]
except KeyError as key:
print("Path metric {0} not found. Valid selections: ".format(key))
for name in path_metrics.keys(): print(" \"{0}\"".format(name))
# except KeyError as key:
# err_str = "Path metric {0} not found. Valid selections: ".format(key)
# err_str += " ".join(["\"{0}\"".format(name) for name in path_metrics.keys()])
# raise KeyError(err_str)
err_str = "Path metric {0} not found. Valid selections: ".format(key)
err_str += " ".join(["\"{0}\"".format(name) for name in path_metrics.keys()])
raise KeyError(err_str)
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You can use multiline strings

raise KeyError("Path metric {} not found. Valid Selections: {}".format(
                           key, ' '.join(['"{}"'.format(name) for name in path_metrics.keys()]))



def sqnorm(v, axis=None):
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6 changes: 1 addition & 5 deletions testsuite/MDAnalysisTests/analysis/test_psa.py
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Expand Up @@ -171,17 +171,13 @@ class TestPSAExceptions(TestCase):
def test_get_path_metric_func_bad_key(self):
'''Test that KeyError is caught by
get_path_metric_func().'''

try:
with self.assertRaises(KeyError):
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with pytest.raises(KeyError):
    PSA.get_path_metric_func('foobar')

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Yeah, I put my changes on hold since, once I rebased properly, realized everything is now pytest-specific. Hoping to finish this PR within the week.

PSA.get_path_metric_func('123456')
except KeyError:
self.fail('KeyError should be caught')

def test_get_coord_axes_bad_dims(self):
"""Test that ValueError is raised when
numpy array with incorrect dimensions
is fed to get_coord_axes()."""

with self.assertRaises(ValueError):
PSA.get_coord_axes(np.zeros((5,5,5,5)))

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