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Pytest Style analysis/test_base.py #1547

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Jul 29, 2017
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Pytest Style analysis/test_base.py #1547

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Pytest Style analysis/test_base.py
utkbansal Jul 23, 2017
cc6b94a
Drop the class
utkbansal Jul 26, 2017
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110 changes: 53 additions & 57 deletions testsuite/MDAnalysisTests/analysis/test_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,14 +20,13 @@
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
from __future__ import division, absolute_import

import pytest
from six.moves import range
from unittest import TestCase

import numpy as np

from numpy.testing import (
assert_, dec, raises, assert_raises, assert_equal, assert_array_equal
)
from numpy.testing import assert_equal, assert_array_equal

import MDAnalysis as mda
from MDAnalysis.analysis import base
Expand Down Expand Up @@ -61,51 +60,49 @@ def _single_frame(self):
pass


class TestAnalysisBase(TestCase):
def setUp(self):
# has 98 frames
self.u = mda.Universe(PSF, DCD)

def tearDown(self):
del self.u
class TestAnalysisBase(object):
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no need to have this as a class actually

@staticmethod
@pytest.fixture()
def u():
return mda.Universe(PSF, DCD)

def test_default(self):
an = FrameAnalysis(self.u.trajectory).run()
assert_equal(an.n_frames, len(self.u.trajectory))
assert_equal(an.frames, list(range(len(self.u.trajectory))))
def test_default(self, u):
an = FrameAnalysis(u.trajectory).run()
assert an.n_frames == len(u.trajectory)
assert_equal(an.frames, list(range(len(u.trajectory))))
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assert_array_equal

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please also change for similar cases in this file

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See discussion on #1444.

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@kain88-de my understanding is that assert_equal is preferred over assert_array_equal as discussed in 1444?

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@utkbansal It is my understanding too.


def test_start(self):
an = FrameAnalysis(self.u.trajectory, start=20).run()
assert_equal(an.n_frames, len(self.u.trajectory) - 20)
assert_equal(an.frames, list(range(20, len(self.u.trajectory))))
def test_start(self, u):
an = FrameAnalysis(u.trajectory, start=20).run()
assert an.n_frames == len(u.trajectory) - 20
assert_equal(an.frames, list(range(20, len(u.trajectory))))

def test_stop(self):
an = FrameAnalysis(self.u.trajectory, stop=20).run()
assert_equal(an.n_frames, 20)
def test_stop(self, u):
an = FrameAnalysis(u.trajectory, stop=20).run()
assert an.n_frames == 20
assert_equal(an.frames, list(range(20)))

def test_step(self):
an = FrameAnalysis(self.u.trajectory, step=20).run()
assert_equal(an.n_frames, 5)
def test_step(self, u):
an = FrameAnalysis(u.trajectory, step=20).run()
assert an.n_frames == 5
assert_equal(an.frames, list(range(98))[::20])

def test_verbose(self):
a = FrameAnalysis(self.u.trajectory, verbose=True)
assert_(a._verbose)
assert_(not a._quiet)
def test_verbose(self, u):
a = FrameAnalysis(u.trajectory, verbose=True)
assert a._verbose
assert not a._quiet

@raises(NotImplementedError)
def test_incomplete_defined_analysis(self):
IncompleteAnalysis(self.u.trajectory).run()
def test_incomplete_defined_analysis(self, u):
with pytest.raises(NotImplementedError):
IncompleteAnalysis(u.trajectory).run()

def test_old_api(self):
OldAPIAnalysis(self.u.trajectory).run()
def test_old_api(self, u):
OldAPIAnalysis(u.trajectory).run()

def test_start_stop_step_conversion(self):
an = FrameAnalysis(self.u.trajectory)
assert_equal(an.start, 0)
assert_equal(an.stop, self.u.trajectory.n_frames)
assert_equal(an.step, 1)
def test_start_stop_step_conversion(self, u):
an = FrameAnalysis(u.trajectory)
assert an.start == 0
assert an.stop == u.trajectory.n_frames
assert an.step == 1


def test_filter_baseanalysis_kwargs():
Expand All @@ -117,19 +114,20 @@ def good_f(mobile, ref):

kwargs = {'step': 3, 'foo': None}

assert_raises(ValueError, base._filter_baseanalysis_kwargs, bad_f, kwargs)
with pytest.raises(ValueError):
base._filter_baseanalysis_kwargs(bad_f, kwargs)

base_kwargs, kwargs = base._filter_baseanalysis_kwargs(good_f, kwargs)

assert_equal(1, len(kwargs))
assert_equal(kwargs['foo'], None)
assert 1 == len(kwargs)
assert kwargs['foo'] == None

assert_equal(5, len(base_kwargs))
assert_equal(base_kwargs['start'], None)
assert_equal(base_kwargs['step'], 3)
assert_equal(base_kwargs['stop'], None)
assert_equal(base_kwargs['quiet'], None)
assert_equal(base_kwargs['verbose'], None)
assert 5 == len(base_kwargs)
assert base_kwargs['start'] is None
assert base_kwargs['step'] == 3
assert base_kwargs['stop'] is None
assert base_kwargs['quiet'] is None
assert base_kwargs['verbose'] is None


def simple_function(mobile):
Expand All @@ -139,12 +137,9 @@ def simple_function(mobile):
def test_AnalysisFromFunction():
u = mda.Universe(PSF, DCD)
step = 2
ana1 = base.AnalysisFromFunction(simple_function, mobile=u.atoms,
step=step).run()
ana2 = base.AnalysisFromFunction(simple_function, u.atoms,
step=step).run()
ana3 = base.AnalysisFromFunction(simple_function, u.trajectory, u.atoms,
step=step).run()
ana1 = base.AnalysisFromFunction(simple_function, mobile=u.atoms, step=step).run()
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please don't change this formatting. I'm sure this was done to conform to the 80 char limit of pep8

ana2 = base.AnalysisFromFunction(simple_function, u.atoms, step=step).run()
ana3 = base.AnalysisFromFunction(simple_function, u.trajectory, u.atoms, step=step).run()

results = []
for ts in u.trajectory[::step]:
Expand All @@ -157,8 +152,8 @@ def test_AnalysisFromFunction():

def test_analysis_class():
ana_class = base.analysis_class(simple_function)
assert_(issubclass(ana_class, base.AnalysisBase))
assert_(issubclass(ana_class, base.AnalysisFromFunction))
assert issubclass(ana_class, base.AnalysisBase)
assert issubclass(ana_class, base.AnalysisFromFunction)

u = mda.Universe(PSF, DCD)
step = 2
Expand All @@ -170,8 +165,9 @@ def test_analysis_class():
results = np.asarray(results)

assert_array_equal(results, ana.results)
with pytest.raises(ValueError):
ana_class(2)

assert_raises(ValueError, ana_class, 2)

def test_analysis_class_decorator():
# Issue #1511
Expand Down