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Pytest Style: auxiliary/base.py #1492

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merged 4 commits into from
Jul 18, 2017
Merged

Pytest Style: auxiliary/base.py #1492

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77d1ace
Pytest style auxiliary/base.py
utkbansal Jul 15, 2017
bc8b1cb
Fix raises
utkbansal Jul 16, 2017
3ee718a
Fix raises errors
utkbansal Jul 16, 2017
3da7539
Fix assert calls
utkbansal Jul 18, 2017
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46 changes: 19 additions & 27 deletions testsuite/MDAnalysisTests/auxiliary/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,14 +24,15 @@
from six.moves import range
import pytest
import numpy as np
from numpy.testing import (assert_equal, assert_raises, assert_almost_equal,
raises)
from numpy.testing import assert_almost_equal


import MDAnalysis as mda

from MDAnalysisTests.datafiles import (COORDINATES_XTC, COORDINATES_TOPOLOGY)

@raises(ValueError)

@pytest.mark.raises(exception=ValueError)
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please use the pytest.raises context manager

def test_get_bad_auxreader_format_raises_ValueError():
# should raise a ValueError when no AuxReaders with match the specified format
mda.auxiliary.core.get_auxreader_for(format='bad-format')
Expand Down Expand Up @@ -132,16 +133,13 @@ def format_data(self, data):
class BaseAuxReaderTest(object):

def test_n_steps(self, ref, reader):
assert_equal(len(reader), ref.n_steps,
"number of steps does not match")
assert len(reader) == ref.n_steps, "number of steps does not match"

def test_dt(self, ref, reader):
assert_equal(reader.dt, ref.dt,
"dt does not match")
assert reader.dt == ref.dt, "dt does not match"

def test_initial_time(self, ref, reader):
assert_equal(reader.initial_time, ref.initial_time,
"initial time does not match")
assert reader.initial_time == ref.initial_time, "initial time does not match"

def test_first_step(self, ref, reader):
# on first loading we should start at step 0
Expand Down Expand Up @@ -173,7 +171,8 @@ def test_next_past_last_step_raises_StopIteration(self, ref, reader):
# should take us to the last step
reader[-1]
# if we try to move to next step from here, should raise StopIteration
assert_raises(StopIteration, reader.next)
with pytest.raises(StopIteration):
reader.next

def test_move_to_invalid_step_raises_IndexError(self, ref, reader):
# last step is number n_steps -1 ; if we try move to step number
Expand Down Expand Up @@ -228,17 +227,15 @@ def test_time_selector(self, ref):
time_selector = ref.time_selector)
# time should still match reference time for each step
for i, val in enumerate(reader):
assert_equal(val.time, ref.select_time_ref[i],
"time for step {} does not match".format(i))
assert val.time == ref.select_time_ref[i], "time for step {} does not match".format(i)

def test_data_selector(self, ref):
# reload reader, passing in a data selector
reader = ref.reader(ref.testdata,
data_selector=ref.data_selector)
# data should match reference data for each step
for i, val in enumerate(reader):
assert_equal(val.data, ref.select_data_ref[i],
"data for step {0} does not match".format(i))
assert val.data == ref.select_data_ref[i], "data for step {0} does not match".format(i)

def test_no_constant_dt(self, ref):
## assume we can select time...
Expand All @@ -248,8 +245,7 @@ def test_no_constant_dt(self, ref):
constant_dt=False)
# time should match reference for selecting time, for each step
for i, val in enumerate(reader):
assert_equal(val.time, ref.select_time_ref[i],
"data for step {} does not match".format(i))
assert val.time == ref.select_time_ref[i], "data for step {} does not match".format(i)

def test_update_ts_without_auxname_raises_ValueError(self, ref):
# reload reader without auxname
Expand Down Expand Up @@ -319,7 +315,7 @@ def test_read_higher_freq_timestep(self, ref, reader):
def test_get_auxreader_for(self, ref, reader):
# check guesser gives us right reader
reader = mda.auxiliary.core.get_auxreader_for(ref.testdata)
assert_equal(reader, ref.reader)
assert reader == ref.reader

def test_iterate_through_trajectory(self, ref):
# add to trajectory
Expand All @@ -329,9 +325,8 @@ def test_iterate_through_trajectory(self, ref):
# trajectory here has same dt, offset; so there's a direct correspondence
# between frames and steps
for i, ts in enumerate(u.trajectory):
assert_equal(ts.aux.test, ref.auxsteps[i].data,
"representative value does not match when iterating through "
"all trajectory timesteps")
assert ts.aux.test == ref.auxsteps[i].data, "representative value does not match when iterating through "\
"all trajectory timesteps"
u.trajectory.close()

def test_iterate_as_auxiliary_from_trajectory(self, ref):
Expand All @@ -342,22 +337,19 @@ def test_iterate_as_auxiliary_from_trajectory(self, ref):
# trahectory here has same dt, offset, so there's a direct correspondence
# between frames and steps, and iter_as_aux will run through all frames
for i, ts in enumerate(u.trajectory.iter_as_aux('test')):
assert_equal(ts.aux.test, ref.auxsteps[i].data,
"representative value does not match when iterating through "
"all trajectory timesteps")
assert ts.aux.test == ref.auxsteps[i].data, "representative value does not match when iterating through "\
"all trajectory timesteps"
u.trajectory.close()

def test_get_description(self, ref, reader):
description = reader.get_description()
for attr in ref.description:
assert_equal(description[attr], ref.description[attr],
"'Description' does not match for {}".format(attr))
assert description[attr] == ref.description[attr], "'Description' does not match for {}".format(attr)

def test_load_from_description(self, reader):
description = reader.get_description()
new = mda.auxiliary.core.auxreader(**description)
assert_equal(new, reader,
"AuxReader reloaded from description does not match")
assert new == reader, "AuxReader reloaded from description does not match"


def assert_auxstep_equal(A, B):
Expand Down