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Port auxiliary module to pytest #1439

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merged 7 commits into from Jun 28, 2017
Merged

Port auxiliary module to pytest #1439

merged 7 commits into from Jun 28, 2017

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@utkbansal utkbansal commented Jun 27, 2017

Fixes #

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  • CHANGELOG updated?
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@utkbansal utkbansal force-pushed the utkbansal:pytest-aux branch from c860a3a to eb049d4 Jun 27, 2017
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@utkbansal utkbansal commented Jun 27, 2017

@kain88-de @richardjgowers Have a look at this.
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@richardjgowers richardjgowers commented Jun 27, 2017

@utkbansal it looks like you might have to turn BaseAuxReference into a fixture. Then the tests in BaseAuxReader should all be parametrised to use it, rather than referring to it through self.

I wouldn't blindly put everything from BaseAuxReference into the fixture though, there's a lot of junk in there that could get moved out, for example iter_list isn't actually reference data, and that could exist only in the test methods which use it.
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@utkbansal utkbansal commented Jun 27, 2017

I'm guessing, the error is arising because setUp can't take arguments?!
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@utkbansal utkbansal commented Jun 27, 2017 •
edited

@richardjgowers Okay, I'll try that.

Interesting to note that the minimal build exits once the pytest suite fails and it doesn't try to run the nose test suite. This is against our assumptions!
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kain88-de reviewed Jun 27, 2017
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testsuite/MDAnalysisTests/auxiliary/base.py Outdated
@@ -34,14 +37,17 @@ 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')

class BaseAuxReference(object):
class BaseAuxReference(TestCase):

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this contains reference data. No need to declare it as a test class
testsuite/MDAnalysisTests/auxiliary/test_xvg.py Outdated
@@ -33,8 +33,11 @@
from MDAnalysisTests.auxiliary.base import (BaseAuxReaderTest, BaseAuxReference)

class XVGReference(BaseAuxReference):
def __init__(self):

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these are normal classes.
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Use fixtures
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@utkbansal utkbansal force-pushed the utkbansal:pytest-aux branch from 6715bbf to 853f646 Jun 27, 2017
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Move auxiliary to PYTEST_LIST
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@utkbansal utkbansal commented Jun 27, 2017

@kain88-de @richardjgowers I have made some progress. I still have 3 test cases failing. I'm looking into that. A quick review would be helpful. basically what I want to know is - if this the direction we want to proceed in?
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Drop the module scope of the fixture
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@utkbansal utkbansal commented Jun 27, 2017

Got those errors, apparently having the scope set to module causes some problem. Maybe some methods are updating some attributes?
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@richardjgowers richardjgowers commented Jun 27, 2017

Don't worry about scope yet, that's an optimisation
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Use fixtures in TestXVGFileReader
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@utkbansal utkbansal commented Jun 27, 2017

This should fix the drop in coverage. I still have to do some cleanup stuff.
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@kain88-de kain88-de commented Jun 27, 2017

@utkbansal. There is a possible minimal fix in #1440. You can just take the code. No need for commit attribution. Choose better names though! Simply doing the init/setup in a different named method fixes everything. As long as coverage doesn't drop this is OK for now but should be fixed with a better solution long term.
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Minor cleanups
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@utkbansal utkbansal commented Jun 27, 2017

@kain88-de @richardjgowers All green and no drop in coverage! Have cleaned this up. Please review.
@utkbansal utkbansal changed the title [WIP]Port auxiliary module to pytest Port auxiliary module to pytest Jun 27, 2017
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Looks good
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kain88-de reviewed Jun 27, 2017
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testsuite/MDAnalysisTests/auxiliary/test_xvg.py
def test_changing_n_col_raises_ValueError(self):
@staticmethod
@pytest.fixture()
def ref():

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what happens when I define a global fixture ref in the same file?

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I tried making both of them global. 3 tests failed. So I switched back.

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So if I now create a global fixture the tests will break?
testsuite/MDAnalysisTests/auxiliary/test_xvg.py Outdated
def reader(ref):
return ref.reader(ref.testdata, initial_time=ref.initial_time,
dt=ref.dt, auxname=ref.name,
time_selector=None, data_selector=None)

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kain88-de Jun 27, 2017
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indentation
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Indentation fixes
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@utkbansal utkbansal commented Jun 27, 2017

@richardjgowers Should be ready to be merged now.
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@utkbansal utkbansal commented Jun 27, 2017 •
edited

Can someone explain why test_xvg_bz2 function has the same name as another function just above it!? https://github.com/utkbansal/mdanalysis/blob/27a9cb2ed3a0ad34b19671c28522c6a4c7c4a365/testsuite/MDAnalysisTests/auxiliary/test_xvg.py#L132

Looks like a bug.
@utkbansal utkbansal changed the title Port auxiliary module to pytest [WIP]Port auxiliary module to pytest Jun 27, 2017
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@kain88-de kain88-de commented Jun 27, 2017

Can someone explain why test_xvg_bz2 function has the same name as another function just above it!?

Looks like a mistake. You can rename the functions.
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kain88-de reviewed Jun 28, 2017
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testsuite/MDAnalysisTests/auxiliary/test_xvg.py Outdated

def test_xvg_bz2():
reader = mda.auxiliary.XVG.XVGReader(XVG_BZ2)
assert_array_equal(reader.read_all_times(), np.array([0., 50., 100.]))


def test_xvg_bz2():

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kain88-de Jun 28, 2017
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If you rename the function so that the test is run as well the PR is good to go.
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Fix function name repetition
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@utkbansal utkbansal changed the title [WIP]Port auxiliary module to pytest Port auxiliary module to pytest Jun 28, 2017
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@utkbansal utkbansal commented Jun 28, 2017

@richardjgowers @kain88-de Can be merged now!
@richardjgowers richardjgowers merged commit be8db1c into MDAnalysis:develop Jun 28, 2017
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@richardjgowers richardjgowers commented Jun 28, 2017

Another one down!
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