larry-discuss team mailing list archive

[Keith Goodman <kwgoodman@xxxxxxxxx>]

On Thu, Feb 4, 2010 at 9:11 AM,  <josef.pktd@xxxxxxxxx> wrote:
> On Thu, Feb 4, 2010 at 11:17 AM, Keith Goodman <kwgoodman@xxxxxxxxx> wrote:
>> On Thu, Feb 4, 2010 at 8:04 AM,  <josef.pktd@xxxxxxxxx> wrote:
>>> On Thu, Feb 4, 2010 at 10:33 AM, Keith Goodman <kwgoodman@xxxxxxxxx> wrote:
>>>> On Wed, Feb 3, 2010 at 7:04 PM,  <josef.pktd@xxxxxxxxx> wrote:
>>>>> On Wed, Feb 3, 2010 at 9:54 PM,  <josef.pktd@xxxxxxxxx> wrote:
>>>>>> On Wed, Feb 3, 2010 at 9:16 PM, Keith Goodman <kwgoodman@xxxxxxxxx> wrote:
>>>>>>> On Wed, Feb 3, 2010 at 6:06 PM, joep <josef.pktd@xxxxxxxxx> wrote:
>>>>>>>> Blueprint changed by joep:
>>>>>>>>
>>>>>>>> Whiteboard set to:
>>>>>>>>
>>>>>>>> assert_larry
>>>>>>>> http://bazaar.launchpad.net/~kwgoodman/larry/trunk/annotate/head%3A/la/tests/deflarry_nose_test.py#L49
>>>>>>>>
>>>>>>>> and the method check_function in test class
>>>>>>>>
>>>>>>>> http://bazaar.launchpad.net/~kwgoodman/larry/trunk/annotate/head%3A/la/tests/deflarry_nose_test.py#L128
>>>>>>>>
>>>>>>>> already contain the extracted boiler plate assert function to compare a
>>>>>>>> larry with desired data matrix x and labels
>>>>>>>>
>>>>>>>> the later has a view keyword to choose whether to verify nocopy or
>>>>>>>> noreference
>>>>>>>>
>>>>>>>> used in nosetests for larry methods
>>>>>>>
>>>>>>> I moved this to the larry-discuss list since it is hard to discuss it
>>>>>>> through the whiteboard on the blueprint.
>>>>>>>
>>>>>>> Yes, let's start with those functions and then prettify them.
>>>>>>>
>>>>>>> What should the signature be?
>>>>>>>
>>>>>>> The current signature is:
>>>>>>>
>>>>>>> assert_larry(opname, la, t, lab, msgstr)
>>>>>>>
>>>>>>> How about changing that to the same signature as np.testing.assert_equal? So:
>>>>>>>
>>>>>>> assert_equal(actual, desired, err_msg='', verbose=True)
>>>>>>>
>>>>>>> Then we don't have to separate the data and the label. And instead of
>>>>>>> nancode we can use the numpy nan aware assert in numpy 1.4.
>>>>>>>
>>>>>>> Oops...dinner time!
>>>>>>
>>>>>> I'm just browsing the code and adding some notes.
>>>>>>
>>>>>> Yes, matching the numpy signature for assert_equal and
>>>>>> assert_almost_equal is a good idea.
>>>>>> If you require numpy 1.4 for the test suite, then most of the boiler
>>>>>> plate is gone (nan handling)
>>>>>>
>>>>>> I think that assert_larry_equal is equivalent to
>>>>>> assert_equal(la1.x, la2.x)
>>>>>> assert_equal(la1.label, la2.label)
>>>>>>
>>>>>> slicing_test.py/test_slicing and test_morph use directly an assert_
>>>>>> which could be replaced by np.testing.assert_equal
>>>>>
>>>>> just another comment:
>>>>>
>>>>> there are 3 patterns in the test suite corresponding to the previous comments
>>>>>
>>>>> * python unittest with boilerplate
>>>>> * numpy 1.3 nosetests with explicit nan handling
>>>>> * numpy 1.4 nosetests where numpy.testing assert do the nan handling
>>>>>
>>>>> In the 4th option an explicit function assert_larry_xxx is not really
>>>>> necessary, and the test for x and labels and nocopy/noreference could
>>>>> also be "yielded" directly from the test function/method.
>>>>
>>>> Instead of making many unit tests out of one call to larry's
>>>> assert_equal, which would occur if we used yield, I think it is better
>>>> for the whole thing be one unit test. That would mean that we'd have
>>>> to wrap calls to np.testing.assert_equal in try...except blocks,
>>>> collect any error messages, and raise an AssertionError at the end of
>>>> the function if needed.
>>>
>>> several asserts don't have to be yielded, if you want them to be only
>>> one unittest that fails at the first assertion error, e.g.
>>> def test_movingsum32(self)  in deflarry_nose_test.py
>>
>> I think it is better for debugging if all the info is printed out when
>> the test fails. For example, if a test fails on the label, Id like to
>> know if it passed on the array.
>>
>>>>
>>>> As for signature, how about
>>>>
>>>> assert_equal(actual, desired, msg='', dtype=True, noreference=True,
>>>> nocopy=False, verbose=True)
>>>
>>> this doesn't work, since noreference and nocopy also need the original larry,
>>> the signature of check function is
>>
>> Good point.
>>
>> An alternative to passing in the original and the actual is to pass in
>> the original and the function that modifies the original to produce
>> the actual. Then two larrys are always passed in. But that sounds
>> messy.
>>
>>> check_function(self, t, label, p, orig, view=False)
>>>
>>> the signature could be
>>> assert_larry_equal(actual, desired, msg='', dtype=True, original=None,
>>> noreference=True,
>>> nocopy=False, verbose=True)
>>
>> Should we go with the signature above?
>>
>>> but for noreference=True check an original has to be included
>>>
>>> with
>>> assert_larry_equal(actual, desired, original, msg='', dtype=True,
>>> noreference=True,
>>> nocopy=False, verbose=True)
>>>
>>> the original would have to be passed in even if both noreference and
>>> nocopy are False
>>>
>>>
>>>> So by default the dtype would be compared. Sometimes you expect the
>>>> dtype to change so maybe an option would be to pass in the dtype for
>>>> the "desired" larry.
>>>>
>>>> I think that would cover the most common use cases.
>>>
>>> Yes, I think so for the comparison of two larrys
>>>
>>> slicing tests e.g. test_slicing, would need a new function for
>>> noreference, nocopy that verifies e.g. that a slice is really a view.
>>> (I don't know what the numpy tests for view versus copy are for fancy
>>> slicing/indexing)
>>>
>>> Josef
>
> I attached a draft of the assert_larry_equal function. it imports some
> helper functions from test.py in the la/tests folder, which
> could/should also be rewritten into assert form.
> It's a draft, I haven't checked if it is working correctly yet for all cases.
>
> Also, I think it would be better to add the testing helper functions
> to la.utils so that they can be imported and don't need to have a copy
> in the test folder, as in the case of test.py.

I made a few tweaks. To get all tests to run even if the first one
(check labels) fails, I wrapped the asserts in try...except (just the
first two for now).

Also added a check that original is not None when doing a noreference
check ro nocopy check. And changed an assert to assert_equal.

def assert_larry_equal(actual, desired, msg='', dtype=True, original=None,
                       noreference=True, nocopy=False, verbose=True):
    #assert equality of attributes of two larries

    fail = []

    try:
        assert_equal(actual.x, desired.x, 'x')
    except AssertionError, err:
        fail.append(str(err))
    try:
        assert_equal(actual.label, desired.label, 'label')
    except AssertionError, errmsg:
        fail.append(str(err))

    if dtype:
        msg = printfail(actual.x.dtype, desired.x.dtype, 'x.dtype')
        assert_equal(actual.x.dtype, desired.x.dtype, msg)

    if noreference:
        if original is None:
            raise ValueError, 'original must be a larry to run
noreference check.'
        assert_(assert_noreference(actual, original), 'Reference found')
    elif nocopy:
        if original is None:
            raise ValueError, 'original must be a larry to run nocopy
check.'
        assert_(assert_nocopy(actual, original), 'copy instead of
reference found')
    else:   #FIXME check view for different dimensional larries
        pass

    if len(fail) > 0:
        msg = ''.join(fail)
        raise AssertionError, msg