larry-discuss team mailing list archive

[Keith Goodman <kwgoodman@xxxxxxxxx>]

On Thu, Feb 4, 2010 at 10:35 AM,  <josef.pktd@xxxxxxxxx> wrote:
> On Thu, Feb 4, 2010 at 1:25 PM, Keith Goodman <kwgoodman@xxxxxxxxx> wrote:
>> On Thu, Feb 4, 2010 at 10:08 AM, Keith Goodman <kwgoodman@xxxxxxxxx> wrote:
>>> 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
>>
>> I get this:
>>
>>>> x = larry([1,2,3])
>>>> y = larry([2,2,3], [['a', 'b', 'c']])
>>>>
>>>> assert_larry_equal(x, y, 'cumsum test', noreference=False)
>> ---------------------------------------------------------------------------
>> AssertionError:
>> Items are not equal:
>> item=0
>> item=0
>> label
>>  ACTUAL: 0
>>  DESIRED: 'a'
>> Arrays are not equal
>> x
>> (mismatch 33.3333333333%)
>>  x: array([1, 2, 3])
>>  y: array([2, 2, 3])
>>
>> with the code below. Hmm, the AssertionError message needs to be cleaned up.
>>
>> 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 = []
>>
>>    # label
>>    try:
>>        assert_equal(actual.label, desired.label, 'label')
>>    except AssertionError, err:
>>        fail.append(str(err))
>>
>>    # Data array
>>    try:
>>        assert_equal(actual.x, desired.x, 'x')
>>    except AssertionError, err:
>>        fail.append(str(err))
>>
>>    # dtype
>>    if dtype:
>>        try:
>>            assert_equal(actual.x.dtype, desired.x.dtype, 'dtype')
>>        except AssertionError, err:
>>            fail.append(str(err))
>>
>>    # Check for references or copies
>>    if noreference:
>>        if original is None:
>>            raise ValueError, 'original must be a larry to run
>> noreference check.'
>>        try:
>>            assert_(assert_noreference(actual, original), 'Reference found')
>>        except AssertionError, err:
>>            fail.append(str(err))
>>    elif nocopy:
>>        if original is None:
>>            raise ValueError, 'original must be a larry to run nocopy check.'
>>        try:
>>            assert_(assert_nocopy(actual, original), 'copy instead of
>> reference found')
>>        except AssertionError, err:
>>            fail.append(str(err))
>>    else:   #FIXME check view for different dimensional larries
>>        pass
>>
>>    # Did the test pass?
>>    if len(fail) > 0:
>>        # No
>>        msg = ''.join(fail)
>>        raise AssertionError, msg
>>
>
>
> Another possibility to look at, might be to use a yield inside the
> assert_larry instead of the try .. except, which might result in
> pretty much the same outcome, except for raising the test count. But
> if it's just in one function in doesn't increase boiler plate so it's
> fine.
>
> mabye '\n'.join(fail) would make it easier to read.
>
> Can you send it as an attachment or add it to the blueprint? gmail
> destroys the correct intend when I copy from the mail.

https://blueprints.launchpad.net/larry/+spec/simplify-unit-testing