larry-discuss team mailing list archive

[Keith Goodman <kwgoodman@xxxxxxxxx>]

On Thu, Feb 4, 2010 at 11:07 AM,  <josef.pktd@xxxxxxxxx> wrote:
> On Thu, Feb 4, 2010 at 1:59 PM, Keith Goodman <kwgoodman@xxxxxxxxx> wrote:
>> On Thu, Feb 4, 2010 at 10:54 AM,  <josef.pktd@xxxxxxxxx> wrote:
>>> On Thu, Feb 4, 2010 at 1:38 PM, Keith Goodman <kwgoodman@xxxxxxxxx> wrote:
>>>> 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
>>>>
>>>
>>> looks good, we can make minor adjustments after we see actual test output
>>> (One thought I tried is to remove the extra newline after
>>> ------------------, but it doesn't make much difference.)
>>>
>>> the second function would be almost a copy of this with only one
>>> assert_equal replace by assert_almost_equal for x
>>>
>>> def assert_larry_almost_equal(actual, desired, decimal=7, msg='',
>>> dtype=True, original=None,
>>>                       noreference=True, nocopy=False, verbose=True):
>>
>> Hmm, could we do almost equal whenever one of the dtypes is float;
>> equal otherwise?
>
> Yes,
> In general I never use assert_equal with floats. In this case, I would
> add the decimal keyword to assert_equal.
> Also, to be less confusing, I would set decimal=14 (or similar) so the
> function corresponds better to its name

That sounds good. Then we just need a check to see if both x's are
scalar (almost_equal) or not (equal).