np.testing.assert_almost_equal Issue in Python 3.5 for numpy==1.15.0 #11743

foohyfooh · 2018-08-15T12:16:37Z

The issues seems to be that in numpy/testing/_private/utils.py (x_id == y_id).all() on Line 707 is returning a bool in Python 3.5 and thus calling all on it is giving an AttributeError.
This is causing errors when testing the Pyrr package.

Note: This issue occurs with numpy==1.15.0 but not numpy==1.14.5

Reproducing code example:

This is one of the four code snippets that has the error is occurring.

from __future__ import absolute_import, division, print_function
try:
    import unittest2 as unittest
except:
    import unittest
import numpy as np
from pyrr import Quaternion, Matrix44, Matrix33, Vector3, Vector4, euler

class test_matrix_quaternion(unittest.TestCase):
    def test_m44_q_equivalence(self):
        """Test for equivalance of matrix and quaternion rotations.

        Create a matrix and quaternion, rotate each by the same values
        then convert matrix<->quaternion and check the results are the same.
        """
        m = Matrix44.from_x_rotation(np.pi / 2.)
        mq = Quaternion.from_matrix(m)

        q = Quaternion.from_x_rotation(np.pi / 2.)
        qm = Matrix44.from_quaternion(q)

        self.assertTrue(np.allclose(np.dot([1., 0., 0., 1.], m), [1., 0., 0., 1.]))
        self.assertTrue(np.allclose(np.dot([1., 0., 0., 1.], qm), [1., 0., 0., 1.]))

        self.assertTrue(np.allclose(q * Vector4([1., 0., 0., 1.]), [1., 0., 0., 1.]))
        self.assertTrue(np.allclose(mq * Vector4([1., 0., 0., 1.]), [1., 0., 0., 1.]))

        np.testing.assert_almost_equal(q, mq, decimal=5)
        np.testing.assert_almost_equal(m, qm, decimal=5)

Error message:

The errors can be found at https://travis-ci.org/adamlwgriffiths/Pyrr/jobs/415907003
Lines: 486, 502, 518, 534

The following is the Traceback from Travis CI

======================================================================
ERROR: Test for equivalance of matrix and quaternion rotations.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/adamlwgriffiths/Pyrr/pyrr/tests/objects/test_equivalence.py", line 29, in test_m44_q_equivalence
    np.testing.assert_almost_equal(q, mq, decimal=5)
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 568, in assert_almost_equal
    return assert_array_almost_equal(actual, desired, decimal, err_msg)
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 964, in assert_array_almost_equal
    precision=decimal)
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 736, in assert_array_compare
    flagged = func_assert_same_pos(x, y, func=isnan, hasval='nan')
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 707, in func_assert_same_pos
    if (x_id == y_id).all() != True:
AttributeError: 'bool' object has no attribute 'all'
======================================================================
ERROR: test_decompose (pyrr.tests.objects.test_matrix44.test_object_matrix44)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/adamlwgriffiths/Pyrr/pyrr/tests/objects/test_matrix44.py", line 326, in test_decompose
    np.testing.assert_almost_equal(m, expected_model)
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 568, in assert_almost_equal
    return assert_array_almost_equal(actual, desired, decimal, err_msg)
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 964, in assert_array_almost_equal
    precision=decimal)
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 736, in assert_array_compare
    flagged = func_assert_same_pos(x, y, func=isnan, hasval='nan')
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 707, in func_assert_same_pos
    if (x_id == y_id).all() != True:
AttributeError: 'bool' object has no attribute 'all'
======================================================================
ERROR: test_normalize (pyrr.tests.objects.test_vector3.test_object_vector3)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/adamlwgriffiths/Pyrr/pyrr/tests/objects/test_vector3.py", line 77, in test_normalize
    np.testing.assert_almost_equal(v.normalized, [0.57735, 0.57735, 0.57735], decimal=5)
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 568, in assert_almost_equal
    return assert_array_almost_equal(actual, desired, decimal, err_msg)
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 964, in assert_array_almost_equal
    precision=decimal)
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 736, in assert_array_compare
    flagged = func_assert_same_pos(x, y, func=isnan, hasval='nan')
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 707, in func_assert_same_pos
    if (x_id == y_id).all() != True:
AttributeError: 'bool' object has no attribute 'all'
======================================================================
ERROR: test_normalize (pyrr.tests.objects.test_vector4.test_object_vector4)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/adamlwgriffiths/Pyrr/pyrr/tests/objects/test_vector4.py", line 60, in test_normalize
    np.testing.assert_almost_equal(v.normalized, [0.5, 0.5, 0.5, 0.5], decimal=5)
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 568, in assert_almost_equal
    return assert_array_almost_equal(actual, desired, decimal, err_msg)
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 964, in assert_array_almost_equal
    precision=decimal)
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 736, in assert_array_compare
    flagged = func_assert_same_pos(x, y, func=isnan, hasval='nan')
  File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/numpy/testing/_private/utils.py", line 707, in func_assert_same_pos
    if (x_id == y_id).all() != True:
AttributeError: 'bool' object has no attribute 'all'

Numpy/Python version information:

1.15.0 3.5.5 |Anaconda, Inc.| (default, Apr 7 2018, 04:52:34) [MSC v.1900 64 bit (AMD64)]

The text was updated successfully, but these errors were encountered:

charris · 2018-08-15T13:50:24Z

Problem came in with #11122. What happens if you replace if (x_id == y_id).all() != True: by if not np.all(x_id == y_id): ?

@mhvk Thoughts?

mhvk · 2018-08-15T14:24:16Z

Weird. But your suggestion should work. (I'm on holidays so won't be able to check too much or make a PR; @foohyfooh - if you can, that would be great!)

charris · 2018-08-15T17:31:39Z

8000

@foohyfooh Can you come up with simpler code that triggers the problem?

foohyfooh · 2018-08-15T20:01:12Z

import numpy as np
from pyrr.objects import Vector3
np.testing.assert_almost_equal(Vector3(), Vector3())

charris · 2018-08-15T20:03:13Z

@foohyfooh I'm looking for something without outside dependencies so it can be added to numpy as a test.

foohyfooh · 2018-08-15T23:12:33Z

@charris Sorry I didn't recognize that is what you were looking for. I don't think I have a test other than what is happening in the Pyrr library.

charris · 2018-08-15T23:17:07Z

What is special about Vector3? We can make a testing class if needed.

foohyfooh · 2018-08-15T23:32:12Z

Nothing is special about it. It is just that the classes in Pyrr allow for positional element access just like numpy arrays.
It is just that the interaction between np.testing.assert_almost_equal and Pyrr classes is broken in Python 3.5 but works fine in Python 3.3, 3.4 and 3.6.

charris · 2018-08-15T23:44:47Z

So this is a Python change, not a NumPy 1.15 thing? Now you have me wondering why it should work. Are the Vector3 classes instances of list or some other sequence type?

foohyfooh · 2018-08-15T23:51:03Z

But the test worked fine with NumPy 1.14.5 when using Python 3.5.
Is there any change that was made between 1.14.5 and 1.15.0 that a specific effect in Python 3.5 only?

ewmoore · 2018-08-15T23:55:33Z

A quick look says that they are ndarray subclasses.

…

On Wed, Aug 15, 2018 at 7:51 PM Jonathan Herbert ***@***.***> wrote: But the test worked fine with NumPy 1.14.5 when using Python 3.5. Is there any change that was made between 1.14.5 and 1.15.0 that a specific effect in Python 3.5 only? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#11743 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACNRkWR9LkkdjHZo_X6AOSQWipcWU7NWks5uRLPpgaJpZM4V-Ap6> .

charris · 2018-08-16T00:10:17Z

It looks like Vector3 subclasses ndarray, but the == operator returns boolean.

n [1]: from pyrr.objects import Vector3

In [2]: Vector3() == Vector3()
Out[2]: True

In [3]: array(()) == array(())
Out[3]: array([], dtype=bool)

Note that comparing arrays returns an array, but I suspect you have overloaded that operator and Vector3 no longer behaves like an array. That, in combination with the changes in testing, where it checks that it is working with an array and wrongly assumes that Vector3 acts like one -- it is an instance of ndarray after all -- and calls a method that the comparison result should have.

So, we can work around that maybe, but the base class you are using maybe should not inherit from ndarray.

foohyfooh · 2018-08-16T00:10:40Z

@ewmoore Thanks for pointing that out. I can't believe that I missed that.

foohyfooh · 2018-08-16T00:33:03Z

Thank you for helping me sort out this issue. I will attempt to resolve the issue in Pyrr and verify that everything is working as it should.
Sorry for blaming NumPy.

charris · 2018-08-16T00:42:08Z

If you are looking for other ways to do things, the mailing list is a good resource. There have been recent additions to numpy, __array_ufunc__ in particular, that might be useful.

charris · 2018-08-16T00:51:19Z

I'm thinking we should still make the suggested change on our end, as the dos and don'ts of subclassing are probably not as clearly set out as might be desired. In particular, scalars vs 1-D array returns can be a problem with a lot of functions.

@charris

Implement fix suggested by @charris See numpy#11743

mhvk · 2018-08-16T11:29:01Z

@foohyfooh - definitely don't worry about making a bug report if we break something, even if it turns out to be something that really one shouldn't have relied upon!

Use np.all instead of the *.all method to be a bit more robust against bad subclasses of ndarray that may change the behavior of the method. Closes numpy#11743.

foohyfooh mentioned this issue Aug 15, 2018

Remove Python 2.6 Support adamlwgriffiths/Pyrr#76

Merged

adamlwgriffiths mentioned this issue Aug 15, 2018

Numpy issues with Python 3.5 adamlwgriffiths/Pyrr#77

Closed

charris added the 06 - Regression label Aug 15, 2018

charris added this to the 1.15.1 release milestone Aug 15, 2018

foohyfooh changed the title ~~numpy/testing/_private/utils.py Issue in Python 3.5 for numpy==1.15.0~~ np.testing.assert_almost_equal Issue in Python 3.5 for numpy==1.15.0 Aug 15, 2018

foohyfooh added a commit to foohyfooh/numpy that referenced this issue Aug 16, 2018

BUG: Fix Python 3.5 np.testing.assert_almost_equal issue

3eeb38a

Implement fix suggested by @charris See numpy#11743

foohyfooh mentioned this issue Aug 16, 2018

BUG: Fix Python 3.5 np.testing.assert_almost_equal issue #11751

Closed

charris mentioned this issue Aug 16, 2018

MAINT: Make assert_array_compare more generic. #11756

Merged

charris closed this as completed in #11756 Aug 17, 2018

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np.testing.assert_almost_equal Issue in Python 3.5 for numpy==1.15.0 #11743

np.testing.assert_almost_equal Issue in Python 3.5 for numpy==1.15.0 #11743

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np.testing.assert_almost_equal Issue in Python 3.5 for numpy==1.15.0 #11743

np.testing.assert_almost_equal Issue in Python 3.5 for numpy==1.15.0 #11743

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Reproducing code example:

Error message:

Numpy/Python version information:

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