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Re: Remaining numpy 1.24 issues on 32bit architectures

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Hi,

I made some tiny steps forward ("only" 84 failures instead of 89 when I
wrote my first mail) in the numpy 1.24 migration for 32bit architectures
but I'm facing issues I do not have a real clue for.  In

   https://salsa.debian.org/med-team/python-skbio/-/blob/master/debian/patches/numpy-1.24.patch#L123-L126

I tried three variants how I could fix

_______________________ AlphaDiversityTests.test_no_ids ________________________
self = <skbio.diversity.tests.test_driver.AlphaDiversityTests testMethod=test_no_ids>
    def test_no_ids(self):
        # expected values hand-calculated
        expected = pd.Series([3, 3, 3, 3])
        # All this does not help
        # expected = pd.Series(np.array([3, 3, 3, 3], int32))
        # actual = np.int64(alpha_diversity('observed_otus', self.table1))
        # actual = np.dtype('int64').type(alpha_diversity('observed_otus', self.table1))
        actual = alpha_diversity('observed_otus', self.table1)
>       assert_series_almost_equal(actual, expected)
skbio/diversity/tests/test_driver.py:260: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
left = 0    3
1    3
2    3
3    3
dtype: int32
right = 0    3
1    3
2    3
3    3
dtype: int64
    def assert_series_almost_equal(left, right):
        # pass all kwargs to ensure this function has consistent behavior even if
        # `assert_series_equal`'s defaults change
>       pdt.assert_series_equal(left, right,
                                check_dtype=True,
                                check_index_type=True,
                                check_series_type=True,
                                check_names=True,
                                check_exact=False,
                                check_datetimelike_compat=False,
                                obj='Series')
E       AssertionError: Attributes of Series are different
E       
E       Attribute "dtype" are different
E       [left]:  int32
E       [right]: int64
skbio/util/_testing.py:323: AssertionError
____________________ AlphaDiversityTests.test_observed_otus ____________________
self = <skbio.diversity.tests.test_driver.AlphaDiversityTests testMethod=test_observed_otus>
    def test_observed_otus(self):
        # expected values hand-calculated
        expected = pd.Series([3, 3, 3, 3], index=self.sids1)
        actual = alpha_diversity('observed_otus', self.table1, self.sids1)
>       assert_series_almost_equal(actual, expected)
skbio/diversity/tests/test_driver.py:223: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
left = A    3
B    3
C    3
D    3
dtype: int32
right = A    3
B    3
C    3
D    3
dtype: int64
    def assert_series_almost_equal(left, right):
        # pass all kwargs to ensure this function has consistent behavior even if
        # `assert_series_equal`'s defaults change
>       pdt.assert_series_equal(left, right,
                                check_dtype=True,
                                check_index_type=True,
                                check_series_type=True,
                                check_names=True,
                                check_exact=False,
                                check_datetimelike_compat=False,
                                obj='Series')
E       AssertionError: Attributes of Series are different
E       
E       Attribute "dtype" are different
E       [left]:  int32
E       [right]: int64
skbio/util/_testing.py:323: AssertionError
______________________ AlphaDiversityTests.test_optimized ______________________
self = <skbio.diversity.tests.test_driver.AlphaDiversityTests testMethod=test_optimized>
    def test_optimized(self):
        # calling optimized faith_pd gives same results as calling unoptimized
        # version
>       optimized = alpha_diversity('faith_pd', self.table1, tree=self.tree1,
                                    otu_ids=self.oids1)
skbio/diversity/tests/test_driver.py:265: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 


which obviosly[2] failed.  I wonder whether someone might give some
hints how to get dtypes consistently to one integer representation which
is the background of nearly all these test suite issues.

Kind regards
    Andreas.

[2] https://salsa.debian.org/med-team/python-skbio/-/jobs/3868951

Am Sun, Jan 29, 2023 at 12:11:15PM +0100 schrieb Andreas Tille:
> Hi,
> 
> I think there are some remaining issues with numpy 1.24 migration on 32
> bit architectures[1].
> 
> Here is one example:
> 
> _________ TestSequence.test_getitem_with_slice_has_positional_metadata _________
> 
> self = <skbio.sequence.tests.test_sequence.TestSequence testMethod=test_getitem_with_slice_has_positional_metadata>
> 
>     def test_getitem_with_slice_has_positional_metadata(self):
>         s = "0123456789abcdef"
>         length = len(s)
>         seq = Sequence(s, metadata={'id': 'id3', 'description': 'dsc3'},
>                        positional_metadata={'quality': np.arange(length)})
>     
>         eseq = Sequence("012", metadata={'id': 'id3', 'description': 'dsc3'},
>                         positional_metadata={'quality': np.arange(3)})
>         self.assertEqual(seq[0:3], eseq)
>         self.assertEqual(seq[:3], eseq)
>         self.assertEqual(seq[:3:1], eseq)
>     
>         eseq = Sequence("def", metadata={'id': 'id3', 'description': 'dsc3'},
>                         positional_metadata={'quality': [13, 14, 15]})
> >       self.assertEqual(seq[-3:], eseq)
> E       AssertionError: Seque[128 chars]: int32>
> E       Stats:
> E           length: 3
> E       ----------------[14 chars]0 def != Seque[128 chars]: int64>
> E       Stats:
> E           length: 3
> E       ----------------[14 chars]0 def
> 
> skbio/sequence/tests/test_sequence.py:748: AssertionError
> 
> How can I ensure that in both cases the arrays have the same type (I think it makes
> no difference whether it is np.int32 or np.int64 as long as they are of same type.
> 
> Kind regards
> 
>      Andreas.
> 
> [1] https://buildd.debian.org/status/package.php?p=python-skbio&suite=experimental
> 
> -- 
> http://fam-tille.de
> 
> 

-- 
http://fam-tille.de

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Remaining numpy 1.24 issues on 32bit architectures Andreas Tille <andreas@an3as.eu> - 2023-01-29 12:20 +0100
  Re: Remaining numpy 1.24 issues on 32bit architectures Andreas Tille <andreas@an3as.eu> - 2023-01-30 09:20 +0100
    Re: Remaining numpy 1.24 issues on 32bit architectures Nilesh Patra <nilesh@debian.org> - 2023-01-30 12:40 +0100
      Re: Remaining numpy 1.24 issues on 32bit architectures Andreas Tille <tille@debian.org> - 2023-01-30 13:50 +0100

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