dtype issues on Windows

[mataton]

In skbio/stats, the function subsample_counts and it's underlying Cython function _subsample_counts_without_replacement throw the following errors when run on Windows systems:

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ERROR: test_subsample_counts_nonrandom (__main__.SubsampleCountsTests.test_subsample_counts_nonrandom)
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Traceback (most recent call last):
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\stats\tests\test_subsample.py", line 38, in test_subsample_counts_nonrandom
    npt.assert_equal(subsample_counts(a, 2), exp)
                     ^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\stats\_subsample.py", line 247, in subsample_counts
    result = _subsample_counts_without_replacement(counts, n, counts_sum)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "skbio\\stats\\__subsample.pyx", line 13, in skbio.stats.__subsample._subsample_counts_without_replacement
    def _subsample_counts_without_replacement(
ValueError: Buffer dtype mismatch, expected 'int64_t' but got 'long'

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ERROR: test_subsample_counts_without_replacement (__main__.SubsampleCountsTests.test_subsample_counts_without_replacement)
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Traceback (most recent call last):
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\stats\tests\test_subsample.py", line 54, in test_subsample_counts_without_replacement
    obs = subsample_counts(a, 2)
          ^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\stats\_subsample.py", line 247, in subsample_counts
    result = _subsample_counts_without_replacement(counts, n, counts_sum)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "skbio\\stats\\__subsample.pyx", line 13, in skbio.stats.__subsample._subsample_counts_without_replacement
    def _subsample_counts_without_replacement(
ValueError: Buffer dtype mismatch, expected 'int64_t' but got 'long'

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It seems that there is a difference in the underlying data types of integers on Windows vs UNIX, as well as something regarding Cython. See here, here, here, and here. I have tried casting things to np.int64 to no avail.

EDIT: The issues surrounding subsample have been resolved with PR #2016. The other issues here still remain.

[mataton]

There are very similar, but slightly different errors occurring in the _tip_distances function in diversity/beta/_unifrac.py and the associated Cython code.

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ERROR: test_weighted_normalized_root_not_observed (__main__.UnifracTests.test_weighted_normalized_root_not_observed)
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Traceback (most recent call last):
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\diversity\beta\tests\test_unifrac.py", line 160, in test_weighted_normalized_root_not_observed
    actual = weighted_unifrac([1, 0, 0, 0], [1, 1, 0, 0],
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\diversity\beta\_unifrac.py", line 317, in weighted_unifrac
    node_to_root_distances = _tip_distances(branch_lengths, tree, tip_indices)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "skbio\\diversity\\_phylogenetic.pyx", line 17, in skbio.diversity._phylogenetic._tip_distances
    @cython.boundscheck(False)
ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'long'

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ERROR: test_weighted_unifrac_identity_normalized (__main__.UnifracTests.test_weighted_unifrac_identity_normalized)
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Traceback (most recent call last):
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\diversity\beta\tests\test_unifrac.py", line 517, in test_weighted_unifrac_identity_normalized
    actual = weighted_unifrac(
             ^^^^^^^^^^^^^^^^^
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\diversity\beta\_unifrac.py", line 317, in weighted_unifrac
    node_to_root_distances = _tip_distances(branch_lengths, tree, tip_indices)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "skbio\\diversity\\_phylogenetic.pyx", line 17, in skbio.diversity._phylogenetic._tip_distances
    @cython.boundscheck(False)
ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'long'

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ERROR: test_weighted_unifrac_non_overlapping_normalized (__main__.UnifracTests.test_weighted_unifrac_non_overlapping_normalized)
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Traceback (most recent call last):
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\diversity\beta\tests\test_unifrac.py", line 535, in test_weighted_unifrac_non_overlapping_normalized
    actual = weighted_unifrac(
             ^^^^^^^^^^^^^^^^^
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\diversity\beta\_unifrac.py", line 317, in weighted_unifrac
    node_to_root_distances = _tip_distances(branch_lengths, tree, tip_indices)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "skbio\\diversity\\_phylogenetic.pyx", line 17, in skbio.diversity._phylogenetic._tip_distances
    @cython.boundscheck(False)
ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'long'

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ERROR: test_weighted_unifrac_normalized (__main__.UnifracTests.test_weighted_unifrac_normalized)
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Traceback (most recent call last):
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\diversity\beta\tests\test_unifrac.py", line 568, in test_weighted_unifrac_normalized
    actual = weighted_unifrac(
             ^^^^^^^^^^^^^^^^^
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\diversity\beta\_unifrac.py", line 317, in weighted_unifrac
    node_to_root_distances = _tip_distances(branch_lengths, tree, tip_indices)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "skbio\\diversity\\_phylogenetic.pyx", line 17, in skbio.diversity._phylogenetic._tip_distances
    @cython.boundscheck(False)
ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'long'

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ERROR: test_weighted_unifrac_symmetry_normalized (__main__.UnifracTests.test_weighted_unifrac_symmetry_normalized)
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Traceback (most recent call last):
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\diversity\beta\tests\test_unifrac.py", line 525, in test_weighted_unifrac_symmetry_normalized
    actual = weighted_unifrac(
             ^^^^^^^^^^^^^^^^^
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\diversity\beta\_unifrac.py", line 317, in weighted_unifrac
    node_to_root_distances = _tip_distances(branch_lengths, tree, tip_indices)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "skbio\\diversity\\_phylogenetic.pyx", line 17, in skbio.diversity._phylogenetic._tip_distances
    @cython.boundscheck(False)
ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'long'

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ERROR: test_weighted_unifrac_zero_counts_normalized (__main__.UnifracTests.test_weighted_unifrac_zero_counts_normalized)
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Traceback (most recent call last):
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\diversity\beta\tests\test_unifrac.py", line 549, in test_weighted_unifrac_zero_counts_normalized
    actual = weighted_unifrac(
             ^^^^^^^^^^^^^^^^^
  File "C:\Users\maton\qlab\skbio\windows\github\scikit-bio\skbio\diversity\beta\_unifrac.py", line 317, in weighted_unifrac
    node_to_root_distances = _tip_distances(branch_lengths, tree, tip_indices)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "skbio\\diversity\\_phylogenetic.pyx", line 17, in skbio.diversity._phylogenetic._tip_distances
    @cython.boundscheck(False)
ValueError: Buffer dtype mismatch, expected 'DTYPE_t' but got 'long'

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