Control: tags -1 help Control: tags -1 upstream Control: forwarded -1 https://github.com/biocore/scikit-bio/issues/1678
Hi Rebecca, thanks a lot for working on the Pandas migration. On Wed, Nov 13, 2019 at 10:19:56PM +0000, Rebecca N. Palmer wrote: > The ones that are blocking pandas [1] are python-skbio, > > [1] https://qa.debian.org/excuses.php?package=pandas (cnvkit since fixed) I've checked the issue with some patch from upstream[1] but failed. I also tried to build HEAD from upstream which also leaves three remaining errors which I reported in issue #1678[2]: ====================================================================== ERROR: test_munging_invalid_type_to_self_type (skbio.sequence.tests.test_sequence.TestDistance) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/sequence/tests/test_sequence.py", line 2369, in test_munging_invalid_type_to_self_type Sequence("ACGT").distance(42) File "/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/sequence/_sequence.py", line 1539, in distance other = self._munge_to_self_type(other, 'distance') File "/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/sequence/_sequence.py", line 2161, in _munge_to_self_type return self.__class__(other) File "/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/sequence/_sequence.py", line 622, in __init__ s = np.frombuffer(sequence, dtype=np.uint8) TypeError: a bytes-like object is required, not 'int' ====================================================================== ERROR: test_init_invalid_sequence (skbio.sequence.tests.test_sequence.TestSequence) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/sequence/tests/test_sequence.py", line 465, in test_init_invalid_sequence Sequence(('a', 'b', 'c')) File "/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/sequence/_sequence.py", line 622, in __init__ s = np.frombuffer(sequence, dtype=np.uint8) TypeError: a bytes-like object is required, not 'tuple' ====================================================================== FAIL: test_no_variation_pearson (skbio.stats.distance.tests.test_mantel.MantelTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/python-skbio-0.5.5a/.pybuild/cpython3_3.7_skbio/build/skbio/stats/distance/tests/test_mantel.py", line 247, in test_no_variation_pearson npt.assert_equal(obs, (np.nan, np.nan, 3)) File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 355, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k, err_msg), verbose) File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 427, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=0 ACTUAL: 0.0 DESIRED: nan ---------------------------------------------------------------------- Ran 2352 tests in 44.011s FAILED (SKIP=30, errors=2, failures=1) I somehow suspect that the two errors above might be caused by a broken Python3 conversion - any help to fix this would be welcome. Kind regards Andreas. [1] https://github.com/biocore/scikit-bio/commit/9c061da7e2746aee403b41621f71b118ce5c52f8 [2] https://github.com/biocore/scikit-bio/issues/1678 -- http://fam-tille.de
