Bug#951222: scikit-learn breaks python-skbio autopkgtest: skbio.stats.distance._permdisp.permdisp

[Paul Gevers]

Source: scikit-learn, python-skbio
Control: found -1 scikit-learn/0.22.1+dfsg-1
Control: found -1 python-skbio/0.5.5-3
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks needs-update

Dear maintainers,

With a recent upload of scikit-learn the autopkgtest of python-skbio
fails in testing when that autopkgtest is run with the binary packages
of scikit-learn from unstable. It passes when run with only packages
from testing. In tabular form:
                       pass            fail
scikit-learn           from testing    0.22.1+dfsg-1
python-skbio           from testing    0.5.5-3
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration of scikit-learn to
testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul
PS: scikit-learn also FTBFS on several architectures.


[1] https://qa.debian.org/excuses.php?package=scikit-learn

https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-skbio/4266056/log.gz

=================================== FAILURES
===================================
______________ [doctest] skbio.stats.distance._permdisp.permdisp
_______________
129     ...                       ['s1', 's2', 's3', 's4', 's5', 's6'])
130     >>> grouping = ['G1', 'G1', 'G1', 'G2', 'G2', 'G2']
131
132     Run PERMDISP using 99 permutations to caluculate the p-value:
133
134     >>> from skbio.stats.distance import permdisp
135     >>> import numpy as np
136     >>> #make output deterministic, should not be included during
normal use
137     >>> np.random.seed(0)
138     >>> permdisp(dm, grouping, permutations=99)
Differences (unified diff with -expected +actual):
    @@ -4,5 +4,5 @@
     number of groups                 2
     test statistic             1.03296
    -p-value                       0.35
    +p-value                       0.29
     number of permutations          99
     Name: PERMDISP results, dtype: object

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