[Debian-med-packaging] Bug#920545: python-intervaltree breaks python-intervaltree-bio autopkgtest

[Paul Gevers]

Source: python-intervaltree, python-intervaltree-bio
Control: found -1 python-intervaltree/3.0.2-1
Control: found -1 python-intervaltree-bio/1.0.1-2
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: important
User: debian-ci at lists.debian.org
Usertags: breaks needs-update

Dear maintainers,

With a recent upload of python-intervaltree the autopkgtest of
python-intervaltree-bio fails in testing when that autopkgtest is run
with the binary packages of python-intervaltree from unstable. It passes
when run with only packages from testing. In tabular form:
                        pass            fail
python-intervaltree     from testing    3.0.2-1
python-intervaltree-bio from testing    1.0.1-2
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
python-intervaltree 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? If needed,
please change the bug's severity.

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

Paul

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

https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-intervaltree-bio/1785537/log.gz

=================================== FAILURES
===================================
________________________________ test_knownGene
________________________________

    def test_knownGene():
        # To speed up testing, we'll download the file and reuse the
downloaded copy
        knownGene_url =
'http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/knownGene.txt.gz'
        # Mirror. Slightly faster and more stable, I believe:
        knownGene_url =
'http://kt.era.ee/distribute/pyintervaltree/knownGene.txt.gz'

        # To speed up testing, we'll download the file and reuse the
downloaded copy
        knownGene_file, headers = urlretrieve(knownGene_url)

        knownGene_localurl = 'file:///%s' % os.path.abspath(knownGene_file)
        knownGene =
GenomeIntervalTree.from_table(url=knownGene_localurl, decompress=True) #
Py3 downloads .gz files to local files with names not ending with .gz
        assert len(knownGene) == 82960
>       result = knownGene[b'chr1'].search(100000, 138529)
E       AttributeError: 'IntervalTree' object has no attribute 'search'

.pc/offline-test-data.patch/tests/genomeintervaltree_test.py:28:
AttributeError
 test_knownGene[file:///tmp/autopkgtest-lxc.z3ra1nek/downtmp/build.Szw/src/debian/data/]

base_url =
'file:///tmp/autopkgtest-lxc.z3ra1nek/downtmp/build.Szw/src/debian/data/'

    def test_knownGene(base_url):
        # To speed up testing, we'll download the file and reuse the
downloaded copy
        knownGene_url = base_url + 'knownGene.txt.gz'

        # To speed up testing, we'll download the file and reuse the
downloaded copy
        knownGene_file, headers = urlretrieve(knownGene_url)

        knownGene_localurl = 'file:///%s' % os.path.abspath(knownGene_file)
        knownGene =
GenomeIntervalTree.from_table(url=knownGene_localurl, decompress=True) #
Py3 downloads .gz files to local files with names not ending with .gz
        assert len(knownGene) == 82960
>       result = knownGene[b'chr1'].search(100000, 138529)
E       AttributeError: 'IntervalTree' object has no attribute 'search'

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