Your message dated Thu, 10 Dec 2020 21:48:43 +0000
with message-id <[email protected]>
and subject line Bug#977067: fixed in cwltool 3.0.20200807132242-3
has caused the Debian Bug report #977067,
regarding igdiscover FTBFS with pytest 6
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
977067: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=977067
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: igdiscover
Version: 0.11-3
Severity: important
User: [email protected]
Usertags: pytest-v6
Hi,
igdiscover FTBFS with pytest 6 in experimental.
The error log below has more details.
> I: pybuild base:232: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_igdiscover/build; python3.9 -m pytest
> tests
> ============================= test session starts
> ==============================
> platform linux -- Python 3.9.1, pytest-6.0.2, py-1.9.0, pluggy-0.13.0
> rootdir: /<<PKGBUILDDIR>>, configfile: setup.cfg
> collected 36 items
>
> tests/test_cluster.py .. [
> 5%]
> tests/test_commands.py ..... [
> 19%]
> tests/test_merger.py ............ [
> 52%]
> tests/test_parse.py . [
> 55%]
> tests/test_species.py FFF [
> 63%]
> tests/test_trie.py ..... [
> 77%]
> tests/test_utils.py F.......
> [100%]
>
> =================================== FAILURES
> ===================================
> __________________________ test_cdr3_detection_heavy
> ___________________________
>
> def test_cdr3_detection_heavy():
> heavy = """
> ARRLHSGSYILFDY
> CAGGTGACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGTATGGGTGTGGGCTGGATCCGTCAGCCCTCACGGAAGACCCTGGAGTGGCTTGCACACATTTATTGGAATGATGATAAATACTACAGCACATCGCTGAAGAGCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTTCTAACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACGGAGACTTCATAGTGGGAGCTACATTCTCTTTGACTACTGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCAGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGA
>
> ARIKWLRSPGYGYFDF
> CAGGTGACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAGACCCACACAGACCCTCACTCTGACCTGCACCTTCTCTGGGTTCTCAATCAGCACCTCTGGAACAGGTGTGGGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAATGGCTTGCAAGCATTTATTGGACTGATGCTAAATACTATAGCACATCGCAGAAGAGCAGGCTCACCATCTCCAAGGACACCTCCAGAAACCAGGTGATTCTAACAATGACCAACATGGAGCCTGTGGACATAGCCACATATTTCTGTGCACGGATAAAGTGGCTGCGGTCCCCAGGCTATGGATACTTCGATTTCTGGGGCCCTGGCACCCCAATCACCATCTCCTCAGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGA
>
> ARHGIAAAGTHNWFDP
> TCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGGATTACTGTGCGAGACATGGGATAGCAGCAGCTGGTACCCACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGCAGGTTGTT
> """
>> assert_cdr3_detection('VH', heavy)
>
> tests/test_species.py:30:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> _
>
> chain = 'VH'
> s = '\n\tARRLHSGSYILFDY
> CAGGTGACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGG...ACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGCAGGTTGTT\n\t'
>
> def assert_cdr3_detection(chain, s):
> for amino_acids, sequence in split(s):
> for offset in range(3):
> target = sequence[offset:]
> match = find_cdr3(target, chain)
>> assert match is not None
> E assert None is not None
>
> tests/test_species.py:18: AssertionError
> __________________________ test_cdr3_detection_kappa
> ___________________________
>
> def test_cdr3_detection_kappa():
> kappa = """
> QQYDSSPRT
> TTCAGTGGCAGTGGAGCAGGGACAGATTTCACTCTCACCATCAGCAGTCTGGAACCTGAGGATGTCGCAACTTACTACTGTCAGCAGTATGATAGCAGCCCCCGGACGTTCGGCGCTGGGACCAAGCTGGAAATCAAACGGAGTGTGCAGAAGCCAACTATCTCCCTCTTCCCTCCATCATCTGAGGAGG
>
> QQYSSYPYT
> GAGCTGGCCTCGGGAGTCCCAGCTCGCTTCAGTGGGAGTGGGTCAGGGACTTCTTTCTCTCTCACAATCAGCAACGTGGAGGCTGAAGATGTTGCAACCTATTACTGTCAGCAGTATAGCAGTTATCCGTACACGTTCGGCGCAGGGACCAAGCTGGAAATCAAACGGAGTGTGCAGAAGCCAACTATCTCCCTCTTCCCTCCATCATCTGAGGAGG
>
> LQYDSSPYT
> ATTCTCACCATCAGCAGCCTGCAGCCTGAAGACTTTGCAACTTACTACTGTCTACAGTATGATAGTTCCCCGTACACGTTCGGCGCAGGGACCAAGCTGGAAATCAAACGGAGTGTGCAGAAGCCAACTATCTCCCTCTTCCCTCCATCATCTGAGGAGG
>
> FQYYSGRLT
> ACAGACTTCACTCTCACCATCAGCAGCCTGCAGCCTGAGGACATTGCAGTTTATTACTGTTTCCAGTATTACAGCGGGAGACTCACGTTCGGAGGAGGGACCCGCTTGGAAATCAAACGGAGTGTGCAGAAGCCAACTATCTCCCTCTTCCCTCCATCATCTGAGGAGG
> """
>> assert_cdr3_detection('VK', kappa)
>
> tests/test_species.py:43:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> _
>
> chain = 'VK'
> s = '\nQQYDSSPRT
> TTCAGTGGCAGTGGAGCAGGGACAGATTTCACTCTCACCATCAGCAGTCTGGAACCTGAGGATGTCGCAACTTACTACTGTCAGCAGTATGATAGCAGCCCCCGG...ACTGTTTCCAGTATTACAGCGGGAGACTCACGTTCGGAGGAGGGACCCGCTTGGAAATCAAACGGAGTGTGCAGAAGCCAACTATCTCCCTCTTCCCTCCATCATCTGAGGAGG\n\t'
>
> def assert_cdr3_detection(chain, s):
> for amino_acids, sequence in split(s):
> for offset in range(3):
> target = sequence[offset:]
> match = find_cdr3(target, chain)
>> assert match is not None
> E assert None is not None
>
> tests/test_species.py:18: AssertionError
> __________________________ test_cdr3_detection_lambda
> __________________________
>
> def test_cdr3_detection_lambda():
> lambda_ = """
> LTYHGNSGTFV
> GGATCCAAAAACCCCTCAGCCAATGCAGGAATTTTGCTCATCTCTGAACTCCAGAATGAGGATGAGGCTGACTATTACTGTCTGACATATCATGGTAATAGTGGTACTTTTGTATTCGGTGGAGGAACCAAGCTGACCGTCCTAGGTCAGCCCAAGTCTGCCCCCACAGTCAGCCTGTTCC
>
> QLWDANSTV
> ATGGCCACACTGACCATCACTGGCGCCCAGGGTGAGGACGAGGCCGACTATTGCTGTCAGTTGTGGGATGCTAACAGTACTGTGTTCGGTGGAGGAACCACGCTGACCGTCCTAGGTCAGCCCAAGTCTGCCCCCACAGTCAGCCTGTTCCCGCCCTCCTC
>
> GVGYSGGYV
> GATCGCTACTTAACCATCTCCAACATCCAGCCTGAAGACGAGGCTGACTATTTCTGTGGTGTGGGTTATAGCGGTGGTTATGTATTCGGTGGAGGAACCAAGTTGACCGTCCTAGGTCAGCCCAAGTCTGCTCCCACAGTCAGCCTGTTCCCGCCCTCCTC
> """
>> assert_cdr3_detection('VL', lambda_)
>
> tests/test_species.py:54:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> _
>
> chain = 'VL'
> s = '\nLTYHGNSGTFV
> GGATCCAAAAACCCCTCAGCCAATGCAGGAATTTTGCTCATCTCTGAACTCCAGAATGAGGATGAGGCTGACTATTACTGTCTGACATATCATGGTAATAGTG...CTATTTCTGTGGTGTGGGTTATAGCGGTGGTTATGTATTCGGTGGAGGAACCAAGTTGACCGTCCTAGGTCAGCCCAAGTCTGCTCCCACAGTCAGCCTGTTCCCGCCCTCCTC\n\t'
>
> def assert_cdr3_detection(chain, s):
> for amino_acids, sequence in split(s):
> for offset in range(3):
> target = sequence[offset:]
> match = find_cdr3(target, chain)
>> assert match is not None
> E assert None is not None
>
> tests/test_species.py:18: AssertionError
> ________________________________ test_has_stop
> _________________________________
>
> def test_has_stop():
>> assert has_stop('TAA')
> E AssertionError: assert False
> E + where False = has_stop('TAA')
>
> tests/test_utils.py:11: AssertionError
> =========================== short test summary info
> ============================
> FAILED tests/test_species.py::test_cdr3_detection_heavy - assert None is not
> ...
> FAILED tests/test_species.py::test_cdr3_detection_kappa - assert None is not
> ...
> FAILED tests/test_species.py::test_cdr3_detection_lambda - assert None is
> not...
> FAILED tests/test_utils.py::test_has_stop - AssertionError: assert False
> ========================= 4 failed, 32 passed in 2.21s
> =========================
> E: pybuild pybuild:353: test: plugin distutils failed with: exit code=1: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_igdiscover/build; python3.9 -m pytest
> tests
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9
> returned exit code 13
> make: *** [debian/rules:8: build] Error 25
> dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: cwltool
Source-Version: 3.0.20200807132242-3
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
cwltool, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated cwltool package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Thu, 10 Dec 2020 22:19:00 +0100
Source: cwltool
Architecture: source
Version: 3.0.20200807132242-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 977067
Changes:
cwltool (3.0.20200807132242-3) unstable; urgency=medium
.
* Team upload.
* Abbreviated option names are no longer allowed in pytest 6
Closes: #977067
* Standards-Version: 4.5.1
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