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[Advent bug squashing] Bug#1001535: marked as done (busco: (autopkgtest) needs update for python3.10)

Maybe not the best way to fix this, but it is only a test-specific thingy, no big deal.
Please add this as well to calendar.

Regards,
Nilesh


-------- Forwarded Message --------
Subject: Bug#1001535: marked as done (busco: (autopkgtest) needs update for python3.10)
Date: Sun, 12 Dec 2021 16:39:03 +0000
From: Debian Bug Tracking System <owner@bugs.debian.org>
Reply-To: 1001535@bugs.debian.org
To: Nilesh Patra <nilesh@debian.org>

Your message dated Sun, 12 Dec 2021 16:34:17 +0000
with message-id <E1mwRnl-000C81-TC@fasolo.debian.org>
and subject line Bug#1001535: fixed in busco 5.2.2-2
has caused the Debian Bug report #1001535,
regarding busco: (autopkgtest) needs update for python3.10
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.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


--
1001535: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1001535
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Source: busco
Version: 5.2.2-1
Severity: serious
X-Debbugs-CC: debian-ci@lists.debian.org
User: debian-ci@lists.debian.org
Usertags: needs-update
User: debian-python@lists.debian.org
Usertags: python3.10
Control: affects -1 src:python3-defaults

Hi Maintainer

As can be seen [1], the autopkgtests of busco fail when python3.10 is
a supported version.
This currently blocks the migration of python3-defaults to testing [2].

I've copied what I hope is the relevant part of the log below.

Regards
Graham


[1] https://ci.debian.net/packages/b/busco/unstable/amd64/
[2] https://qa.debian.org/excuses.php?package=python3-defaults


======================================================================
ERROR: test_init_tools_eukaryota_metaeuk
(tests.unittests.GenomeAnalysis_unittests.TestConfigManager)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3.10/unittest/mock.py", line 1366, in patched
    with self.decoration_helper(patched,
  File "/usr/lib/python3.10/contextlib.py", line 135, in __enter__
    return next(self.gen)
  File "/usr/lib/python3.10/unittest/mock.py", line 1348, in decoration_helper
    arg = exit_stack.enter_context(patching)
  File "/usr/lib/python3.10/contextlib.py", line 492, in enter_context
    result = _cm_type.__enter__(cm)
  File "/usr/lib/python3.10/unittest/mock.py", line 1528, in __enter__
    raise InvalidSpecError(
unittest.mock.InvalidSpecError: Cannot autospec attr 'config' from
target 'BuscoAnalysis' as it has already been mocked out.
[target=<class 'busco.analysis.BuscoAnalysis.BuscoAnalysis'>,
attr=<Mock id='140560674098768'>]

======================================================================
ERROR: test_init_tools_prokaryota
(tests.unittests.GenomeAnalysis_unittests.TestConfigManager)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3.10/unittest/mock.py", line 1366, in patched
    with self.decoration_helper(patched,
  File "/usr/lib/python3.10/contextlib.py", line 135, in __enter__
    return next(self.gen)
  File "/usr/lib/python3.10/unittest/mock.py", line 1348, in decoration_helper
    arg = exit_stack.enter_context(patching)
  File "/usr/lib/python3.10/contextlib.py", line 492, in enter_context
    result = _cm_type.__enter__(cm)
  File "/usr/lib/python3.10/unittest/mock.py", line 1528, in __enter__
    raise InvalidSpecError(
unittest.mock.InvalidSpecError: Cannot autospec attr 'config' from
target 'BuscoAnalysis' as it has already been mocked out.
[target=<class 'busco.analysis.BuscoAnalysis.BuscoAnalysis'>,
attr=<Mock id='140560674098768'>]

======================================================================
ERROR: test_run_analysis_metaeuk
(tests.unittests.GenomeAnalysis_unittests.TestConfigManager)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3.10/unittest/mock.py", line 1366, in patched
    with self.decoration_helper(patched,
  File "/usr/lib/python3.10/contextlib.py", line 135, in __enter__
    return next(self.gen)
  File "/usr/lib/python3.10/unittest/mock.py", line 1348, in decoration_helper
    arg = exit_stack.enter_context(patching)
  File "/usr/lib/python3.10/contextlib.py", line 492, in enter_context
    result = _cm_type.__enter__(cm)
  File "/usr/lib/python3.10/unittest/mock.py", line 1528, in __enter__
    raise InvalidSpecError(
unittest.mock.InvalidSpecError: Cannot autospec attr 'config' from
target 'BuscoAnalysis' as it has already been mocked out.
[target=<class 'busco.analysis.BuscoAnalysis.BuscoAnalysis'>,
attr=<Mock id='140560674098768'>]

----------------------------------------------------------------------
Ran 99 tests in 2.065s

FAILED (errors=3, skipped=1)
autopkgtest [19:49:27]: test run-unit-test: -----------------------]
autopkgtest [19:49:28]: test run-unit-test:  - - - - - - - - - -
results - - - - - - - - - -
run-unit-test        FAIL non-zero exit status 1

--- End Message ---
--- Begin Message --- 
Source: busco
Source-Version: 5.2.2-2
Done: Nilesh Patra <nilesh@debian.org>

We believe that the bug you reported is fixed in the latest version of
busco, 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 1001535@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Nilesh Patra <nilesh@debian.org> (supplier of updated busco 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 ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Sun, 12 Dec 2021 21:54:24 +0530
Source: busco
Architecture: source
Version: 5.2.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Closes: 1001535
Changes:
 busco (5.2.2-2) unstable; urgency=medium
 .
   * Do not autospec mocked instances (Closes: #1001535)
Checksums-Sha1:
 0566d896eb0af84ead22edfc9e585f82d86d99df 2039 busco_5.2.2-2.dsc
 b191e02fea89ec727c3b1d8b6fb750ed87e842e5 6652 busco_5.2.2-2.debian.tar.xz
 7f6cfd9ee7a63949e006aa0967e1018710dd22ee 6355 busco_5.2.2-2_amd64.buildinfo
Checksums-Sha256:
 df9b245beed17b2ecc8056514380bdaa5d42bfdb9c8b1cbb818081762a81b96e 2039 busco_5.2.2-2.dsc
 628588deb0bee8c6aa0b8b0d6d3d1b55b9610671fac473c8b80469b998200e43 6652 busco_5.2.2-2.debian.tar.xz
 9310353ff7b9841500d1bc385a5086bc9c763c445210b2afd4685becd03bac9c 6355 busco_5.2.2-2_amd64.buildinfo
Files:
 4a7261d91785c7464f58b8dcadd5ea08 2039 science optional busco_5.2.2-2.dsc
 bb2b543ca30d9b7be7ea7a66507d0b80 6652 science optional busco_5.2.2-2.debian.tar.xz
 d00beaae5b383337bd4382e12fef6143 6355 science optional busco_5.2.2-2_amd64.buildinfo

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