[Debichem-devel] Bug#1019515: gemmi: autopkgtest regression on arm64 i386 s390x and ppc64el: numerical deltas

[Paul Gevers]

Source: gemmi
Version: 0.5.6+ds-2
Severity: serious
User: debian-ci at lists.debian.org
Usertags: regression

Dear maintainer(s),

With a recent upload of gemmi the autopkgtest of gemmi fails in testing 
when that autopkgtest is run with the binary packages of gemmi from 
unstable. It passes when run with only packages from testing. In tabular 
form:

                        pass            fail
gemmi                  from testing    0.5.6+ds-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 to testing [1]. Can 
you please investigate the situation and fix it?

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=gemmi

https://ci.debian.net/data/autopkgtest/testing/arm64/g/gemmi/25899714/log.gz

=================================== FAILURES 
===================================
__________________________ TestProg.test_sfcalc_1pfe 
___________________________

self = <test_prog.TestProg testMethod=test_sfcalc_1pfe>

         @unittest.skipIf(sys.platform == 'win32', 'with MSVC it differs 
slightly')
         def test_sfcalc_1pfe(self):
>           self.do('''\
     $ gemmi sfcalc --dmin=9 --rate=4 --blur=60 --rcut=1e-7 --test -v 
tests/1pfe.cif.gz
     [...]
     RMSE=0.0010414  0.0001639%  max|dF|=0.003530  R=0.000% 
<dPhi>=8.067e-06
     ''')  # noqa: E501

tests/test_prog.py:89: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_prog.py:36: in do
     self.assertEqual(expected_lines, output_lines)
E   AssertionError: Lists differ: ['RMSE=0.0010414  0.0001639% 
max|dF|=0.003530  R=0.000%  <dPhi>=8.067e-06'] != ['RMSE=0.0010127 
0.0001594%  max|dF|=0.003041  R=0.000%  <dPhi>=7.880e-06']
E   E   First differing element 0:
E   'RMSE=0.0010414  0.0001639%  max|dF|=0.003530  R=0.000% 
<dPhi>=8.067e-06'
E   'RMSE=0.0010127  0.0001594%  max|dF|=0.003041  R=0.000% 
<dPhi>=7.880e-06'
E   E   - ['RMSE=0.0010414  0.0001639%  max|dF|=0.003530  R=0.000% 
<dPhi>=8.067e-06']
E   ?              - ^        ^^                 --                     ^ --
E   E   + ['RMSE=0.0010127  0.0001594%  max|dF|=0.003041  R=0.000% 
<dPhi>=7.880e-06']
E   ?               ^^        ^ +                 ++                   ++ ^
__________________________ TestProg.test_sfcalc_5wkd 
___________________________

self = <test_prog.TestProg testMethod=test_sfcalc_5wkd>

         @unittest.skipIf(sys.platform == 'win32', 'with MSVC it differs 
slightly')
         def test_sfcalc_5wkd(self):
>           self.do('''\
     $ gemmi sfcalc --blur=12 --dmin=2.5 --rate=2.5 --rcut=1e-7 --test 
-v tests/5wkd.pdb
     [...]
     RMSE=3.3342e-05  4.703e-05%  max|dF|=0.0001706  R=0.000% 
<dPhi>=4.718e-06
     ''')  # noqa: E501

tests/test_prog.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_prog.py:36: in do
     self.assertEqual(expected_lines, output_lines)
E   AssertionError: Lists differ: ['RMSE=3.3342e-05  4.703e-05% 
max|dF|=0.0001706  R=0.000%  <dPhi>=4.718e-06'] != ['RMSE=3.2830e-05 
4.630e-05%  max|dF|=0.0001628  R=0.000%  <dPhi>=4.665e-06']
E   E   First differing element 0:
E   'RMSE=3.3342e-05  4.703e-05%  max|dF|=0.0001706  R=0.000% 
<dPhi>=4.718e-06'
E   'RMSE=3.2830e-05  4.630e-05%  max|dF|=0.0001628  R=0.000% 
<dPhi>=4.665e-06'
E   E   - ['RMSE=3.3342e-05  4.703e-05%  max|dF|=0.0001706  R=0.000% 
<dPhi>=4.718e-06']
E   ?           ^^^        ^ -                     -- 
   ^^^
E   E   + ['RMSE=3.2830e-05  4.630e-05%  max|dF|=0.0001628  R=0.000% 
<dPhi>=4.665e-06']
E   ?          ++ ^        ^^                       ++ 
   ^^^
=========================== short test summary info 
============================
FAILED tests/test_prog.py::TestProg::test_sfcalc_1pfe - AssertionError: 
Lists...
FAILED tests/test_prog.py::TestProg::test_sfcalc_5wkd - AssertionError: 
Lists...
======================== 2 failed, 169 passed in 1.42s 
=========================
autopkgtest [17:13:32]: test command1

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