[Debichem-devel] Bug#980661: python-griddataformats: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13

[Lucas Nussbaum]

Source: python-griddataformats
Version: 0.5.0-3
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20210120 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
>  debian/rules build
> dh build --with python3 --buildsystem=pybuild
>    dh_update_autotools_config -O--buildsystem=pybuild
>    dh_autoreconf -O--buildsystem=pybuild
>    dh_auto_configure -O--buildsystem=pybuild
> I: pybuild base:232: python3.9 setup.py config 
> running config
>    dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:232: /usr/bin/python3 setup.py build 
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData
> copying gridData/core.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData
> copying gridData/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData
> copying gridData/OpenDX.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData
> copying gridData/_version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData
> copying gridData/gOpenMol.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData
> copying gridData/CCP4.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/tests
> copying gridData/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/tests
> copying gridData/tests/test_grid.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/tests
> copying gridData/tests/test_gOpenMol.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/tests
> copying gridData/tests/test_dx.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/tests
> copying gridData/tests/test_ccp4.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/tests
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/tests/datafiles
> copying gridData/tests/datafiles/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/tests/datafiles
> copying gridData/tests/datafiles/test.dx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/tests/datafiles
> copying gridData/tests/datafiles/test.ccp4 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/tests/datafiles
> copying gridData/tests/datafiles/1jzv.ccp4 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/tests/datafiles
> copying gridData/tests/datafiles/nAChR_M2_water.plt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/tests/datafiles
> UPDATING /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/_version.py
> set /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build/gridData/_version.py to '0.5.0'
>    dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:232: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build; python3.9 -m pytest 
> ============================= test session starts ==============================
> platform linux -- Python 3.9.1+, pytest-6.0.2, py-1.10.0, pluggy-0.13.0
> rootdir: /<<PKGBUILDDIR>>
> collected 87 items
> 
> gridData/tests/test_ccp4.py ..................................           [ 39%]
> gridData/tests/test_dx.py ...............                                [ 56%]
> gridData/tests/test_gOpenMol.py .                                        [ 57%]
> gridData/tests/test_grid.py .............s.......F......xxx......        [100%]
> 
> =================================== FAILURES ===================================
> ________________________ TestGrid.test_resample_factor _________________________
> 
> self = <gridData.tests.test_grid.TestGrid object at 0x7f9db042f400>
> data = {'delta': array([1., 1., 1.]), 'grid': <<class 'gridData.core.Grid'> with (3, 3, 3) bins>, 'griddata': array([[[ 1,  2...    [16, 17, 18]],
> 
>        [[19, 20, 21],
>         [22, 23, 24],
>         [25, 26, 27]]]), 'origin': array([0., 0., 0.])}
> 
>     def test_resample_factor(self, data):
>         pytest.importorskip('scipy')
>     
>         g = data['grid'].resample_factor(2)
>         assert_array_equal(g.delta, np.ones(3) * .5)
>         assert_array_equal(g.grid.shape, np.ones(3) * 6)
>         # check that the edges are the same
> >       assert_array_almost_equal(g.grid[::5, ::5, ::5],
>                                   data['grid'].grid[::2, ::2, ::2])
> E       AssertionError: 
> E       Arrays are not almost equal to 6 decimals
> E       
> E       Mismatched elements: 8 / 8 (100%)
> E       Max absolute difference: 5.12890625
> E       Max relative difference: 5.12890625
> E        x: array([[[-4.128906, -1.339844],
> E               [ 4.238281,  7.027344]],
> E       ...
> E        y: array([[[ 1,  3],
> E               [ 7,  9]],
> E       ...
> 
> gridData/tests/test_grid.py:171: AssertionError
> =========================== short test summary info ============================
> FAILED gridData/tests/test_grid.py::TestGrid::test_resample_factor - Assertio...
> ============== 1 failed, 82 passed, 1 skipped, 3 xfailed in 0.58s ==============
> E: pybuild pybuild:353: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_gridData/build; python3.9 -m pytest 
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13

The full build log is available from:
   http://qa-logs.debian.net/2021/01/20/python-griddataformats_0.5.0-3_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with me
so that we can identify if something relevant changed in the meantime.

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.