[Debian-med-packaging] Bug#964610: nibabel: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.8 returned exit code 13

[Nilesh Patra]

On Tue, 21 Jul 2020 15:52:22 +0200 Andreas Tille <tille at debian.org> wrote:
> Control: tags -1 - upstream
> Control: tags -1 pending
>
> The build time test issue was solved thanks to upstream (switched from
> nose to pytest). Unfortunately there are now issues with sphinx to
> build the docs. My dirty workaroung did not worked so I simply added
> ' || true ' behind the sphinx call. This needs to be sorted out before
> uploading.
>
> Moreover autopkgtest should be switched from nose to pytest.
>
> Any help is welcome

I don't see such an error in the build log on my system. Pasting the
relevant part below:

PYTHONPATH=/<<PKGBUILDDIR>> /usr/bin/make -C doc html
SPHINXBUILD=/usr/share/sphinx/scripts/python3/sphinx-build PYTHON=python3
make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
mkdir -p ../build/html ../build/doctrees
python3 tools/build_modref_templates.py nibabel source/reference False
/usr/share/sphinx/scripts/python3/sphinx-build -b html -d
../build/doctrees   source ../build/html
/<<PKGBUILDDIR>>/doc/tools/apigen.py:210: UserWarning: The DICOM readers
are highly experimental, unstable, and only work for Siemens time-series
at the moment
Please use with caution.  We would be grateful for your help in
improving them
  mod = __import__(uri, fromlist=[uri.split('.')[-1]])
*** 3.1.1
Generating docs for nibabel:
  -> nibabel
Generating docs for nibabel._h5py_compat:
  -> nibabel._h5py_compat
WARNING: Empty - nibabel._h5py_compat
Generating docs for nibabel._version:
  -> nibabel._version
Generating docs for nibabel.affines:
  -> nibabel.affines
Generating docs for nibabel.analyze:
  -> nibabel.analyze
Generating docs for nibabel.arrayproxy:
  -> nibabel.arrayproxy
Generating docs for nibabel.arraywriters:
  -> nibabel.arraywriters
Generating docs for nibabel.batteryrunners:
  -> nibabel.batteryrunners
Generating docs for nibabel.benchmarks:
  -> nibabel.benchmarks
WARNING: Empty - nibabel.benchmarks
  -> nibabel.benchmarks.bench_array_to_file
  -> nibabel.benchmarks.bench_arrayproxy_slicing
  -> nibabel.benchmarks.bench_fileslice
  -> nibabel.benchmarks.bench_finite_range
  -> nibabel.benchmarks.bench_load_save
  -> nibabel.benchmarks.bench_streamlines
  -> nibabel.benchmarks.butils
Generating docs for nibabel.brikhead:
  -> nibabel.brikhead
Generating docs for nibabel.casting:
  -> nibabel.casting
Generating docs for nibabel.cifti2:
  -> nibabel.cifti2
WARNING: Empty - nibabel.cifti2
  -> nibabel.cifti2.cifti2
  -> nibabel.cifti2.cifti2_axes
  -> nibabel.cifti2.parse_cifti2
Generating docs for nibabel.cmdline:
  -> nibabel.cmdline
WARNING: Empty - nibabel.cmdline
  -> nibabel.cmdline.conform
  -> nibabel.cmdline.dicomfs
  -> nibabel.cmdline.diff
  -> nibabel.cmdline.ls
  -> nibabel.cmdline.nifti_dx
  -> nibabel.cmdline.parrec2nii
  -> nibabel.cmdline.tck2trk
  -> nibabel.cmdline.trk2tck
  -> nibabel.cmdline.utils
Generating docs for nibabel.data:
  -> nibabel.data
Generating docs for nibabel.dataobj_images:
  -> nibabel.dataobj_images
Generating docs for nibabel.deprecated:
  -> nibabel.deprecated
Generating docs for nibabel.deprecator:
  -> nibabel.deprecator
Generating docs for nibabel.dft:
  -> nibabel.dft
Generating docs for nibabel.ecat:
  -> nibabel.ecat
Generating docs for nibabel.environment:
  -> nibabel.environment
Generating docs for nibabel.eulerangles:
  -> nibabel.eulerangles
Generating docs for nibabel.filebasedimages:
  -> nibabel.filebasedimages
Generating docs for nibabel.fileholders:
  -> nibabel.fileholders
Generating docs for nibabel.filename_parser:
  -> nibabel.filename_parser
Generating docs for nibabel.fileslice:
  -> nibabel.fileslice
Generating docs for nibabel.fileutils:
  -> nibabel.fileutils
Generating docs for nibabel.freesurfer:
  -> nibabel.freesurfer
WARNING: Empty - nibabel.freesurfer
  -> nibabel.freesurfer.io
  -> nibabel.freesurfer.mghformat
Generating docs for nibabel.funcs:
  -> nibabel.funcs
Generating docs for nibabel.gifti:
  -> nibabel.gifti
WARNING: Empty - nibabel.gifti
  -> nibabel.gifti.gifti
  -> nibabel.gifti.giftiio
  -> nibabel.gifti.parse_gifti_fast
  -> nibabel.gifti.util
WARNING: Empty - nibabel.gifti.util
Generating docs for nibabel.imageclasses:
  -> nibabel.imageclasses
Generating docs for nibabel.imageglobals:
  -> nibabel.imageglobals
Generating docs for nibabel.keywordonly:
  -> nibabel.keywordonly
Generating docs for nibabel.loadsave:
  -> nibabel.loadsave
Generating docs for nibabel.minc1:
  -> nibabel.minc1
Generating docs for nibabel.minc2:
  -> nibabel.minc2
Generating docs for nibabel.mriutils:
  -> nibabel.mriutils
Generating docs for nibabel.nicom:
  -> nibabel.nicom
WARNING: Empty - nibabel.nicom
  -> nibabel.nicom.csareader
  -> nibabel.nicom.dicomreaders
  -> nibabel.nicom.dicomwrappers
  -> nibabel.nicom.dwiparams
  -> nibabel.nicom.structreader
  -> nibabel.nicom.utils
Generating docs for nibabel.nifti1:
  -> nibabel.nifti1
Generating docs for nibabel.nifti2:
  -> nibabel.nifti2
Generating docs for nibabel.onetime:
  -> nibabel.onetime
Generating docs for nibabel.openers:
  -> nibabel.openers
Generating docs for nibabel.optpkg:
  -> nibabel.optpkg
Generating docs for nibabel.orientations:
  -> nibabel.orientations
Generating docs for nibabel.parrec:
  -> nibabel.parrec
Generating docs for nibabel.processing:
  -> nibabel.processing
Generating docs for nibabel.pydicom_compat:
  -> nibabel.pydicom_compat
Generating docs for nibabel.quaternions:
  -> nibabel.quaternions
Generating docs for nibabel.rstutils:
  -> nibabel.rstutils
Generating docs for nibabel.spaces:
  -> nibabel.spaces
Generating docs for nibabel.spatialimages:
  -> nibabel.spatialimages
Generating docs for nibabel.spm2analyze:
  -> nibabel.spm2analyze
Generating docs for nibabel.spm99analyze:
  -> nibabel.spm99analyze
Generating docs for nibabel.streamlines:
  -> nibabel.streamlines
  -> nibabel.streamlines.array_sequence
  -> nibabel.streamlines.header
  -> nibabel.streamlines.tck
  -> nibabel.streamlines.tractogram
  -> nibabel.streamlines.tractogram_file
  -> nibabel.streamlines.trk
  -> nibabel.streamlines.utils
Generating docs for nibabel.tmpdirs:
  -> nibabel.tmpdirs
Generating docs for nibabel.trackvis:
  -> nibabel.trackvis
Generating docs for nibabel.tripwire:
  -> nibabel.tripwire
Generating docs for nibabel.viewers:
  -> nibabel.viewers
Generating docs for nibabel.volumeutils:
  -> nibabel.volumeutils
Generating docs for nibabel.wrapstruct:
  -> nibabel.wrapstruct
Generating docs for nibabel.xmlutils:
  -> nibabel.xmlutils
60 files written
Running Sphinx v2.4.3
Build API docs...done.
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 115 source files that are out of date
updating environment: [new config] 115 added, 0 changed, 0 removed
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/usr/lib/python3.8/importlib/__init__.py:127: UserWarning: The DICOM
readers are highly experimental, unstable, and only work for Siemens
time-series at the moment
Please use with caution.  We would be grateful for your help in
improving them
  return _bootstrap._gcd_import(name[level:], package, level)
/<<PKGBUILDDIR>>/nibabel/cifti2/__init__.py:docstring of
nibabel.cifti2.rst:5: WARNING: autosummary: stub file not found
'nibabel.cifti2.cifti2'. Check your autosummary_generate setting.
/<<PKGBUILDDIR>>/nibabel/cifti2/__init__.py:docstring of
nibabel.cifti2.rst:5: WARNING: autosummary: stub file not found
'nibabel.cifti2.cifti2_axes'. Check your autosummary_generate setting.
/<<PKGBUILDDIR>>/nibabel/gifti/__init__.py:docstring of
nibabel.gifti.rst:5: WARNING: autosummary: stub file not found
'nibabel.gifti.giftiio'. Check your autosummary_generate setting.
/<<PKGBUILDDIR>>/nibabel/gifti/__init__.py:docstring of
nibabel.gifti.rst:5: WARNING: autosummary: stub file not found
'nibabel.gifti.gifti'. Check your autosummary_generate setting.
/<<PKGBUILDDIR>>/nibabel/nicom/__init__.py:docstring of
nibabel.nicom.rst:5: WARNING: autosummary: stub file not found
'nibabel.nicom.csareader'. Check your autosummary_generate setting.
/<<PKGBUILDDIR>>/nibabel/nicom/__init__.py:docstring of
nibabel.nicom.rst:5: WARNING: autosummary: stub file not found
'nibabel.nicom.dicomreaders'. Check your autosummary_generate setting.
/<<PKGBUILDDIR>>/nibabel/nicom/__init__.py:docstring of
nibabel.nicom.rst:5: WARNING: autosummary: stub file not found
'nibabel.nicom.dicomwrappers'. Check your autosummary_generate setting.
/<<PKGBUILDDIR>>/nibabel/nicom/__init__.py:docstring of
nibabel.nicom.rst:5: WARNING: autosummary: stub file not found
'nibabel.nicom.dwiparams'. Check your autosummary_generate setting.
/<<PKGBUILDDIR>>/nibabel/nicom/__init__.py:docstring of
nibabel.nicom.rst:5: WARNING: autosummary: stub file not found
'nibabel.nicom.structreader'. Check your autosummary_generate setting.
/<<PKGBUILDDIR>>/nibabel/processing.py:docstring of
nibabel.processing.conform:7: WARNING: Unexpected indentation.
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build succeeded, 18 warnings.

The HTML pages are in ../build/html.

Build finished. The HTML pages are in ../build/html.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
# but remove jquery copy (later on link to Debian's version)
rm build/html/_static/jquery.js
# objects inventory is of no use for the package
rm build/html/objects.inv
# also doc source files only consume space
rm -r build/html/_sources


Is this a false postive for you (As happened a few times earlier)?

Kind Regards,
Nilesh

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