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Help with new sphinx version needed (Was: Bug#966983: Most likely fixed in sphinx (2.4.3-5))

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  Help with new sphinx version needed (Was: Bug#966983: Most likely  fixed in sphinx (2.4.3-5)) Andreas Tille <andreas@an3as.eu> - 2020-08-11 14:30 +0200
    Re: Help with new sphinx version needed (Was: Bug#966983: Most  likely fixed in sphinx (2.4.3-5)) Dmitry Shachnev <mitya57@debian.org> - 2020-08-11 15:30 +0200

#12816 — Help with new sphinx version needed (Was: Bug#966983: Most likely fixed in sphinx (2.4.3-5))

Hi,

I need some help with a sphinx error for python-skbio:

On Tue, Aug 11, 2020 at 10:26:10AM +0200, Sebastiaan Couwenberg wrote:
> On 8/11/20 9:41 AM, Andreas Tille wrote:
> > On Tue, Aug 11, 2020 at 07:17:30AM +0200, Sebastiaan Couwenberg wrote:
> >> A smiliar issue was reported for mapproxy in #966979, which was not an
> >> issue in mapproxy but in sphinx, and fixed in sphinx (2.4.3-5).
> >>
> >> I have not tested the build of this package, but the dh_sphinxdoc issue
> >> is mostl likely fixed with sphinx (2.4.3-5) as well.
> > 
> > Thanks for the hint but I get:
> > 
> > reading sources... [  0%] generated/skbio.alignment.AlignmentStructure
> > /build/python-skbio-0.5.6/.pybuild/cpython3_3.8_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.011492611219229537 and the largest is 16.021722090908206.
> >   warn(
> > /build/python-skbio-0.5.6/.pybuild/cpython3_3.8_skbio/build/skbio/stats/ordination/_ordination_results.py:285: UserWarning: Tight layout not applied. The left and right margins cannot be made large enough to accommodate all axes decorations. 
> >   fig.tight_layout()
> > 
> > Extension error:
> > Handler <function _process_docstring at 0x7f951324b1f0> for event 'autodoc-process-docstring' threw an exception (exception: module, class, method, function, traceback, frame, or code object was expected, got method_descriptor)
> > make[1]: *** [debian/rules:20: override_dh_auto_build-indep] Error 2
> 
> That's not the dh_sphinxdoc error this issue was filed for.
> 
> This failure is most likely caused by an extension not being compatible
> with sphinx 3.2.0.
> 
> sphinx was upgraded in unstable from 2.4.3-5 to 3.2.0-1 two days ago.

Any idea how to fix this?

Kind regards

       Andreas.

-- 
http://fam-tille.de

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#12817 — Re: Help with new sphinx version needed (Was: Bug#966983: Most likely fixed in sphinx (2.4.3-5))

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Control: reassign -1 python3-sphinx 3.2.0-1
Control: affects -1 + src:python-skbio

Hi Andreas!

On Tue, Aug 11, 2020 at 02:26:40PM +0200, Andreas Tille wrote:
> I need some help with a sphinx error for python-skbio:
>
> > > Extension error:
> > > Handler <function _process_docstring at 0x7f951324b1f0> for event
> > > 'autodoc-process-docstring' threw an exception (exception: module,
> > > class, method, function, traceback, frame, or code object was expected,
> > > got method_descriptor)
>
> Any idea how to fix this?

This is https://github.com/sphinx-doc/sphinx/issues/8074.

Upstream promises to make a new release within a week. If you don't mind,
I will wait for that and then upload the new release to Debian.

--
Dmitry Shachnev

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