[Debian-med-packaging] Bug#1000864: python-skbio: FTBFS with Python 3.10

[Graham Inggs]

Source: python-skbio
Version: 0.5.6-5
Severity: serious
Tags: ftbfs patch
User: debian-python at lists.debian.org
Usertags: python3.10

Hi Maintainer

Now that scikit-learn has at least built on amd64 [1], we can now see
a new failure in python-skbio [2].  I have copied part of the log
below.

This is due to .c files in the upstream tarball being generated by an
old version of cython.  The solution is to add cython3 as a
build-dependency and regenerate the .c files at build time.

I've attached a patch that does this.

Regards
Graham


[1] https://buildd.debian.org/status/package.php?p=scikit-learn
[2] https://buildd.debian.org/status/package.php?p=python-skbio&suite=sid


skbio/alignment/_ssw_wrapper.c: In function
‘__pyx_tp_dealloc_5skbio_9alignment_12_ssw_wrapper_AlignmentStructure’:
skbio/alignment/_ssw_wrapper.c:10363:5: error: lvalue required as
increment operand
10363 |     ++Py_REFCNT(o);
      |     ^~
skbio/alignment/_ssw_wrapper.c:10365:5: error: lvalue required as
decrement operand
10365 |     --Py_REFCNT(o);
      |     ^~
skbio/alignment/_ssw_wrapper.c: In function
‘__pyx_tp_dealloc_5skbio_9alignment_12_ssw_wrapper_StripedSmithWaterman’:
skbio/alignment/_ssw_wrapper.c:10570:5: error: lvalue required as
increment operand
10570 |     ++Py_REFCNT(o);
      |     ^~
skbio/alignment/_ssw_wrapper.c:10572:5: error: lvalue required as
decrement operand
10572 |     --Py_REFCNT(o);
      |     ^~
skbio/alignment/_ssw_wrapper.c: In function ‘__Pyx_ParseOptionalKeywords’:
skbio/alignment/_ssw_wrapper.c:12453:21: warning:
‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
12453 |                     (PyUnicode_GET_SIZE(**name) !=
PyUnicode_GET_SIZE(key)) ? 1 :
      |                     ^
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