[Debian-med-packaging] Bug#1055692: macs ftbfs with Python 3.12

[Matthias Klose]

Package: src:macs
Version:
Severity: important
Tags: sid trixie
User: debian-python at lists.debian.org
Usertags: python3.12

macs ftbfs with Python 3.12 (note that also cython 3.0.5 was used)

[...]
    dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:310: python3.12 setup.py config

Error compiling Cython file:
------------------------------------------------------------
...
     crick_right = right_sum(crick, search_start, window_size)

     wtd_list = np.zeros( search_end - search_start + 1, dtype="float32")
     i = 0
     for j in range(search_start, search_end+1):
         wtd_list[i] = max((2 * (watson_left * crick_right)**0.5 - 
watson_right - crick_left),0) # minimum score is 0
 
                      ^
------------------------------------------------------------

MACS2/IO/CallPeakUnit.pyx:200:93: complex types are unordered
Compiling MACS2/Prob.pyx because it changed.
Compiling MACS2/IO/Parser.pyx because it changed.
Compiling MACS2/Pileup.pyx because it changed.
Compiling MACS2/PeakModel.pyx because it changed.
Compiling MACS2/PeakDetect.pyx because it changed.
Compiling MACS2/Signal.pyx because it changed.
Compiling MACS2/IO/PeakIO.pyx because it changed.
Compiling MACS2/IO/BedGraphIO.pyx because it changed.
Compiling MACS2/IO/FixWidthTrack.pyx because it changed.
Compiling MACS2/IO/PairedEndTrack.pyx because it changed.
Compiling MACS2/IO/BedGraph.pyx because it changed.
Compiling MACS2/IO/ScoreTrack.pyx because it changed.
Compiling MACS2/IO/CallPeakUnit.pyx because it changed.
[ 1/13] Cythonizing MACS2/IO/BedGraph.pyx
[ 2/13] Cythonizing MACS2/IO/BedGraphIO.pyx
[ 3/13] Cythonizing MACS2/IO/CallPeakUnit.pyx
Traceback (most recent call last):
   File "/<<PKGBUILDDIR>>/setup.py", line 102, in <module>
     main()
   File "/<<PKGBUILDDIR>>/setup.py", line 98, in main
     ext_modules = cythonize( ext_modules ),
                   ^^^^^^^^^^^^^^^^^^^^^^^^
   File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", 
line 1154, in cythonize
     cythonize_one(*args)
   File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", 
line 1321, in cythonize_one
     raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: MACS2/IO/CallPeakUnit.pyx
E: pybuild pybuild:395: configure: plugin distutils failed with: exit 
code=1: python3.12 setup.py config
dh_auto_configure: error: pybuild --configure -i python{version} -p 
"3.12 3.11" returned exit code 13
make: *** [debian/rules:14: binary] Error 25