[Debian-astro-maintainers] Bug#1081693: FTBFS with Python 3.13

[Stefano Rivera]

Source: pybdsf
Version: 1.11.1-1
Severity: normal
User: debian-python at lists.debian.org
Usertags: python3.13

This package failed build from source when test-built against a version of
python3-defaults that includes 3.13 as a supported version.

To reproduce this issue, build against python3-defaults (python3-all-dev etc.)
from Debian experimental.

What's new in Python 3.13:
https://docs.python.org/3.13/whatsnew/3.13.html

Log snippet:

[136/139] Building CXX object CMakeFiles/_cbdsm.dir/src/c++/stat.cc.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from /<<PKGBUILDDIR>>/src/c++/boost_python.h:14,
                 from /<<PKGBUILDDIR>>/src/c++/stat.cc:12:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
/<<PKGBUILDDIR>>/src/c++/stat.cc: In instantiation of ‘std::pair<double, double> _stat(pyndarray, boost::python::api::object, double, double) [with T = double; pyndarray = boost::python::numpy::ndarray]’:
/<<PKGBUILDDIR>>/src/c++/stat.cc:226:19:   required from ‘boost::python::api::object _bstat(pyndarray, boost::python::api::object, double) [with T = double; pyndarray = boost::python::numpy::ndarray]’
  226 |     res = _stat<T>(arr, mask, mean.back(), kappa*dev.back());
      |           ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/c++/stat.cc:257:30:   required from here
  257 |     return _bstat<npy_double>(arr, mask, kappa);
      |            ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/c++/stat.cc:204:1: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  204 | _stat(pyndarray arr, object mask, double _mean, double _threshold)
      | ^~~~~
[137/139] Building CXX object CMakeFiles/_cbdsm.dir/src/c++/num_util/num_util.cpp.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from /<<PKGBUILDDIR>>/src/c++/num_util/num_util.h:14,
                 from /<<PKGBUILDDIR>>/src/c++/num_util/num_util.cpp:8:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
/<<PKGBUILDDIR>>/src/c++/num_util/num_util.cpp: In function ‘boost::python::numpy::dtype num_util::type2dtype(char)’:
/<<PKGBUILDDIR>>/src/c++/num_util/num_util.cpp:435:54: warning: control reaches end of non-void function [-Wreturn-type]
  435 |       std::cout << "Invalid character code!" << std::endl;
      |                                                      ^~~~
[138/139] Linking CXX shared module _cbdsm.cpython-313-aarch64-linux-gnu.so
[138/139] Install the project...
-- Install configuration: "Release"
CMake Error at cmake_install.cmake:46 (file):
  file INSTALL cannot find
  "/<<PKGBUILDDIR>>/_skbuild/linux-aarch64-3.13/cmake-build/_pytesselate.cpython-313-aarch64-linux-gnu.so":
  No such file or directory.


FAILED: CMakeFiles/install.util 
cd /<<PKGBUILDDIR>>/_skbuild/linux-aarch64-3.13/cmake-build && /usr/bin/cmake -P cmake_install.cmake
ninja: build stopped: subcommand failed.
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/skbuild/setuptools_wrap.py", line 668, in setup
    cmkr.make(make_args, install_target=cmake_install_target, env=env)
    ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/skbuild/cmaker.py", line 696, in make
    self.make_impl(clargs=clargs, config=config, source_dir=source_dir, install_target=install_target, env=env)
    ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/skbuild/cmaker.py", line 741, in make_impl
    raise SKBuildError(msg)

An error occurred while building with CMake.
  Command:
    /usr/bin/cmake --build . --target install --config Release --
  Install target:
    install
  Source directory:
    /<<PKGBUILDDIR>>
  Working directory:
    /<<PKGBUILDDIR>>/_skbuild/linux-aarch64-3.13/cmake-build
Please check the install target is valid and see CMake's output for more information.


ERROR Backend subprocess exited when trying to invoke build_wheel
E: pybuild pybuild:389: build: plugin pyproject failed with: exit code=1: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13  

If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/712745/

This bug has been filed at "normal" severity, as we haven't started the
transition to add 3.13 as a supported version, yet. This will be raised to RC
as soon as that happens, hopefully well before trixie.

Thanks,

Stefano