f2py use is broken under Python 3.12

[mathomp4]

GEOSpyD recently moved to Python 3.12. Unfortunately, this breaks our use of f2py as the scripts here assume distutils (or at least work with it). My first test shows a failure much like that in numpy/numpy#24874:

Traceback (most recent call last):
  File "/ford1/share/gmao_SIteam/GEOSpyD/24.1.2-0_py3.12/2024-04-11/bin/f2py", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/ford1/share/gmao_SIteam/GEOSpyD/24.1.2-0_py3.12/2024-04-11/lib/python3.12/site-packages/numpy/f2py/f2py2e.py", line 766, in main
    run_compile()
  File "/ford1/share/gmao_SIteam/GEOSpyD/24.1.2-0_py3.12/2024-04-11/lib/python3.12/site-packages/numpy/f2py/f2py2e.py", line 738, in run_compile
    builder.compile()
  File "/ford1/share/gmao_SIteam/GEOSpyD/24.1.2-0_py3.12/2024-04-11/lib/python3.12/site-packages/numpy/f2py/_backends/_meson.py", line 176, in compile
    self.sources = _prepare_sources(self.modulename, self.sources, self.build_dir)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/ford1/share/gmao_SIteam/GEOSpyD/24.1.2-0_py3.12/2024-04-11/lib/python3.12/site-packages/numpy/f2py/_backends/_meson.py", line 188, in _prepare_sources
    shutil.copy(source, bdir)
  File "/ford1/share/gmao_SIteam/GEOSpyD/24.1.2-0_py3.12/2024-04-11/lib/python3.12/shutil.py", line 435, in copy
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/ford1/share/gmao_SIteam/GEOSpyD/24.1.2-0_py3.12/2024-04-11/lib/python3.12/shutil.py", line 240, in copyfile
    raise SameFileError("{!r} and {!r} are the same file".format(src, dst))
shutil.SameFileError: '/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/MAPL_cfio_r4/f2py3-ShaveMantissa_/ShaveMantissa_.pyf' and '/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/MAPL_cfio_r4/f2py3-ShaveMantissa_/ShaveMantissa_.pyf' are the same file

I'm not sure how to fix this yet. I know some flags aren't in the meson style of f2py, see https://numpy.org/devdocs/f2py/buildtools/distutils-to-meson.html

My hope is that I can follow around @HaoZeke on the numpy repo and figure out the fix...

[mathomp4]

First update. It looks like it is the second step that fails. Step 1 (which I think makes the .pyf file) works:

/ford1/share/gmao_SIteam/GEOSpyD/24.1.2-0_py3.12/2024-04-11/bin/f2py \
   -m ShaveMantissa_ \
   -h ShaveMantissa_.pyf \
   --build-dir /home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/MAPL_cfio_r4/f2py3-ShaveMantissa_ \
   --include-paths /home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/MAPL_cfio_r4:/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/lib:/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/include/MAPL_cfio_r4 \
   --overwrite-signature \ 
   /home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/MAPL_cfio/ShaveMantissa_py.F90 \ 
   /home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/MAPL_cfio/ShaveMantissa.c

But then we try the second step (which uses the .pyf file):

/ford1/share/gmao_SIteam/GEOSpyD/24.1.2-0_py3.12/2024-04-11/bin/f2py \
   -m ShaveMantissa_ \
   --build-dir /home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/MAPL_cfio_r4/f2py3-ShaveMantissa_ \
   -c /home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/MAPL_cfio_r4/f2py3-ShaveMantissa_/ShaveMantissa_.pyf 
   --f77flags='' \
   --f90flags='' \
   -I/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/MAPL_cfio_r4 \
   -I/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/lib \
   -I/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/include/MAPL_cfio_r4 
   -L/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/MAPL_cfio_r4 \
   -L/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/lib \
   -L/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/include/MAPL_cfio_r4 \
   /home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/MAPL_cfio/ShaveMantissa_py.F90 \
   /home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/MAPL_cfio/ShaveMantissa.c \
   -L/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/MAPL_cfio_r4 \
   -L/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/lib \
   -L/home/mathomp4/Models/MAPL2-IFX-2024.1/MAPL/build-Debug/include/MAPL_cfio_r4

and it fails.

Now, I see some stupid library duplication in there, but hmm...

[mathomp4]

Wait...I'm not sure we ever use the two-step process in GEOS. We probably inherited that...