Python 3.13 Issues/Support

[mathomp4]

@mrkwjc A query: Have you built/installed ffnet with Python 3.13 yet? I'm trying to today and it's not working. I get this output:

> /ford1/share/gmao_SIteam/GEOSpyD/24.11.3-0/2025-02-21/envs/py3.13/bin/pip install git+https://github.com/mrkwjc/ffnet
Collecting git+https://github.com/mrkwjc/ffnet
  Cloning https://github.com/mrkwjc/ffnet to ./tmp-for-ffnet/pip-req-build-6aerriss
  Running command git clone --filter=blob:none --quiet https://github.com/mrkwjc/ffnet /ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-req-build-6aerriss
  Resolved https://github.com/mrkwjc/ffnet to commit 69b848438e6e9aed7415b7c6e3c54d1f16f445f9
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy in /ford1/share/gmao_SIteam/GEOSpyD/24.11.3-0/2025-02-21/envs/py3.13/lib/python3.13/site-packages (from ffnet==0.8.6) (2.1.3)
Requirement already satisfied: meson in /ford1/share/gmao_SIteam/GEOSpyD/24.11.3-0/2025-02-21/envs/py3.13/lib/python3.13/site-packages (from ffnet==0.8.6) (1.7.0)
Collecting meson-python (from ffnet==0.8.6)
  Using cached meson_python-0.17.1-py3-none-any.whl.metadata (4.1 kB)
Requirement already satisfied: packaging>=19.0 in /ford1/share/gmao_SIteam/GEOSpyD/24.11.3-0/2025-02-21/envs/py3.13/lib/python3.13/site-packages (from meson-python->ffnet==0.8.6) (24.2)
Collecting pyproject-metadata>=0.7.1 (from meson-python->ffnet==0.8.6)
  Using cached pyproject_metadata-0.9.0-py3-none-any.whl.metadata (6.9 kB)
Using cached meson_python-0.17.1-py3-none-any.whl (27 kB)
Using cached pyproject_metadata-0.9.0-py3-none-any.whl (18 kB)
Building wheels for collected packages: ffnet
  Building wheel for ffnet (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Building wheel for ffnet (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [92 lines of output]
      Traceback (most recent call last):
        File "/ford1/share/gmao_SIteam/GEOSpyD/24.11.3-0/2025-02-21/envs/py3.13/bin/f2py", line 7, in <module>
          from numpy.f2py.f2py2e import main
      ModuleNotFoundError: No module named 'numpy'
      Traceback (most recent call last):
        File "/ford1/share/gmao_SIteam/GEOSpyD/24.11.3-0/2025-02-21/envs/py3.13/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
          main()
          ~~~~^^
        File "/ford1/share/gmao_SIteam/GEOSpyD/24.11.3-0/2025-02-21/envs/py3.13/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
                                   ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
        File "/ford1/share/gmao_SIteam/GEOSpyD/24.11.3-0/2025-02-21/envs/py3.13/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
          return _build_backend().build_wheel(
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
              wheel_directory, config_settings, metadata_directory
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          )
          ^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 438, in build_wheel
          return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 426, in _build
          return self._build_with_temp_dir(
                 ~~~~~~~~~~~~~~~~~~~~~~~~~^
              cmd,
              ^^^^
          ...<3 lines>...
              self._arbitrary_args(config_settings),
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          )
          ^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 407, in _build_with_temp_dir
          self.run_setup()
          ~~~~~~~~~~~~~~^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 522, in run_setup
          super().run_setup(setup_script=setup_script)
          ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 320, in run_setup
          exec(code, locals())
          ~~~~^^^^^^^^^^^^^^^^
        File "<string>", line 62, in <module>
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/_distutils/core.py", line 186, in setup
          return run_commands(dist)
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
          dist.run_commands()
          ~~~~~~~~~~~~~~~~~^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 983, in run_commands
          self.run_command(cmd)
          ~~~~~~~~~~~~~~~~^^^^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
          super().run_command(command)
          ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
          cmd_obj.run()
          ~~~~~~~~~~~^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/command/bdist_wheel.py", line 379, in run
          self.run_command("build")
          ~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/_distutils/cmd.py", line 339, in run_command
          self.distribution.run_command(command)
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
          super().run_command(command)
          ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
          cmd_obj.run()
          ~~~~~~~~~~~^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/_distutils/command/build.py", line 136, in run
          self.run_command(cmd_name)
          ~~~~~~~~~~~~~~~~^^^^^^^^^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/_distutils/cmd.py", line 339, in run_command
          self.distribution.run_command(command)
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
          super().run_command(command)
          ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
          cmd_obj.run()
          ~~~~~~~~~~~^^
        File "<string>", line 51, in run
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/_distutils/cmd.py", line 339, in run_command
          self.distribution.run_command(command)
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
          super().run_command(command)
          ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/ford1/share/gmao_SIteam/GEOSpyD-Github/tmp-for-ffnet/pip-build-env-4ss_6muj/overlay/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
          cmd_obj.run()
          ~~~~~~~~~~~^^
        File "<string>", line 40, in run
        File "/ford1/share/gmao_SIteam/GEOSpyD/24.11.3-0/2025-02-21/envs/py3.13/lib/python3.13/subprocess.py", line 421, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['f2py', '-m', '_ffnet', '-c', 'ffnet.f']' returned non-zero exit status 1.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for ffnet
Failed to build ffnet
ERROR: Failed to build installable wheels for some pyproject.toml based projects (ffnet)

Now, go to the bottom and it seems to be saying that:

f2py -m _ffnet -c ffnet.f

is failing. So, I try by hand:

> /ford1/share/gmao_SIteam/GEOSpyD/24.11.3-0/2025-02-21/envs/py3.13/bin/f2py -m _ffnet -c ffnet.f
Cannot use distutils backend with Python>=3.12, using meson backend instead.
Using meson backend
Will pass --lower to f2py
See https://numpy.org/doc/stable/f2py/buildtools/meson.html
Reading fortran codes...
	Reading file 'ffnet.f' (format:fix,strict)
Post-processing...
...
Warning: Unused dummy argument ‘ffn’ at (1) [-Wunused-dummy-argument]
../ffnet.f:754:22:

  754 |       function dmapa(f, a, b, c, d)
      |                      1
Warning: Unused dummy argument ‘f’ at (1) [-Wunused-dummy-argument]
[6/6] Linking target _ffnet.cpython-313-x86_64-linux-gnu.so
> /ford1/share/gmao_SIteam/GEOSpyD/24.11.3-0/2025-02-21/envs/py3.13/bin/python -c 'import _ffnet'
> echo $?
0

So, it builds. There's also a weird thing about numpy at the top but:

> /ford1/share/gmao_SIteam/GEOSpyD/24.11.3-0/2025-02-21/envs/py3.13/bin/python -c 'from numpy.f2py.f2py2e import main'
> echo $?
0

Have you seen this issue?

[mathomp4]

Note: Python 3.12 seems happy. The changes to Python 3.13 for subprocess are fairly minor. I'm going to try the subprocess._USE_POSIX_SPAWN knob they mention to see if that helps. I dunno.

Nope. Did nothing...or I used it wrong. But hard to screw up!

[mrkwjc]

Strange, it compiles, installs and works on my setup. Possibly you need ninja? Here's my build log, maybe this will guide you somehow:

$ pipi --verbose https://github.com/mrkwjc/ffnet/archive/refs/heads/master.zip
Using pip 25.0 from /usr/lib/python3.13/site-packages/pip (python 3.13)
Collecting https://github.com/mrkwjc/ffnet/archive/refs/heads/master.zip
  Using cached https://github.com/mrkwjc/ffnet/archive/refs/heads/master.zip
  Running command python setup.py egg_info
  [02/22/25 00:34:37] ERROR    listing git files failed - pretending     git.py:26
                               there aren't any
  Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /usr/lib/python3.13/site-packages (from ffnet==0.8.6) (2.2.3)
Requirement already satisfied: meson in /usr/lib/python3.13/site-packages (from ffnet==0.8.6) (1.7.0)
Requirement already satisfied: meson-python in /usr/lib/python3.13/site-packages (from ffnet==0.8.6) (0.17.1)
Requirement already satisfied: packaging>=19.0 in /usr/lib/python3.13/site-packages (from meson-python->ffnet==0.8.6) (24.2)
Requirement already satisfied: pyproject-metadata>=0.7.1 in /usr/lib/python3.13/site-packages (from meson-python->ffnet==0.8.6) (0.9.0)
Building wheels for collected packages: ffnet
  Running command python setup.py bdist_wheel
  The Meson build system
  Version: 1.7.0
  Source dir: /tmp/tmpfogltcs6
  Build dir: /tmp/tmpfogltcs6/bbdir
  Build type: native build
  Project name: _ffnet
  Project version: 0.1
  Fortran compiler for the host machine: gfortran (gcc 14.2.1 "GNU Fortran (GCC) 14.2.1 20250128")
  Fortran linker for the host machine: gfortran ld.bfd 2.43.1
  C compiler for the host machine: cc (gcc 14.2.1 "cc (GCC) 14.2.1 20250128")
  C linker for the host machine: cc ld.bfd 2.43.1
  Host machine cpu family: x86_64
  Host machine cpu: x86_64
  Program /usr/bin/python found: YES (/usr/bin/python)
  Found pkg-config: YES (/usr/bin/pkg-config) 2.3.0
  Run-time dependency python found: YES 3.13
  Library quadmath found: YES
  Build targets in project: 1

  Found ninja-1.12.1 at /usr/bin/ninja

  Generating targets:   0%|          | 0/1 eta ?


  Writing build.ninja:   0%|          | 0/33 eta ?

  ninja: Entering directory `/tmp/tmpfogltcs6/bbdir'
  [1/6] Scanning modules
  [2/6] Compiling Fortran object _ffnet.cpython-313-x86_64-linux-gnu.so.p/_ffnet-f2pywrappers.f.o
  [3/6] Compiling C object _ffnet.cpython-313-x86_64-linux-gnu.so.p/a95a963c47a87f2f07a2fe9e68a2455e7ba7798c_.._.._f2py_src_fortranobject.c.o
  [4/6] Compiling Fortran object _ffnet.cpython-313-x86_64-linux-gnu.so.p/ffnet.f.o
  f951: Warning: Nonconforming tab character in column 1 of line 232 [-Wtabs]
  f951: Warning: Nonconforming tab character in column 1 of line 244 [-Wtabs]
  f951: Warning: Nonconforming tab character in column 1 of line 266 [-Wtabs]
  f951: Warning: Nonconforming tab character in column 1 of line 474 [-Wtabs]
  f951: Warning: Nonconforming tab character in column 1 of line 487 [-Wtabs]
  f951: Warning: Nonconforming tab character in column 1 of line 509 [-Wtabs]
  f951: Warning: Nonconforming tab character in column 1 of line 623 [-Wtabs]
  f951: Warning: Nonconforming tab character in column 1 of line 663 [-Wtabs]
  f951: Warning: Nonconforming tab character in column 1 of line 814 [-Wtabs]
  ../ffnet.f:285:43:

    285 |       subroutine func(x, conec, n, bconecno, bn, units, u, inno, i,
        |                                           1
  Warning: Unused dummy argument ‘bconecno’ at (1) [-Wunused-dummy-argument]
  ../ffnet.f:385:32:

    385 |       subroutine pikaiaff(x, ffn, conec, n, units, u, inno, i, outno, o,
        |                                1
  Warning: Unused dummy argument ‘ffn’ at (1) [-Wunused-dummy-argument]
  ../ffnet.f:754:22:

    754 |       function dmapa(f, a, b, c, d)
        |                      1
  Warning: Unused dummy argument ‘f’ at (1) [-Wunused-dummy-argument]
  [5/6] Compiling C object _ffnet.cpython-313-x86_64-linux-gnu.so.p/_ffnetmodule.c.o
  [6/6] Linking target _ffnet.cpython-313-x86_64-linux-gnu.so
  INFO: autodetecting backend as ninja
  INFO: calculating backend command to run: /usr/bin/ninja -C /tmp/tmpfogltcs6/bbdir
  Cannot use distutils backend with Python>=3.12, using meson backend instead.
  Using meson backend
  Will pass --lower to f2py
  See https://numpy.org/doc/stable/f2py/buildtools/meson.html
  Reading fortran codes...
        Reading file 'ffnet.f' (format:fix,strict)
  Post-processing...
        Block: _ffnet
                        Block: prop
                        Block: sqerror
                        Block: grad
                        Block: recall
                        Block: diff
                        Block: func
                        Block: func2
                        Block: pikaiaff
                        Block: normcall
                        Block: normdiff
                        Block: normcall2
                        Block: normdiff2
                        Block: momentum
                        Block: rprop
                        Block: setin
                        Block: getout
                        Block: mapa
                        Block: dmapa
                        Block: vmapa
                        Block: mmapa
  Applying post-processing hooks...
    character_backward_compatibility_hook
  Post-processing (stage 2)...
  Building modules...
      Building module "_ffnet"...
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "prop"...
            units = prop(x,conec,units,[n,u])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "sqerror"...
            sqerr = sqerror(x,conec,units,inno,outno,input,targ,[n,u,i,o,p])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "grad"...
            xprime = grad(x,conec,bconecno,units,inno,outno,input,targ,[n,bn,u,i,o,p])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "recall"...
            output = recall(x,conec,units,inno,outno,input,[n,u,i,o])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "diff"...
            deriv = diff(x,conec,dconecno,dconecmk,units,inno,outno,input,[n,dn,u,i,o])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "func"...
            sqerr = func(x,conec,bconecno,units,inno,outno,input,targ,[n,bn,u,i,o,p])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "func2"...
            sqerr,xprime = func2(x,conec,bconecno,units,inno,outno,input,targ,[n,bn,u,i,o,p])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "pikaiaff"...
            isqerr = pikaiaff(x,ffn,conec,units,inno,outno,input,targ,bound1,bound2,[n,u,i,o,p])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "normcall"...
            output = normcall(x,conec,units,inno,outno,eni,deo,input,[n,u,i,o])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "normdiff"...
            deriv = normdiff(x,conec,dconecno,dconecmk,units,inno,outno,eni,ded,input,[n,dn,u,i,o])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "normcall2"...
            output = normcall2(x,conec,units,inno,outno,eni,deo,input,[n,u,i,o,p])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "normdiff2"...
            deriv = normdiff2(x,conec,dconecno,dconecmk,units,inno,outno,eni,ded,input,[n,dn,u,i,o,p])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "momentum"...
            x = momentum(x,conec,bconecno,units,inno,outno,input,targ,eta,moment,maxiter,[n,bn,u,i,o,p])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "rprop"...
            x,xmi = rprop(x,conec,bconecno,units,inno,outno,input,targ,a,b,mimin,mimax,xmi,maxiter,[n,bn,u,i,o,p])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "setin"...
            units = setin(input,inno,eni,units,[i,u])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "getout"...
            output = getout(units,outno,deo,[u,o])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
                Creating wrapper for Fortran function "mapa"("mapa")...
          Constructing wrapper function "mapa"...
            mapa = mapa(f,a,b,c,d)
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
                Creating wrapper for Fortran function "dmapa"("dmapa")...
          Constructing wrapper function "dmapa"...
            dmapa = dmapa(f,a,b,c,d)
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "vmapa"...
            vout = vmapa(vin,a,b,c,d,[n])
      Generating possibly empty wrappers"
      Maybe empty "_ffnet-f2pywrappers.f"
          Constructing wrapper function "mmapa"...
            mmout = mmapa(mmin,a,b,c,d,[m,n])
      Wrote C/API module "_ffnet" to file "./_ffnetmodule.c"
      Fortran 77 wrappers are saved to "./_ffnet-f2pywrappers.f"
  rmbadname1: Replacing "new" with "new_bn".
  rmbadname1: Replacing "new" with "new_bn".
  rmbadname1: Replacing "rank" with "rank_bn".
  rmbadname1: Replacing "rank" with "rank_bn".
  append_needs: unknown need 'int'
  append_needs: unknown need 'float'
  append_needs: unknown need 'int'
  append_needs: unknown need 'float'
  append_needs: unknown need 'int'
  append_needs: unknown need 'float'
  The Meson build system
  Version: 1.7.0
  Source dir: /tmp/tmp8lblo4z2
  Build dir: /tmp/tmp8lblo4z2/bbdir
  Build type: native build
  Project name: _pikaia
  Project version: 0.1
  Fortran compiler for the host machine: gfortran (gcc 14.2.1 "GNU Fortran (GCC) 14.2.1 20250128")
  Fortran linker for the host machine: gfortran ld.bfd 2.43.1
  C compiler for the host machine: cc (gcc 14.2.1 "cc (GCC) 14.2.1 20250128")
  C linker for the host machine: cc ld.bfd 2.43.1
  Host machine cpu family: x86_64
  Host machine cpu: x86_64
  Program /usr/bin/python found: YES (/usr/bin/python)
  Found pkg-config: YES (/usr/bin/pkg-config) 2.3.0
  Run-time dependency python found: YES 3.13
  Library quadmath found: YES
  Build targets in project: 1

  Found ninja-1.12.1 at /usr/bin/ninja

  Generating targets:   0%|          | 0/1 eta ?


  Writing build.ninja:   0%|          | 0/33 eta ?

  ninja: Entering directory `/tmp/tmp8lblo4z2/bbdir'
  [1/6] Scanning modules
  [2/6] Compiling Fortran object _pikaia.cpython-313-x86_64-linux-gnu.so.p/_pikaia-f2pywrappers.f.o
  [3/6] Compiling C object _pikaia.cpython-313-x86_64-linux-gnu.so.p/a95a963c47a87f2f07a2fe9e68a2455e7ba7798c_.._.._f2py_src_fortranobject.c.o
  [4/6] Compiling Fortran object _pikaia.cpython-313-x86_64-linux-gnu.so.p/pikaia.f.o
  f951: Warning: Nonconforming tab character in column 1 of line 941 [-Wtabs]
  f951: Warning: Nonconforming tab character in column 1 of line 942 [-Wtabs]
  ../pikaia.f:147:27:

    147 |       parameter (SCALE=1./M,EPS=1.2e-7,RNMX=1.-EPS)
        |                           1
  Warning: Change of value in conversion from ‘INTEGER(4)’ to ‘REAL(4)’ at (1) [-Wconversion]
  ../pikaia.f:594:11:

    594 |       np = ctrl(1)
        |           1
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1) [-Wconversion]
  ../pikaia.f:595:13:

    595 |       ngen = ctrl(2)
        |             1
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1) [-Wconversion]
  ../pikaia.f:596:11:

    596 |       nd = ctrl(3)
        |           1
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1) [-Wconversion]
  ../pikaia.f:598:13:

    598 |       imut = ctrl(5)
        |             1
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1) [-Wconversion]
  ../pikaia.f:603:13:

    603 |       irep = ctrl(10)
        |             1
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1) [-Wconversion]
  ../pikaia.f:604:15:

    604 |       ielite = ctrl(11)
        |               1
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1) [-Wconversion]
  ../pikaia.f:605:13:

    605 |       ivrb = ctrl(12)
        |             1
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1) [-Wconversion]
  ../pikaia.f:450:35:

    450 |       integer        gn1(NMAX*DMAX), gn2(NMAX*DMAX)
        |                                   1
  Warning: Array ‘gn1’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising]
  ../pikaia.f:450:51:

    450 |       integer        gn1(NMAX*DMAX), gn2(NMAX*DMAX)
        |                                                   1
  Warning: Array ‘gn2’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising]
  ../pikaia.f:448:67:

    448 |       real           ph(NMAX,2), oldph(NMAX,PMAX), newph(NMAX,PMAX)
        |                                                                   1
  Warning: Array ‘newph’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising]
  ../pikaia.f:448:49:

    448 |       real           ph(NMAX,2), oldph(NMAX,PMAX), newph(NMAX,PMAX)
        |                                                 1
  Warning: Array ‘oldph’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising]
  ../pikaia.f:448:31:

    448 |       real           ph(NMAX,2), oldph(NMAX,PMAX), newph(NMAX,PMAX)
        |                               1
  Warning: Array ‘ph’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising]
  ../pikaia.f:918:43:

    918 |       integer        i,j,k,l,ist,inc,loc,kk
        |                                           1
  Warning: Unused variable ‘kk’ declared at (1) [-Wunused-variable]
  ../pikaia.f:1033:9:

   1033 |       if(rdif.le.rdiflo)then
        |         ^
  Warning: ‘rdif’ may be used uninitialized [-Wmaybe-uninitialized]
  ../pikaia.f:1017:25:

   1017 |       real           rdif, rdiflo, rdifhi, delta
        |                         ^
  note: ‘rdif’ was declared here
  [5/6] Compiling C object _pikaia.cpython-313-x86_64-linux-gnu.so.p/_pikaiamodule.c.o
  [6/6] Linking target _pikaia.cpython-313-x86_64-linux-gnu.so
  INFO: autodetecting backend as ninja
  INFO: calculating backend command to run: /usr/bin/ninja -C /tmp/tmp8lblo4z2/bbdir
  Cannot use distutils backend with Python>=3.12, using meson backend instead.
  Using meson backend
  Will pass --lower to f2py
  See https://numpy.org/doc/stable/f2py/buildtools/meson.html
  Reading fortran codes...
        Reading file 'pikaia.f' (format:fix,strict)
  Line #14 in pikaia.f:"      external twod "
        analyzeline: ignoring program arguments
  Line #56 in pikaia.f:"      parameter (pi=3.1415926536,sigma2=0.15,nn=9) "
        param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  Line #56 in pikaia.f:"      parameter (pi=3.1415926536,sigma2=0.15,nn=9) "
        param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  Line #56 in pikaia.f:"      parameter (pi=3.1415926536,sigma2=0.15,nn=9) "
        param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  Line #149 in pikaia.f:"      parameter (SCALE=1./M,EPS=1.2e-7,RNMX=1.-EPS) "
        param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  Line #149 in pikaia.f:"      parameter (SCALE=1./M,EPS=1.2e-7,RNMX=1.-EPS) "
        param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  Line #149 in pikaia.f:"      parameter (SCALE=1./M,EPS=1.2e-7,RNMX=1.-EPS) "
        param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  Line #1019 in pikaia.f:"      parameter      (rdiflo=0.05, rdifhi=0.25, delta=1.5) "
        param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  Line #1019 in pikaia.f:"      parameter      (rdiflo=0.05, rdifhi=0.25, delta=1.5) "
        param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  Line #1019 in pikaia.f:"      parameter      (rdiflo=0.05, rdifhi=0.25, delta=1.5) "
        param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  Post-processing...
        Block: _pikaia
                        Block: xpkaia
                        Block: twod
  In: :_pikaia:pikaia.f:twod
  param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  In: :_pikaia:pikaia.f:twod
  param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
                        Block: urand
                        Block: rninit
                        Block: ran0
  In: :_pikaia:pikaia.f:ran0
  param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  In: :_pikaia:pikaia.f:ran0
  param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  In: :_pikaia:pikaia.f:ran0
  param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
                        Block: rqsort
                        Block: pikaia
                                        Block: ff
                        Block: setctl
                        Block: report
                        Block: encode
                        Block: decode
                        Block: cross
                        Block: mutate
                        Block: adjmut
  In: :_pikaia:pikaia.f:adjmut
  param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  In: :_pikaia:pikaia.f:adjmut
  param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
  In: :_pikaia:pikaia.f:adjmut
  param_eval: got "eval() arg 1 must be a string, bytes or code object" on 4
                        Block: select
                        Block: rnkpop
                        Block: genrep
                        Block: stdrep
                                        Block: ff
                        Block: newpop
                                        Block: ff
  Applying post-processing hooks...
    character_backward_compatibility_hook
  Post-processing (stage 2)...
  Building modules...
      Constructing call-back function "cb_ff_in_pikaia__user__routines"
        def ff(x,[n]): return f
      Constructing call-back function "cb_ff_in_stdrep__user__routines"
        def ff(x,[n]): return f
      Constructing call-back function "cb_ff_in_newpop__user__routines"
        def ff(x,[n]): return f
      Building module "_pikaia"...
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
                Creating wrapper for Fortran function "twod"("twod")...
          Constructing wrapper function "twod"...
            twod = twod(x,[n])
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
                Creating wrapper for Fortran function "urand"("urand")...
          Constructing wrapper function "urand"...
            urand = urand()
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "rninit"...
            rninit(seed)
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
                Creating wrapper for Fortran function "ran0"("ran0")...
          Constructing wrapper function "ran0"...
            ran0 = ran0(seed)
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "rqsort"...
            p = rqsort(a,[n])
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "pikaia"...
            x,f,status = pikaia(ff,n,ctrl,[ff_extra_args])
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "setctl"...
            setctl(ctrl,n,np,ngen,nd,pcross,pmutmn,pmutmx,pmut,imut,fdif,irep,ielite,ivrb,status)
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "report"...
            report(ivrb,n,nd,oldph,fitns,ifit,pmut,ig,nnew,[ndim,np])
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "encode"...
            encode(nd,ph,gn,[n])
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "decode"...
            decode(n,nd,gn,ph)
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "cross"...
            cross(n,nd,pcross,gn1,gn2)
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "mutate"...
            mutate(n,nd,pmut,gn,imut)
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "adjmut"...
            adjmut(n,oldph,fitns,ifit,pmutmn,pmutmx,pmut,imut,[ndim,np])
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "select"...
            select(jfit,fdif,idad,[np])
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "rnkpop"...
            rnkpop(arrin,indx,rank_bn,[n])
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "genrep"...
            genrep(n,ip,ph,newph,[ndim,np])
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "stdrep"...
            stdrep(ff,n,irep,ielite,ph,oldph,fitns,ifit,jfit,nnew,[ndim,np,ff_extra_args])
      Generating possibly empty wrappers"
      Maybe empty "_pikaia-f2pywrappers.f"
          Constructing wrapper function "newpop"...
            newpop(ff,ielite,n,oldph,newph,ifit,jfit,fitns,nnew,[ndim,np,ff_extra_args])
                Constructing COMMON block support for "rnseed"...
                  iseed
      Wrote C/API module "_pikaia" to file "./_pikaiamodule.c"
      Fortran 77 wrappers are saved to "./_pikaia-f2pywrappers.f"
  /usr/lib/python3.13/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
  !!

          ********************************************************************************
          Please avoid running ``setup.py`` directly.
          Instead, use pypa/build, pypa/installer or other
          standards-based tools.

          See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
          ********************************************************************************

  !!
    self.initialize_options()
  [02/22/25 00:34:41] ERROR    listing git files failed - pretending     git.py:26
                               there aren't any
  Building wheel for ffnet (setup.py) ... done
  Created wheel for ffnet: filename=ffnet-0.8.6-cp313-cp313-linux_x86_64.whl size=158462 sha256=468ed33d3a4365f0f92af6865d812b0b6ad5b8ed56bb38a147d276a22eb8ca82
  Stored in directory: /tmp/pip-ephem-wheel-cache-su9j_sr0/wheels/26/3c/09/e1f8d65d17c9e5caad1ad05269be70650fb76336b122bad2c4
Successfully built ffnet
Installing collected packages: ffnet
Successfully installed ffnet-0.8.6

[mathomp4]

Huh. I definitely have ninja on the systems in question. Now I was using gfortran 12 not 14, but I can't imagine that makes a difference.

I'll try with the zip file on Monday.

[mrkwjc]

Here's the difference. You have:

Building wheels for collected packages: ffnet
  Building wheel for ffnet (pyproject.toml) ... error

and I have:

Building wheels for collected packages: ffnet
  Running command python setup.py bdist_wheel

From where this difference comes, I do not know. ffnet does not even have pyproject.toml file.

BTW: my full install command is this:

$ pip install --user --break-system-packages --verbose git+https://github.com/mrkwjc/ffnet

This works both with git repo and zip.

[mathomp4]

Huh. I didn't know pip even supported setup.py anymore.

I'm going to look at adding a pyproject.toml file and see if that works...

[mathomp4]

Ohhh. Can I ask, what is your pip version? I am running pip 25 and I see bits in their Release Notes about deprecating the setup.py installation

[mathomp4]

Update: Yeah, I bet that's it. I can get it to install with:

pip install setuptools wheel meson
pip install --no-use-pep517 git+https://github.com/mrkwjc/ffnet

I'm going to consult my local python experts on if there is a way to "autoconvert" setup.py to pyproject.toml

ETA: In checking with my experts, he found that this:

  Running command python setup.py bdist_wheel

might be deprecated in Python itself, see: https://packaging.python.org/en/latest/guides/modernize-setup-py-project/#should-setup-py-be-deleted

But, this might be a pip is changing how it works rather than Python. I see:

• Deprecate call to setup.py install when building a wheel failed for source distributions without pyproject.toml pypa/pip#8368
• Deprecate call to setup.py install when wheel is absent for source distributions without pyproject.toml pypa/pip#8559
• Raise a warning when pip falls back to the "legacy" direct install code pypa/pip#8102

For now at least I think I have a workaround.

[mrkwjc]

Help in converting to pyproject.toml would be appreciated :). However, I doubt an automatic conversion is possible because of the f2py compilation. Currently, this compilation is done via custom commands in setup.py. Earlier this was done with distutils. Neverthless, pyproject.toml is a must now.

[mathomp4]

Help in converting to pyproject.toml would be appreciated :). However, I doubt an automatic conversion is possible because of the f2py compilation. Currently, this compilation is done via custom commands in setup.py. Earlier this was done with distutils. Neverthless, pyproject.toml is a must now.

Yeah, my Python experts were pretty much a "only in basic cases" would automatic work. I tried using hatch new --init as someone online said that can do it, but as you say, your setup.py is complex enough it just gave up.

Weirdly, though, it seems like setup.py isn't deprecated, so maybe a simple change in it would make pip happy in the short-term until it can be converted? But there is no explicit "bdist_wheel" in that file! (Python packaging is still magic to me!)

[mrkwjc]

It seems pip needs now setuptools to be installed externally. Maybe pyproject.toml can be as simple as the one suggested here: https://forums.fast.ai/t/legacy-editable-install/113503/4 (just instruct to install setuptools and then use it).