subprocess called process error with meson 1.8.2 and python 3.13.5

[durack1]

Describe the bug
I have been trying to get some f2py code working that I last had working with python 3.10.11 and numpy 1.23.5. I have hit the error below, with a new environment that is built with python 3.13.5 and numpy 2.2.6, this new environment was built adding meson=1.8.2 as an added dependency.

To Reproduce
This is the full example of the issue:

(cmor3110xcd091) machine user$ f2py -c --help-fcompiler
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...
Post-processing...
Applying post-processing hooks...
  character_backward_compatibility_hook
Post-processing (stage 2)...
Building modules...
The Meson build system
Version: 1.8.2
Source dir: /private/var/folders/7d/rkhc67xs5w70chjmlrr6pv440017ch/T/tmpu9xikcek
Build dir: /private/var/folders/7d/rkhc67xs5w70chjmlrr6pv440017ch/T/tmpu9xikcek/bbdir
Build type: native build

meson.build:40:0: ERROR: Expecting rbracket got comma.
,
^
For a block that started at 39,21
                     [
                     ^

A full log can be found at /private/var/folders/7d/rkhc67xs5w70chjmlrr6pv440017ch/T/tmpu9xikcek/bbdir/meson-logs/meson-log.txt
Traceback (most recent call last):
  File "~/miniforge3/envs/cmor3110xcd091/bin/f2py", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "~/miniforge3/envs/cmor3110xcd091/lib/python3.13/site-packages/numpy/f2py/f2py2e.py", line 781, in main
    run_compile()
    ~~~~~~~~~~~^^
  File "~/miniforge3/envs/cmor3110xcd091/lib/python3.13/site-packages/numpy/f2py/f2py2e.py", line 753, in run_compile
    builder.compile()
    ~~~~~~~~~~~~~~~^^
  File "~/miniforge3/envs/cmor3110xcd091/lib/python3.13/site-packages/numpy/f2py/_backends/_meson.py", line 192, in compile
    self.run_meson(self.build_dir)
    ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
  File "~/miniforge3/envs/cmor3110xcd091/lib/python3.13/site-packages/numpy/f2py/_backends/_meson.py", line 185, in run_meson
    self._run_subprocess_command(setup_command, build_dir)
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "~/miniforge3/envs/cmor3110xcd091/lib/python3.13/site-packages/numpy/f2py/_backends/_meson.py", line 181, in _run_subprocess_command
    subprocess.run(command, cwd=cwd, check=True)
    ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "~/miniforge3/envs/cmor3110xcd091/lib/python3.13/subprocess.py", line 577, in run
    raise CalledProcessError(retcode, process.args,
                             output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['meson', 'setup', 'bbdir']' returned non-zero exit status 1.

Expected behavior
I had expected this simple query to work without an issue

system parameters

• Is this a cross build or just a plain native build (for the same computer)?
  This is a conda-forge built library, installed using mamba/Miniforge3.

• what operating system (e.g. MacOS Catalina, Windows 10, CentOS 8.0, Ubuntu 18.04, etc.)
  macOS 15.5; 'uname': uname_result(system='Darwin', node='ml-9953350', release='24.5.0', version='Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:49 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T6000', machine='arm64')}

• what Python version are you using e.g. 3.8.0
  3.13.5

• what meson --version
1.8.2

• what ninja --version if it's a Ninja build
  $ ninja --version
1.13.1

[eli-schwartz]

Meson's role in this starts and ends with:

The Meson build system
Version: 1.8.2
Source dir: /private/var/folders/7d/rkhc67xs5w70chjmlrr6pv440017ch/T/tmpu9xikcek
Build dir: /private/var/folders/7d/rkhc67xs5w70chjmlrr6pv440017ch/T/tmpu9xikcek/bbdir
Build type: native build

meson.build:40:0: ERROR: Expecting rbracket got comma.
,
^
For a block that started at 39,21
                     [
                     ^

A full log can be found at /private/var/folders/7d/rkhc67xs5w70chjmlrr6pv440017ch/T/tmpu9xikcek/bbdir/meson-logs/meson-log.txt

It indicates that f2py is producing a malformed build file.

/cc @rgommers for numpy stuff -- but also closing because this doesn't seem to be a meson bug.

[durack1]

@eli-schwartz thanks for the quick reply. I have already opened numpy/numpy#29422 - but that doesn't capture the f2py issue you've noted below (it's just a missing meson dependency for python=>3.12. As I am a total meson noob, not sure if this requires a new numpy issue to be opened? I suppose your @rgommers tag might give us that answer - more than happy to raise an issue, I'd just need some guidance to specify actionable details

[eli-schwartz]

I'm expecting @rgommers to have more details, or at least good questions about your environment, for that. :)

He works on both numpy and meson and should know a lot more than I do about how f2py constructs its generated build file.

[rgommers]

A separate issue on the numpy repo would be good, yes. A malformed meson.build file being generated is different from a dependency handling issue, so I'd prefer to not mix them.

Could you please add a more complete reproducer to the new issue @durack1? I don't think it was f2py -c --help-fcompiler, which prints some help output and then exits, but rather you were feeding a source file to f2py -c?

[durack1]

Could you please add a more complete reproducer to the new issue @durack1? I don't think it was f2py -c --help-fcompiler, which prints some help output and then exits, but rather you were feeding a source file to f2py -c?

Sure, see below. These are for two different environments, with differing versions of python installed.

python 3.11.13

(cmor3110xcd091py311) machine:~ user$ python
Python 3.11.13 | packaged by conda-forge | (main, Jun  4 2025, 14:52:34) [Clang 18.1.8 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> print(np.__version__)
2.2.6
>>> 
(cmor3110xcd091py311) machine:~ user$ f2py -c --help-fcompiler
~/miniforge3/envs/cmor3110xcd091py311/lib/python3.11/site-packages/numpy/f2py/f2py2e.py:734: VisibleDeprecationWarning: 
distutils has been deprecated since NumPy 1.26.x
Use the Meson backend instead, or generate wrappers without -c and use a custom build script
  builder = build_backend(
Fortran compilers found:
Compilers available for this platform, but not found:
  --fcompiler=absoft  Absoft Corp Fortran Compiler
  --fcompiler=g95     G95 Fortran Compiler
  --fcompiler=gnu     GNU Fortran 77 compiler
  --fcompiler=gnu95   GNU Fortran 95 compiler
  --fcompiler=ibm     IBM XL Fortran Compiler
  --fcompiler=intel   Intel Fortran Compiler for 32-bit apps
  --fcompiler=nag     NAGWare Fortran 95 Compiler
  --fcompiler=nagfor  NAG Fortran Compiler
  --fcompiler=pg      Portland Group Fortran Compiler
Compilers not available on this platform:
  --fcompiler=arm       Arm Compiler
  --fcompiler=compaq    Compaq Fortran Compiler
  --fcompiler=flang     Portland Group Fortran LLVM Compiler
  --fcompiler=fujitsu   Fujitsu Fortran Compiler
  --fcompiler=hpux      HP Fortran 90 Compiler
  --fcompiler=intele    Intel Fortran Compiler for Itanium apps
  --fcompiler=intelem   Intel Fortran Compiler for 64-bit apps
  --fcompiler=intelev   Intel Visual Fortran Compiler for Itanium apps
  --fcompiler=intelv    Intel Visual Fortran Compiler for 32-bit apps
  --fcompiler=intelvem  Intel Visual Fortran Compiler for 64-bit apps
  --fcompiler=lahey     Lahey/Fujitsu Fortran 95 Compiler
  --fcompiler=mips      MIPSpro Fortran Compiler
  --fcompiler=none      Fake Fortran compiler
  --fcompiler=nv        NVIDIA HPC SDK
  --fcompiler=pathf95   PathScale Fortran Compiler
  --fcompiler=sun       Sun or Forte Fortran 95 Compiler
  --fcompiler=vast      Pacific-Sierra Research Fortran 90 Compiler
For compiler details, run 'config_fc --verbose' setup command.
Removing build directory /var/folders/7d/rkhc67xs5w70chjmlrr6pv440017ch/T/tmpktji4w04

python 3.13.5

(cmor3110xcd091) machine:~ user$ python
Python 3.13.5 | packaged by conda-forge | (main, Jun 16 2025, 08:24:05) [Clang 18.1.8 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> print(np.__version__)
2.2.6
>>> 
(cmor3110xcd091) ml-9953350:~ durack1$ f2py -c --help-fcompiler
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...
Post-processing...
Applying post-processing hooks...
  character_backward_compatibility_hook
Post-processing (stage 2)...
Building modules...
The Meson build system
Version: 1.8.2
Source dir: /private/var/folders/7d/rkhc67xs5w70chjmlrr6pv440017ch/T/tmp5yijtxvg
Build dir: /private/var/folders/7d/rkhc67xs5w70chjmlrr6pv440017ch/T/tmp5yijtxvg/bbdir
Build type: native build

meson.build:40:0: ERROR: Expecting rbracket got comma.
,
^
For a block that started at 39,21
                     [
                     ^

A full log can be found at /private/var/folders/7d/rkhc67xs5w70chjmlrr6pv440017ch/T/tmp5yijtxvg/bbdir/meson-logs/meson-log.txt
Traceback (most recent call last):
  File "~/miniforge3/envs/cmor3110xcd091/bin/f2py", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "~/miniforge3/envs/cmor3110xcd091/lib/python3.13/site-packages/numpy/f2py/f2py2e.py", line 781, in main
    run_compile()
    ~~~~~~~~~~~^^
  File "~/miniforge3/envs/cmor3110xcd091/lib/python3.13/site-packages/numpy/f2py/f2py2e.py", line 753, in run_compile
    builder.compile()
    ~~~~~~~~~~~~~~~^^
  File "~/miniforge3/envs/cmor3110xcd091/lib/python3.13/site-packages/numpy/f2py/_backends/_meson.py", line 192, in compile
    self.run_meson(self.build_dir)
    ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
  File "~/miniforge3/envs/cmor3110xcd091/lib/python3.13/site-packages/numpy/f2py/_backends/_meson.py", line 185, in run_meson
    self._run_subprocess_command(setup_command, build_dir)
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "~/miniforge3/envs/cmor3110xcd091/lib/python3.13/site-packages/numpy/f2py/_backends/_meson.py", line 181, in _run_subprocess_command
    subprocess.run(command, cwd=cwd, check=True)
    ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "~/miniforge3/envs/cmor3110xcd091/lib/python3.13/subprocess.py", line 577, in run
    raise CalledProcessError(retcode, process.args,
                             output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['meson', 'setup', 'bbdir']' returned non-zero exit status 1.