Using via meson
#
Note
Much of this document is now obsoleted, one can run f2py
with
--build-dir
to get a skeleton meson
project with basic dependencies
setup.
Changed in version 1.26.x: The default build system for f2py
is now meson
, see
Status of numpy.distutils and migration advice for some more details..
The key advantage gained by leveraging meson
over the techniques described
in Using via numpy.distutils is that this feeds into existing systems and larger
projects with ease. meson
has a rather pythonic syntax which makes it more
comfortable and amenable to extension for python
users.
Fibonacci walkthrough (F77)#
We will need the generated C
wrapper before we can use a general purpose
build system like meson
. We will acquire this by:
python -m numpy.f2py fib1.f -m fib2
Now, consider the following meson.build
file for the fib
and scalar
examples from Three ways to wrap - getting started section:
project('f2py_examples', 'c',
version : '0.1',
license: 'BSD-3',
meson_version: '>=0.64.0',
default_options : ['warning_level=2'],
)
add_languages('fortran')
py_mod = import('python')
py = py_mod.find_installation(pure: false)
py_dep = py.dependency()
incdir_numpy = run_command(py,
['-c', 'import os; os.chdir(".."); import numpy; print(numpy.get_include())'],
check : true
).stdout().strip()
incdir_f2py = run_command(py,
['-c', 'import os; os.chdir(".."); import numpy.f2py; print(numpy.f2py.get_include())'],
check : true
).stdout().strip()
inc_np = include_directories(incdir_numpy, incdir_f2py)
py.extension_module('fib2',
[
'fib1.f',
'fib2module.c', # note: this assumes f2py was manually run before!
],
incdir_f2py / 'fortranobject.c',
include_directories: inc_np,
dependencies : py_dep,
install : true
)
At this point the build will complete, but the import will fail:
meson setup builddir
meson compile -C builddir
cd builddir
python -c 'import fib2'
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: fib2.cpython-39-x86_64-linux-gnu.so: undefined symbol: FIB_
# Check this isn't a false positive
nm -A fib2.cpython-39-x86_64-linux-gnu.so | grep FIB_
fib2.cpython-39-x86_64-linux-gnu.so: U FIB_
Recall that the original example, as reproduced below, was in SCREAMCASE:
C FILE: FIB1.F
SUBROUTINE FIB(A,N)
C
C CALCULATE FIRST N FIBONACCI NUMBERS
C
INTEGER N
REAL*8 A(N)
DO I=1,N
IF (I.EQ.1) THEN
A(I) = 0.0D0
ELSEIF (I.EQ.2) THEN
A(I) = 1.0D0
ELSE
A(I) = A(I-1) + A(I-2)
ENDIF
ENDDO
END
C END FILE FIB1.F
With the standard approach, the subroutine exposed to python
is fib
and
not FIB
. This means we have a few options. One approach (where possible) is
to lowercase the original Fortran file with say:
tr "[:upper:]" "[:lower:]" < fib1.f > fib1.f
python -m numpy.f2py fib1.f -m fib2
meson --wipe builddir
meson compile -C builddir
cd builddir
python -c 'import fib2'
However this requires the ability to modify the source which is not always
possible. The easiest way to solve this is to let f2py
deal with it:
python -m numpy.f2py fib1.f -m fib2 --lower
meson --wipe builddir
meson compile -C builddir
cd builddir
python -c 'import fib2'
Automating wrapper generation#
A major pain point in the workflow defined above, is the manual tracking of inputs. Although it would require more effort to figure out the actual outputs for reasons discussed in F2PY and build systems.
Note
From NumPy 1.22.4
onwards, f2py
will deterministically generate
wrapper files based on the input file Fortran standard (F77 or greater).
--skip-empty-wrappers
can be passed to f2py
to restore the previous
behaviour of only generating wrappers when needed by the input .
However, we can augment our workflow in a straightforward to take into account files for which the outputs are known when the build system is set up.
project('f2py_examples', 'c',
version : '0.1',
license: 'BSD-3',
meson_version: '>=0.64.0',
default_options : ['warning_level=2'],
)
add_languages('fortran')
py_mod = import('python')
py = py_mod.find_installation(pure: false)
py_dep = py.dependency()
incdir_numpy = run_command(py,
['-c', 'import os; os.chdir(".."); import numpy; print(numpy.get_include())'],
check : true
).stdout().strip()
incdir_f2py = run_command(py,
['-c', 'import os; os.chdir(".."); import numpy.f2py; print(numpy.f2py.get_include())'],
check : true
).stdout().strip()
fibby_source = custom_target('fibbymodule.c',
input : ['fib1.f'], # .f so no F90 wrappers
output : ['fibbymodule.c', 'fibby-f2pywrappers.f'],
command : [py, '-m', 'numpy.f2py', '@INPUT@', '-m', 'fibby', '--lower']
)
inc_np = include_directories(incdir_numpy, incdir_f2py)
py.extension_module('fibby',
['fib1.f', fibby_source],
incdir_f2py / 'fortranobject.c',
include_directories: inc_np,
dependencies : py_dep,
install : true
)
This can be compiled and run as before.
rm -rf builddir
meson setup builddir
meson compile -C builddir
cd builddir
python -c "import numpy as np; import fibby; a = np.zeros(9); fibby.fib(a); print (a)"
# [ 0. 1. 1. 2. 3. 5. 8. 13. 21.]
Salient points#
It is worth keeping in mind the following:
It is not possible to use SCREAMCASE in this context, so either the contents of the
.f
file or the generated wrapper.c
needs to be lowered to regular letters; which can be facilitated by the--lower
option ofF2PY