Add pyproject.toml and support Cython 3

Author: dalcinl

.github/workflows/main.yml

@@ -8,8 +8,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macOS-latest]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
     name: Python ${{ matrix.python-version }} example
 
     steps:

Makefile

@@ -1,7 +1,7 @@
 VERSION=$(shell python3 -c "import mpi4py_fft; print(mpi4py_fft.__version__)")
 
 default:
-	python setup.py build_ext -i
+	python setup.py build build_ext -i
 
 pip:
 	rm -f dist/*
@@ -15,6 +15,6 @@ tag:
 publish: tag pip
 
 clean:
-	git clean mpi4py_fft -fx
+	git clean -dxf mpi4py_fft
 	cd docs && make clean && cd ..
-	@rm -rf *.egg-info/ build/ dist/ .eggs/
+	@rm -rf *.egg-info/ build/ dist/ .eggs/

conf/meta.yaml

@@ -16,7 +16,7 @@ requirements:
     - {{ compiler('cxx') }}
   host:
     - python
-    - cython <3.0
+    - cython
     - numpy
     - pip
     - fftw
@@ -25,7 +25,7 @@ requirements:
   run:
     - python
     - mpi4py
-    - mpich 4.0.2
+    - mpich
     - {{ pin_compatible('numpy') }}
     - fftw
     - hdf5 * mpi_*

mpi4py_fft/fftw/fftw_xfftn.pxd

@@ -1,4 +1,4 @@
-cdef extern from "fftw3.h":
+cdef extern from "fftw3.h" nogil:
 
     ctypedef struct fftw_complex_struct:
         pass
@@ -12,15 +12,15 @@ cdef extern from "fftw3.h":
 
     void fftw_destroy_plan(fftw_plan)
 
-    void fftw_execute_dft(fftw_plan, void *_in, void *_out) nogil
+    void fftw_execute_dft(fftw_plan, void *_in, void *_out)
 
-    void fftw_execute_dft_c2r(fftw_plan, void *_in, void *_out) nogil
+    void fftw_execute_dft_c2r(fftw_plan, void *_in, void *_out)
 
-    void fftw_execute_dft_r2c(fftw_plan, void *_in, void *_out) nogil
+    void fftw_execute_dft_r2c(fftw_plan, void *_in, void *_out)
 
-    void fftw_execute_r2r(fftw_plan, void *_in, void *_out) nogil
+    void fftw_execute_r2r(fftw_plan, void *_in, void *_out)
 
-    void fftw_execute(fftw_plan) nogil
+    void fftw_execute(fftw_plan)
 
     void fftw_init_threads()
 
@@ -43,7 +43,7 @@ cdef extern from "fftw3.h":
     void fftw_print_plan(fftw_plan)
 
 
-cdef extern from "fftw_planxfftn.h":
+cdef extern from "fftw_planxfftn.h" nogil:
 
     ctypedef double fftw_real
 

mpi4py_fft/fftw/fftw_xfftn.pyx

@@ -1,5 +1,5 @@
-cimport fftw_xfftn
 #cython: language_level=3
+from . cimport fftw_xfftn
 cimport numpy as np
 from .utilities import *
 import numpy as np
@@ -26,16 +26,16 @@ cpdef void cleanup():
     fftw_cleanup()
     fftw_cleanup_threads()
 
-cdef void _fftw_execute_dft(void *plan, void *_in, void *_out) nogil:
+cdef void _fftw_execute_dft(void *plan, void *_in, void *_out) noexcept nogil:
     fftw_execute_dft(<fftw_plan>plan, <fftw_complex *>_in, <fftw_complex *>_out)
 
-cdef void _fftw_execute_dft_r2c(void *plan, void *_in, void *_out) nogil:
+cdef void _fftw_execute_dft_r2c(void *plan, void *_in, void *_out) noexcept nogil:
     fftw_execute_dft_r2c(<fftw_plan>plan, <fftw_real *>_in, <fftw_complex *>_out)
 
-cdef void _fftw_execute_dft_c2r(void *plan, void *_in, void *_out) nogil:
+cdef void _fftw_execute_dft_c2r(void *plan, void *_in, void *_out) noexcept nogil:
     fftw_execute_dft_c2r(<fftw_plan>plan, <fftw_complex *>_in, <fftw_real *>_out)
 
-cdef void _fftw_execute_r2r(void *plan, void *_in, void *_out) nogil:
+cdef void _fftw_execute_r2r(void *plan, void *_in, void *_out) noexcept nogil:
     fftw_execute_r2r(<fftw_plan>plan, <fftw_real *>_in, <fftw_real *>_out)
 
 cdef generic_function _get_execute_function(kind):

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools >= 42", "numpy", "cython >= 0.29.32"]
+build-backend = "setuptools.build_meta"

setup.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+"""mpi4py-fft -- Parallel Fast Fourier Transforms (FFTs) using MPI for Python"""
 
 import os
 import sys
@@ -33,6 +34,8 @@ def get_prefix_dirs():
     append(dirs, sys.prefix)
     if 'CONDA_BUILD' not in os.environ:
         append(dirs, '/usr')
+        append(dirs, '/usr/local')
+        append(dirs, '/opt/homebrew')
     return dirs
 
 def get_include_dirs():
@@ -101,10 +104,10 @@ def generate_extensions(fftwlibs, force=True):
 def remove_extensions(fftwlibs):
     """Remove generated files"""
     for fname in (
-            'utilities.c',
-            'fftw_xfftn.c',
-            'fftwf_xfftn.c',
-            'fftwl_xfftn.c',
+        'utilities.c',
+        'fftw_xfftn.c',
+        'fftwf_xfftn.c',
+        'fftwl_xfftn.c',
     ):
         dst = os.path.join(fftwdir, fname)
         try:
@@ -116,10 +119,10 @@ def remove_extensions(fftwlibs):
             continue
         p = 'fftw'+prec_map[d]+'_'
         for fname in (
-                'fftw_planxfftn.h',
-                'fftw_planxfftn.c',
-                'fftw_xfftn.pyx',
-                'fftw_xfftn.pxd',
+            'fftw_planxfftn.h',
+            'fftw_planxfftn.c',
+            'fftw_xfftn.pyx',
+            'fftw_xfftn.pxd',
         ):
             dst = os.path.join(fftwdir, fname.replace('fftw_', p))
             try:
@@ -131,20 +134,31 @@ def get_extensions():
     """Return list of extension modules"""
     include_dirs = get_include_dirs()
     library_dirs = get_library_dirs()
-    ext = [Extension("mpi4py_fft.fftw.utilities",
-                     sources=[os.path.join(fftwdir, "utilities.pyx")],
-                     include_dirs=include_dirs)]
+    ext = [
+        Extension(
+            "mpi4py_fft.fftw.utilities",
+            sources=[os.path.join(fftwdir, "utilities.pyx")],
+            define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
+            include_dirs=include_dirs,
+        ),
+    ]
 
     fftwlibs = get_fftw_libs()
     for d, libs in fftwlibs.items():
-        p = 'fftw'+prec_map[d]+'_'
-        ext.append(Extension("mpi4py_fft.fftw.{}xfftn".format(p),
-                             sources=[os.path.join(fftwdir, "{}xfftn.pyx".format(p)),
-                                      os.path.join(fftwdir, "{}planxfftn.c".format(p))],
-                             #define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
-                             libraries=libs,
-                             include_dirs=include_dirs,
-                             library_dirs=library_dirs))
+        p = 'fftw' + prec_map[d] + '_'
+        ext.append(
+            Extension(
+                "mpi4py_fft.fftw.{}xfftn".format(p),
+                sources=[
+                    os.path.join(fftwdir, "{}xfftn.pyx".format(p)),
+                    os.path.join(fftwdir, "{}planxfftn.c".format(p)),
+                ],
+                define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
+                libraries=libs,
+                include_dirs=include_dirs,
+                library_dirs=library_dirs,
+            )
+        )
     return ext
 
 
@@ -190,14 +204,19 @@ def version():
 if __name__ == '__main__':
     setup(name="mpi4py-fft",
           version=version(),
-          description="mpi4py-fft -- Parallel Fast Fourier Transforms (FFTs) using MPI for Python",
+          description=__doc__.strip(),
           long_description=long_description,
+          long_description_content_type='text/x-rst',
           author="Lisandro Dalcin and Mikael Mortensen",
-          url='https://github.com/mpi4py/mpi4py-fft',
-          packages=["mpi4py_fft",
-                    "mpi4py_fft.fftw",
-                    "mpi4py_fft.io"],
-          package_dir={"mpi4py_fft": "mpi4py_fft"},
+          url="https://github.com/mpi4py/mpi4py-fft",
+          packages=[
+              "mpi4py_fft",
+              "mpi4py_fft.fftw",
+              "mpi4py_fft.io",
+          ],
+          package_dir={
+              "mpi4py_fft": "mpi4py_fft",
+          },
           classifiers=[
               'Development Status :: 4 - Beta',
               'Environment :: Console',
@@ -209,10 +228,9 @@ def version():
               'License :: OSI Approved :: BSD License',
               'Topic :: Scientific/Engineering :: Mathematics',
               'Topic :: Software Development :: Libraries :: Python Modules',
-              ],
+          ],
+          keywords=['Python', 'FFTW', 'FFT', 'DCT', 'DST', 'MPI'],
           distclass=Dist,
           ext_modules=get_extensions(),
           install_requires=["mpi4py", "numpy"],
-          setup_requires=["setuptools>=18.0", "cython>=0.25"],
-          keywords=['Python', 'FFTW', 'FFT', 'DCT', 'DST', 'MPI']
          )

tests/test_speed.py

@@ -1,10 +1,15 @@
 from time import time
 import numpy as np
-import pyfftw
 import scipy.fftpack as sp
 from mpi4py_fft import fftw
 import pickle
 
+try:
+    import pyfftw
+except ImportError:
+    print('pyFFTW not available')
+    raise SystemExit(0)
+
 try:
     #fftw.import_wisdom('wisdom.dat')
     pyfftw.import_wisdom(pickle.load(open('pyfftw.wisdom', 'rb')))