Merge pull request #13 from MP-Gadget/fixes

Fix the build! Enable github action tests!

.github/workflows/main.yaml

@@ -0,0 +1,49 @@
+# main test workflow; ported from .travis.yaml
+name: main
+
+on:
+  push:
+    branches: [ '*', $default-branch ]
+  pull_request:
+    branches: [ $default-branch ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+        matrix:
+            python-version: ['3.10', '3.12']
+    steps:
+    - name: Checkout source code
+      uses: actions/checkout@v4
+    - name: Install build deps
+      run: |
+        sudo apt-get update
+        sudo apt-get -y install openmpi-bin libopenmpi-dev
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Build
+      run: |
+        python -m pip install setuptools wheel nose mpi4py numpy cython build runtests
+        python -m build
+    - name: Install
+      run: |
+        python -m pip install `ls dist/pfft_python*.whl`
+    - name: Unit tests
+      run: |
+        python ./runtests.py --mpirun="mpirun -np 4"
+    - name: Roundtrips
+      run: |
+        mpirun -n 1 python $PWD/scripts/pfft-roundtrip-matrix.py -v -diag -Nproc 1 1 -Nmesh 13 15 16
+        mpirun -n 2 python $PWD/scripts/pfft-roundtrip-matrix.py -v -diag -Nproc 2 1 -Nproc 1 2 -Nmesh 13 15 16
+#Not enough slots o github for this test.
+#        mpirun -n 4 python $PWD/scripts/pfft-roundtrip-matrix.py -v -diag -Nproc 2 2 -Nmesh 13 15 16
+#        mpirun -n 4 python $PWD/scripts/pfft-roundtrip-matrix.py -v -diag -Nproc 2 2 -Nmesh 13 15
+    - name: Version
+      run: |
+        bash check_tag.sh pfft/version.py

examples/example.py

@@ -14,9 +14,9 @@
 
 procmesh = pfft.ProcMesh([4], comm=MPI.COMM_WORLD)
 partition = pfft.Partition(
-        pfft.Type.PFFT_C2C, 
-        [8, 8], 
-        procmesh, 
+        pfft.Type.PFFT_C2C,
+        [8, 8],
+        procmesh,
         pfft.Flags.PFFT_TRANSPOSED_OUT | pfft.Flags.PFFT_DESTROY_INPUT
         )
 for irank  in range(4):
@@ -32,7 +32,7 @@
 buffer = pfft.LocalBuffer(partition)
 
 plan = pfft.Plan(partition, pfft.Direction.PFFT_FORWARD, buffer)
-iplan = pfft.Plan(partition, pfft.Direction.PFFT_BACKWARD, buffer, 
+iplan = pfft.Plan(partition, pfft.Direction.PFFT_BACKWARD, buffer,
         flags=pfft.Flags.PFFT_TRANSPOSED_OUT | pfft.Flags.PFFT_DESTROY_INPUT,
         )
 
@@ -50,8 +50,8 @@
 
 output = buffer.view_output()
 
-# denormalize the forward transform 
-output /= numpy.product(partition.n)
+# denormalize the forward transform
+output /= numpy.prod(partition.n)
 
 iplan.execute(buffer)
 

pyproject.toml

@@ -0,0 +1,9 @@
+[build-system]
+requires = [
+    "setuptools>=42",
+    "wheel",
+    "mpi4py",
+    "Cython",  # Ensure Cython is included as a build dependency
+    "numpy"    # It's often necessary to include numpy if using it in setup.py
+]
+build-backend = "setuptools.build_meta"

scripts/pfft-roundtrip-matrix.py

@@ -5,10 +5,10 @@
    given by -Nmesh. Default is [29, 30, 31].
    Tested features are:
        regular transform (r2c + c2r, c2c)
-       transposed in / out, 
-       padded in / out, 
+       transposed in / out,
+       padded in / out,
        destroy input,
-       inplace transform 
+       inplace transform
 
    Examples:
 
@@ -18,7 +18,7 @@
    * for single-rank numpy agreement test, run with
        mpirun -np 1 python roundtrip.py -Nmesh 32 32 32 -Nmesh 3 3 3 -verbose
 
-   * for multi-rank tests, run with 
+   * for multi-rank tests, run with
        mpirun -np 4 python roundtrip.py -Nmesh 32 32 32 -Nmesh 3 3 3 --verbose
 
    n can be any number. procmeshes tested are:
@@ -35,9 +35,9 @@
 
 import os.path
 
-parser = argparse.ArgumentParser(description='Roundtrip testing of pfft', 
+parser = argparse.ArgumentParser(description='Roundtrip testing of pfft',
         epilog=__doc__,
-       formatter_class=argparse.RawDescriptionHelpFormatter 
+       formatter_class=argparse.RawDescriptionHelpFormatter
         )
 
 from pfft import *
@@ -85,7 +85,7 @@ def test_roundtrip_3d(procmesh, type, flags, inplace, Nmesh):
     else:
         buf2 = LocalBuffer(partition)
 
-    input = buf1.view_input() 
+    input = buf1.view_input()
     output = buf2.view_output()
 
     assert input.base == buf1
@@ -95,7 +95,7 @@ def test_roundtrip_3d(procmesh, type, flags, inplace, Nmesh):
 #    print 'input', input.shape
     forward = Plan(
             partition,
-            Direction.PFFT_FORWARD, 
+            Direction.PFFT_FORWARD,
             buf1,
             buf2,
             type=type,
@@ -135,10 +135,10 @@ def test_roundtrip_3d(procmesh, type, flags, inplace, Nmesh):
 
     backward = Plan(
             partition,
-            Direction.PFFT_BACKWARD, 
+            Direction.PFFT_BACKWARD,
             buf2,
             buf1,
-            type=btype, 
+            type=btype,
             flags=bflags,
             )
     #print(repr(backward))
@@ -183,7 +183,7 @@ def test_roundtrip_3d(procmesh, type, flags, inplace, Nmesh):
         bpreserr = 0.0
 
     if input.size > 0:
-        input[:] /= numpy.product(Nmesh)
+        input[:] /= numpy.prod(Nmesh)
         # some distributions have no input value
         c2rerr = numpy.abs(original - input).max()
     else:
@@ -200,7 +200,7 @@ def test_roundtrip_3d(procmesh, type, flags, inplace, Nmesh):
     #    print(repr(forward.type), 'preserve', "error = ", fpreserr)
     #    print(repr(forward.type), 'forward', "error = ", r2cerr)
     #    print(repr(forward.type), 'backward', "error = ", c2rerr)
-    
+
     fpreserr = MPI.COMM_WORLD.allreduce(fpreserr, MPI.MAX)
     bpreserr = MPI.COMM_WORLD.allreduce(bpreserr, MPI.MAX)
     r2cerr = MPI.COMM_WORLD.allreduce(r2cerr, MPI.MAX)
@@ -229,7 +229,7 @@ def main():
     Nmesh = ns.Nmesh
 
     if len(Nmesh) == 0:
-        # default 
+        # default
         Nmesh = [[29, 30, 31]]
 
     if MPI.COMM_WORLD.size == 1 and len(ns.Nproc) == 0:

setup.py

@@ -15,13 +15,13 @@ def build_pfft(prefix, compiler, cflags):
     # Avoid enabling SSE2 by default. aarch64 doesn't have it.
     # optimize="--enable-sse2"
     optimize=""
-    line = ('CFLAGS="%s -fvisibility=hidden" ' % cflags+
+    line = ('CFLAGS="%s -fvisibility=hidden -Wno-error=incompatible-pointer-types" ' % cflags+
             'MPICC="%s" ' % compiler +
             'CC="%s" ' % compiler +
             'sh %s/depends/install_pfft.sh ' % package_basedir +
              os.path.abspath(prefix) +
             ' %s' % optimize)
-    if os.path.exists(os.path.join(prefix, 
+    if os.path.exists(os.path.join(prefix,
         'lib', 'libpfft.a')):
         return
 
@@ -42,10 +42,10 @@ def initialize_options(self):
 
         self.mpicc = os.environ.get('MPICC', compiler)
 
-        build_ext.initialize_options(self)    
+        build_ext.initialize_options(self)
 
     def finalize_options(self):
-        build_ext.finalize_options(self)    
+        build_ext.finalize_options(self)
         self.pfft_build_dir = os.path.join(self.build_temp, 'depends')
 
         self.include_dirs.insert(0, os.path.join(
@@ -56,13 +56,13 @@ def build_extensions(self):
         self.compiler.compiler_so[0] = self.mpicc
         self.compiler.linker_so[0] = self.mpicc
         build_pfft(self.pfft_build_dir, self.mpicc, ' '.join(self.compiler.compiler_so[1:]))
-        link_objects = [ 
-                'libpfft.a', 
+        link_objects = [
+                'libpfft.a',
                 'libpfftf.a',
-                'libfftw3_mpi.a', 
-                'libfftw3.a', 
-                'libfftw3f_mpi.a', 
-                'libfftw3f.a', 
+                'libfftw3_mpi.a',
+                'libfftw3.a',
+                'libfftw3f_mpi.a',
+                'libfftw3f.a',
                 ]
 
         link_objects = [list(glob.glob(os.path.join(self.pfft_build_dir, '*', i)))[0] for i in link_objects]
@@ -96,19 +96,21 @@ def find_version(path):
     install_requires=['cython', 'numpy', 'mpi4py'],
     packages= ['pfft', 'pfft.tests'],
     requires=['numpy'],
-    ext_modules = cythonize([Extension( 
-                "pfft.core", 
+    ext_modules = cythonize([Extension(
+                "pfft.core",
                 ["pfft/core.pyx"],
-                include_dirs=["./", 
+                include_dirs=["./",
                 numpy.get_include(),
+                mpi4py.get_include(),
                 ],
                 libraries=['m'],
                 cython_directives = {"embedsignature": True}
-                )]),
+                )],
+                include_path=[os.path.join(mpi4py.get_include(),"../"),],
+                ),
     license='GPL3',
     scripts=['scripts/pfft-roundtrip-matrix.py'],
     cmdclass = {
         "build_py":build_py,
         "build_ext": build_ext_subclass}
 )
-