Updating to circleci2.0 and adding Makefile

.circleci/config.yml

@@ -0,0 +1,48 @@
+version: 2
+jobs:
+  build:
+    machine: true
+    steps:
+      - checkout
+
+      - restore_cache:
+          key: v2-miniconda-{{ .Branch }}
+
+      - run:
+          name: install miniconda
+          command: |
+            if [[ ! -d /home/circleci/miniconda ]]; then
+                wget https://repo.continuum.io/miniconda/Miniconda3-4.5.1-Linux-x86_64.sh -O miniconda.sh &&
+                bash miniconda.sh -b -f -p /home/circleci/miniconda;
+            else
+                echo "Using cached miniconda";
+            fi
+            source ~/miniconda/bin/activate root
+            conda config --set always_yes yes
+            conda config --add channels conda-forge
+            conda config --add channels spectralDNS
+            conda clean --lock
+            conda install --yes --quiet conda-forge-ci-setup=1
+            source run_conda_forge_build_setup
+
+      - save_cache:
+          key: v2-miniconda-{{ .Branch }}
+          paths:
+            - /home/circleci/miniconda
+
+      - run:
+          name: Build and test
+          command: |
+            source ~/miniconda/bin/activate root
+            cd /home/circleci/project
+            conda build --python 2.7 ./conf/conda
+            conda build --python 3.6 ./conf/conda
+
+      - run:
+          name: Upload packages
+          command: |
+              source ~/miniconda/bin/activate root
+              cd /home/circleci/project
+              upload_or_check_non_existence ./conf/conda spectralDNS --channel main
+              export CONDA_PY=36
+              upload_or_check_non_existence ./conf/conda spectralDNS --channel main

Makefile

@@ -0,0 +1,21 @@
+VERSION=$(shell python3 -c "import mpiFFT4py; print(mpiFFT4py.__version__)")
+
+default:
+	python setup.py build_ext -i
+
+pip:
+	rm -f dist/*
+	python setup.py sdist
+	twine upload dist/*
+
+tag:
+	git tag $(VERSION)
+	git push --tags
+
+publish: tag pip
+
+clean:
+	git clean mpiFFT4py -fx
+	git clean tests -fx
+	cd docs && make clean && cd ..
+	@rm -rf *.egg-info/ build/ dist/ .eggs/

conf/conda/conda_build_config.yaml

@@ -0,0 +1,2 @@
+numpy:
+  - 1.15

conf/conda/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: mpifft4py
-  version: "1.1.0"
+  version: "{{ GET_DESCRIBE_TAG }}"
 
 source:
   git_url: ../../
@@ -19,9 +19,7 @@ requirements:
     - numpy
     - scipy
     - mpi4py
-    - mpich  #[unix]
-    - openmpi ==1.6.3 #[osx]
-    - cython
+    - fftw
     - pyfftw
 
 test:

mpiFFT4py/__init__.py

@@ -5,3 +5,4 @@
 from .mpibase import work_arrays, datatypes, empty, zeros
 from numpy.fft import fftfreq, rfftfreq
 
+__version__ = '1.1.0'

mpiFFT4py/slab.py

@@ -145,9 +145,9 @@ def complex_local_slice(self):
 
     def complex_local_wavenumbers(self):
         """Returns local wavenumbers of complex space"""
-        return (fftfreq(self.N[0], 1./self.N[0]),
-                fftfreq(self.N[1], 1./self.N[1])[self.complex_local_slice()[1]],
-                rfftfreq(self.N[2], 1./self.N[2]))
+        return (fftfreq(self.N[0], 1./self.N[0]).astype(self.float),
+                fftfreq(self.N[1], 1./self.N[1])[self.complex_local_slice()[1]].astype(self.float),
+                rfftfreq(self.N[2], 1./self.N[2]).astype(self.float))
 
     def get_local_mesh(self):
         """Returns the local decomposed physical mesh"""
@@ -170,13 +170,15 @@ def get_local_wavenumbermesh(self, scaled=False, broadcast=False, eliminate_high
         """
         kx, ky, kz = self.complex_local_wavenumbers()
         if eliminate_highest_freq:
-            ky = fftfreq(self.N[1], 1./self.N[1])
+            ky = fftfreq(self.N[1], 1./self.N[1].astype(self.float))
             for i, k in enumerate((kx, ky, kz)):
                 if self.N[i] % 2 == 0:
                     k[self.N[i]//2] = 0
             ky = ky[self.complex_local_slice()[1]]
 
         Ks = np.meshgrid(kx, ky, kz, indexing='ij', sparse=True)
+        for i in range(3):
+            Ks[i] = Ks[i].astype(self.float)
         if scaled:
             Lp = 2*np.pi/self.L
             for i in range(3):

setup.py

@@ -1,52 +1,66 @@
 #!/usr/bin/env python
 
-import os, sys, platform
-from distutils.core import setup, Extension
-from Cython.Distutils import build_ext
-from Cython.Build import cythonize
+import os
+import re
+import subprocess
+from setuptools import setup, Extension
+from setuptools.command.build_ext import build_ext
 from numpy import get_include
 
-# Version number
-major = 1
-minor = 1
-version = 0
-
 cwd = os.path.abspath(os.path.dirname(__file__))
 cdir = os.path.join(cwd, "mpiFFT4py", "cython")
 
-cmdclass = {}
+def has_flag(compiler, flagname):
+    """Return a boolean indicating whether a flag name is supported on
+    the specified compiler.
+    """
+    devnull = open(os.devnull, "w")
+    p = subprocess.Popen([compiler.compiler[0], '-E', '-'] + [flagname],
+                         stdin=subprocess.PIPE, stdout=devnull, stderr=devnull,
+                         shell=True)
+    p.communicate("")
+    return True if p.returncode == 0 else False
+
 class build_ext_subclass(build_ext):
     def build_extensions(self):
-        extra_compile_args = ['-w', '-Ofast']
-        cmd = "echo | %s -E - %s &>/dev/null" % (
-            self.compiler.compiler[0], " ".join(extra_compile_args))
-        try:
-            subprocess.check_call(cmd, shell=True)
-        except:
-            extra_compile_args = ['-w', '-O3']
+        extra_compile_args = ['-g0']
+        for c in ['-w', '-Ofast', '-ffast-math', '-march=native']:
+            if has_flag(self.compiler, c):
+                extra_compile_args.append(c)
+
         for e in self.extensions:
-            e.extra_compile_args = extra_compile_args
+            e.extra_compile_args += extra_compile_args
+            e.include_dirs.extend([get_include()])
         build_ext.build_extensions(self)
 
-ext = cythonize(os.path.join(cdir, "*.pyx"))
-[e.include_dirs.extend([get_include()]) for e in ext]
-cmdclass = {'build_ext': build_ext_subclass}
+ext = [Extension('mpiFFT4py.cython.maths',
+                 sources=[os.path.join(cdir, "maths.pyx")])]
+
+def version():
+    srcdir = os.path.join(cwd, 'mpiFFT4py')
+    with open(os.path.join(srcdir, '__init__.py')) as f:
+        m = re.search(r"__version__\s*=\s*'(.*)'", f.read())
+        return m.groups()[0]
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
 
 setup(name = "mpiFFT4py",
-      version = "%d.%d.%d" % (major, minor, version),
+      version = version(),
       description = "mpiFFT4py -- Parallel 3D FFT in Python using MPI for Python",
-      long_description = "",
+      long_description = long_description,
       author = "Mikael Mortensen",
       author_email = "[email protected]",
       url = 'https://github.com/spectralDNS/mpiFFT4py',
-      download_url = "https://github.com/spectralDNS/mpiFFT4py/archive/mpiFFT4py-1.1.0.tar.gz",
       classifiers = [
           'Development Status :: 5 - Production/Stable',
           'Environment :: Console',
           'Intended Audience :: Developers',
           'Intended Audience :: Science/Research',
           'Intended Audience :: Education',
           'Programming Language :: Python',
+          'Programming Language :: Python :: 2',
+          'Programming Language :: Python :: 3',
           'License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)',
           'Topic :: Scientific/Engineering :: Mathematics',
           'Topic :: Software Development :: Libraries :: Python Modules',
@@ -57,5 +71,5 @@ def build_extensions(self):
                   ],
       package_dir = {"mpiFFT4py": "mpiFFT4py"},
       ext_modules = ext,
-      cmdclass = cmdclass
+      cmdclass = {'build_ext': build_ext_subclass}
     )