use skbuild

.github/workflows/ci.yml

@@ -35,7 +35,7 @@ jobs:
  - name: Install Python dependencies
  run: |
  python -m pip install --upgrade pip
- pip install pytest numpy h5py numba scipy pandas
+ pip install pytest numpy h5py scipy pandas scikit-build pybind11
  pip install git+https://gitlab.com/reinholdt/polarizationsolver.git@master
 
  - name: Configure CMake (Linux)
@@ -58,5 +58,5 @@ jobs:
  run: |
  rm -rf build
  python setup.py install
- pytest
+ pytest --pyargs cppe
 

.github/workflows/publish.yml

@@ -18,10 +18,10 @@ jobs:
  python -m pip install --user setuptools wheel
  - name: Build a source tarball
  run: |
- pip install pytest numpy h5py numba scipy pandas
+ pip install pytest numpy h5py scipy pandas scikit-build pybind11
  pip install git+https://gitlab.com/reinholdt/polarizationsolver.git@master
  python setup.py install
- pytest
+ pytest --pyargs cppe
  python setup.py sdist
  - name: Publish distribution 📦 to Test PyPI
  if: startsWith(github.ref, 'refs/tags')

cppe/CMakeLists.txt

@@ -6,10 +6,12 @@ include(CMakePackageConfigHelpers)
 include(ExternalProject)
 
 if(ENABLE_OPENMP)
- find_package(OpenMP REQUIRED)
+ find_package(OpenMP)
  if (OPENMP_FOUND)
- set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
- set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+ set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+ set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+ else()
+ message(WARNING "Suitable OpenMP could not be found. Building without OpenMP instead.")
  endif()
 endif()
 
@@ -105,7 +107,7 @@ if(${ENABLE_PYTHON_INTERFACE})
  # install the Python tests
  install(DIRECTORY "../tests"
  DESTINATION ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}${PYMOD_INSTALL_LIBDIR}/cppe
- FILES_MATCHING PATTERN "*.py" PATTERN "*.pot" PATTERN "*.hdf5")
+ FILES_MATCHING PATTERN "*.py" PATTERN "*.pot" PATTERN "*.hdf5" PATTERN "*.csv")
 endif()
 
 target_compile_definitions(cppe INTERFACE USING_${PN})

pyproject.toml

@@ -0,0 +1,2 @@
+[build-system]
+requires = ["setuptools", "wheel", "scikit-build", "cmake", "ninja"]

setup.py

@@ -3,11 +3,17 @@
 """Setup for cppe"""
 import os
 import sys
-import glob
 import setuptools
 
-from setuptools import Extension, find_packages, setup
-from setuptools.command.build_ext import build_ext as BuildCommand
+try:
+ from skbuild import setup
+except ImportError:
+ print("Please update pip, you need pip 10 or greater,\n"
+ " or you need to install the PEP 518 requirements"
+ " in pyproject.toml yourself",
+ file=sys.stderr,
+ )
+ raise
 
 try:
  from sphinx.setup_command import BuildDoc as BuildSphinxDoc
@@ -22,6 +28,13 @@ def initialize_options(self):
  def finalize_options(self):
  pass
 
+try:
+ import pybind11
+except ImportError:
+ print("Please install pybind11 before installing cppe.",
+ file=sys.stderr,
+ )
+ raise
 
 __version__ = "0.3.1"
 
@@ -31,117 +44,12 @@ def strip_readme():
  return "".join([line for line in fp if not line.startswith("<img")])
 
 
-#
-# Pybind11 BuildExt
-#
-class GetPyBindInclude:
- """Helper class to determine the pybind11 include path
-
- The purpose of this class is to postpone importing pybind11
- until it is actually installed, so that the ``get_include()``
- method can be invoked. """
-
- def __init__(self, user=False):
- self.user = user
-
- def __str__(self):
- import pybind11
-
- return pybind11.get_include(self.user)
-
-
-# As of Python 3.6, CCompiler has a `has_flag` method.
-# cf http:https://bugs.python.org/issue26689
-def has_flag(compiler, flagname, opts=[]):
- """Return a boolean indicating whether a flag name is supported on
- the specified compiler.
- """
- import tempfile
- opts += ['-Wno-unused-command-line-argument']
-
- with tempfile.NamedTemporaryFile("w", suffix=".cpp") as f:
- f.write("int main (int argc, char **argv) { return 0; }")
- try:
- extra_postargs = ["-Werror", flagname] + opts
- compiler.compile([f.name], extra_postargs=extra_postargs)
- except setuptools.distutils.errors.CompileError:
- return False
- return True
-
-
-def cpp_flag(compiler, opts=[]):
- """Return the -std=c++[11/14] compiler flag.
-
- The c++14 is preferred over c++11 (when it is available).
- """
- if has_flag(compiler, "-std=c++14", opts):
- return "-std=c++14"
- elif has_flag(compiler, "-std=c++11", opts):
- return "-std=c++11"
- else:
- raise RuntimeError("Unsupported compiler -- at least C++11 support "
- "is needed!")
-
-
-class BuildExt(BuildCommand):
- """A custom build extension for adding compiler-specific options."""
- def build_extensions(self):
- opts = []
- potential_opts = ['-fopenmp']
- potential_linker_args = ['-lgomp']
- if sys.platform == "darwin":
- potential_opts += ["-stdlib=libc++", "-mmacosx-version-min=10.9"]
- if self.compiler.compiler_type == "unix":
- opts.append(cpp_flag(self.compiler, opts))
- potential_opts += ["-fvisibility=hidden", "-Wall", "-Wextra"]
- opts.extend([newopt for newopt in potential_opts
- if has_flag(self.compiler, newopt, opts)])
-
- link_args = [newopt for newopt in potential_linker_args
- if has_flag(self.compiler, newopt, opts)]
-
- for ext in self.extensions:
- ext.extra_compile_args = opts
- ext.extra_link_args = link_args
- BuildCommand.build_extensions(self)
-
-
-#
-# Main setup code
-#
-# Setup RPATH on Linux and MacOS
-if sys.platform == "darwin":
- extra_link_args = ["-Wl,-rpath,@loader_path",]
- runtime_library_dirs = []
-elif sys.platform == "linux":
- extra_link_args = []
- runtime_library_dirs = ["$ORIGIN",]
-else:
- raise OSError("Unsupported platform: {}".format(sys.platform))
-
-# Setup source directories
-sources = glob.glob("cppe/*.cc")
-sources += glob.glob("cppe/core/*.cc")
-sources += glob.glob("cppe/core/tensors/*.cc")
-sources += glob.glob("cppe/core/fmm/*.cc")
-sources += glob.glob("cppe/utils/*.cc")
-sources += glob.glob("cppe/python_iface/*.cc")
+def is_conda_build():
+ return (
+ os.environ.get("CONDA_BUILD", None) == "1"
+ or os.environ.get("CONDA_EXE", None)
+ )
 
-# Setup build of the libadcc extension
-ext_modules = [
- Extension(
- "cppe.pycppe", sources=sources,
- include_dirs=[
- # Path to pybind11 headers
- GetPyBindInclude(),
- GetPyBindInclude(user=True),
- "external/eigen3",
- ],
- extra_link_args=extra_link_args,
- runtime_library_dirs=runtime_library_dirs,
- language="c++",
- ),
-]
 
 setup(
  name="cppe",
@@ -151,11 +59,11 @@ def build_extensions(self):
  keywords=[
  "polarizable", "embedding", "excited", "states", "QM/MM",
  "electronic", "structure", "computational", "chemistry", "quantum",
- "spectroscopy",
+ "spectroscopy", "fast", "multipole", "method",
  ],
  author="Maximilian Scheurer, Peter Reinholdt,"
  " Michael F. Herbst, Lori A. Burns",
- autor_email="[email protected]",
+ author_email="[email protected]",
  license="LGPL v3",
  url="https://github.com/maxscheurer/cppe",
  project_urls={
@@ -178,23 +86,16 @@ def build_extensions(self):
  "Operating System :: MacOS :: MacOS X",
  "Operating System :: POSIX :: Linux",
  ],
- package_dir={'cppe': 'cppe/python_iface'},
- packages=['cppe'],
+ packages=["cppe"],
  package_data={"": ["LICENSE*"]},
- ext_modules=ext_modules,
  zip_safe=False,
  platforms=["Linux", "Mac OS-X"],
  python_requires=">=3.6",
  setup_requires=["pybind11 >= 2.2"],
  install_requires=["pybind11 >= 2.2"],
- tests_require=[
- "pytest", "numpy", "h5py", "numba", "scipy", "pandas"
+ cmake_args=[
+ f'-Dpybind11_DIR={pybind11.get_cmake_dir()}',
+ '-DENABLE_PYTHON_INTERFACE=ON',
+ '-DCMAKE_INSTALL_LIBDIR:PATH=.'
  ],
- # extras_require={
- # "build_docs": ["sphinx>=2", "breathe", "sphinxcontrib-bibtex",
- # "sphinx-automodapi"],
- # },
- cmdclass={"build_ext": BuildExt,
- # "build_docs": BuildDocs,
- },
 )

tests/test_fmm.py

@@ -20,7 +20,7 @@ def test_field_computation(self):
  fs = np.loadtxt(self.fs_file)
  else:
  fmuls = cppe.MultipoleFields(potentials, options)
- fs = fmuls.compute_tree()
+ fs = fmuls.compute()
  np.savetxt(self.fs_file, fs)
 
  ref = pd.read_csv(os.path.join(self.dirname, "ref_fmm_errors.csv"))