fixing build process

.gitignore

@@ -26,3 +26,5 @@ code/Templates/Builder/MyModel.h
 code/Templates/Builder/MyModel.cpp
 ms.out
 dnest4.lib
+build
+dist

MANIFEST.in

@@ -0,0 +1,5 @@
+include LICENSE *.rst python/*.rst *.toml
+
+include code/*.cpp
+include code/Distributions/*.cpp
+include code/RJObject/ConditionalPriors/*.cpp

code/Makefile

@@ -1,6 +1,4 @@
-CXX = g++
-export CXX
-CXXFLAGS = -std=c++11 -O3 -march=native -Wall -Wextra -pedantic -DNDEBUG
+CXXFLAGS = -std=c++11 -O3 -Wall -Wextra -pedantic -DNDEBUG
 
 SRCS = $(wildcard *.cpp) \
        $(wildcard Distributions/*.cpp) \
@@ -15,6 +13,9 @@ libdnest4.a: $(OBJS)
 	@echo Creating $@ library
 	@ar rcs $@ $^
 
+libdnest4: $(OBJS)
+	$(CXX) ${LDFLAGS} -o $@ $^
+
 examples: $(OBJS) libdnest4.a
 	make nolib -C Examples/SpikeSlab
 	make nolib -C Examples/StraightLine

pyproject.toml

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

python/dnest4/__init__.py

@@ -1,22 +1,23 @@
 # -*- coding: utf-8 -*-
 
-__version__ = "0.2.3"
+__version__ = "0.2.4"
 
 try:
     __DNEST4_SETUP__
 except NameError:
     __DNEST4_SETUP__ = False
 
 if not __DNEST4_SETUP__:
-    __all__ = ["DNest4Sampler", "postprocess", "analysis", "my_loadtxt, loadtxt_rows"]
+    __all__ = [
+        "DNest4Sampler",
+        "postprocess",
+        "analysis",
+        "my_loadtxt, loadtxt_rows",
+    ]
 
     from . import analysis
     from .sampler import DNest4Sampler
     from .deprecated import postprocess, postprocess_abc
     from .loading import my_loadtxt, loadtxt_rows
-    from .utils import rand
-    from .utils import randn
-    from .utils import randt2
-    from .utils import randh
-    from .utils import wrap
+    from .utils import rand, randn, randt2, randh, wrap
 

python/dnest4/_dnest4.pyx

@@ -1,4 +1,5 @@
 # distutils: language = c++
+# cython: language_level=3, cdivision=True
 from __future__ import division
 
 cimport cython
@@ -32,7 +33,8 @@ cdef extern from "DNest4.h" namespace "DNest4":
     cdef cppclass Sampler[T]:
         Sampler()
         Sampler(unsigned int num_threads, double compression,
-                const Options options, unsigned save_to_disk)
+                const Options options, unsigned save_to_disk,
+                unsigned _adaptive)
 
         # Setup, running, etc.
         void initialise(unsigned int first_seed) except +
@@ -92,6 +94,7 @@ def sample(
     # "command line" arguments
     seed=None,
     double compression=np.exp(1.0),
+    unsigned int adaptive=0,
 ):
     """
     Sample using a DNest4 model.
@@ -156,7 +159,7 @@ def sample(
 
     # Declarations.
     cdef int i, j, n, error
-    cdef Sampler[PyModel] sampler = Sampler[PyModel](1, compression, options, 0)
+    cdef Sampler[PyModel] sampler = Sampler[PyModel](1, compression, options, 0, adaptive)
     cdef PyModel* particle
     cdef vector[Level] levels
     cdef Level level

python/dnest4/utils.pyx

@@ -1,4 +1,5 @@
-# -*- coding: utf-8 -*-
+# cython: language_level=3, cdivision=True
+
 __all__ = ["rand", "randn", "randt2", "randh", "wrap"]
 
 cimport cython

setup.py

@@ -0,0 +1,123 @@
+#!/usr/bin/env python
+
+import os
+from setuptools import setup, Extension
+
+
+if __name__ == "__main__":
+    import sys
+
+    # Publish the library to PyPI.
+    if "publish" in sys.argv:
+        os.system("python setup.py sdist upload")
+        sys.exit()
+
+    if "--without-cext" in sys.argv:
+        sys.argv.remove("--without-cext")
+        extensions = []
+
+    else:
+        import glob
+        from itertools import chain
+
+        import numpy
+        from Cython.Build import cythonize
+
+        # The root of the DNest4 repo.
+        basedir = os.path.dirname(os.path.abspath(__file__))
+
+        # Set up the C++-extension.
+        libraries = []
+        if os.name == "posix":
+            libraries.append("m")
+        include_dirs = [
+            "dnest4",
+            os.path.join(basedir, "code"),
+            numpy.get_include(),
+        ]
+
+        src = [
+            os.path.join(basedir, "code", fn)
+            for fn in chain(
+                glob.glob(os.path.join(basedir, "code", "*.cpp")),
+                glob.glob(
+                    os.path.join(basedir, "code", "Distributions", "*.cpp")
+                ),
+                glob.glob(
+                    os.path.join(
+                        basedir,
+                        "code",
+                        "RJObject",
+                        "ConditionalPriors",
+                        "*.cpp",
+                    )
+                ),
+            )
+        ]
+        src += [os.path.join(basedir, "python", "dnest4", "_dnest4.pyx")]
+
+        ext = [
+            Extension(
+                "dnest4._dnest4",
+                sources=src,
+                language="c++",
+                libraries=libraries,
+                include_dirs=include_dirs,
+                extra_compile_args=[
+                    "-std=c++11",
+                    "-Wno-unused-function",
+                    "-Wno-uninitialized",
+                    "-DNO_THREADS",
+                ],
+                extra_link_args=["-std=c++11"],
+            ),
+            Extension(
+                "dnest4.utils",
+                sources=[
+                    os.path.join(basedir, "python", "dnest4", "utils.pyx")
+                ],
+                language="c++",
+                libraries=libraries,
+                include_dirs=include_dirs,
+                extra_compile_args=[
+                    "-std=c++11",
+                    "-Wno-unused-function",
+                    "-Wno-uninitialized",
+                    "-DNO_THREADS",
+                ],
+                extra_link_args=["-std=c++11"],
+            ),
+        ]
+        extensions = cythonize(ext)
+
+    # Hackishly inject a constant into builtins to enable importing of the
+    # package before the library is built.
+    if sys.version_info[0] < 3:
+        import __builtin__ as builtins
+    else:
+        import builtins
+    builtins.__DNEST4_SETUP__ = True
+    sys.path.insert(0, os.path.join(basedir, "python"))
+    import dnest4
+
+    setup(
+        name="dnest4",
+        version=dnest4.__version__,
+        author="Daniel Foreman-Mackey",
+        author_email="foreman.mackey@gmail.com",
+        url="https://github.com/eggplantbren/DNest4",
+        license="MIT",
+        packages=["dnest4"],
+        package_dir={"": "python"},
+        ext_modules=extensions,
+        description="Diffusive nested sampling in Python",
+        long_description=open("python/README.rst").read(),
+        classifiers=[
+            # "Development Status :: 5 - Production/Stable",
+            "Intended Audience :: Developers",
+            "Intended Audience :: Science/Research",
+            "License :: OSI Approved :: MIT License",
+            "Operating System :: OS Independent",
+            "Programming Language :: Python",
+        ],
+    )