formatting and packaging

.isort.cfg

@@ -0,0 +1,4 @@
+[settings]
+line_length=79
+multi_line_output=3
+known_third_party = h5py,matplotlib,numpy,pytest,scipy,setuptools

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.3.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: debug-statements
+
+- repo: https://github.com/asottile/seed-isort-config
+  rev: v1.9.2
+  hooks:
+  - id: seed-isort-config
+    args: [--application-directories=src]
+
+- repo: https://github.com/pre-commit/mirrors-isort
+  rev: v4.3.20
+  hooks:
+  - id: isort
+    args: []
+
+- repo: https://github.com/psf/black
+  rev: 19.3b0
+  hooks:
+  - id: black
+    language_version: python3.6
+
+- repo: https://github.com/dfm/black_nbconvert
+  rev: v0.1.1
+  hooks:
+  - id: black_nbconvert

MANIFEST.in

@@ -1 +1 @@
-include README.rst LICENSE HISTORY.rst AUTHORS.rst
+include LICENSE *.rst

docs/conf.py

@@ -3,11 +3,12 @@
 import os
 import sys
 
+from emcee import __version__  # NOQA
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath(".."))
-from emcee import __version__  # NOQA
+sys.path.insert(0, os.path.join(os.path.abspath(".."), "src"))
 
 extensions = [
     "sphinx.ext.autodoc",

document/plots/oned.py

@@ -1,15 +1,15 @@
 import os
 import sys
 import time
+from multiprocessing import Pool
 
-import numpy as np
-import matplotlib.pyplot as pl
 import h5py
+import matplotlib.pyplot as pl
+import numpy as np
 
-from multiprocessing import Pool
+import emcee
 
 sys.path.append(os.path.abspath(os.path.join(__file__, "..", "..", "..")))
-import emcee
 
 # import acor
 
@@ -20,8 +20,9 @@ def lnprobfn(p, icov):
 
 def random_cov(ndim, dof=1):
     v = np.random.randn(ndim * (ndim + dof)).reshape((ndim + dof, ndim))
-    return (sum([np.outer(v[i], v[i]) for i in range(ndim + dof)])
-            / (ndim + dof))
+    return sum([np.outer(v[i], v[i]) for i in range(ndim + dof)]) / (
+        ndim + dof
+    )
 
 
 _rngs = {}
@@ -31,33 +32,34 @@ def _worker(args):
     i, outfn, nsteps = args
 
     pid = os.getpid()
-    _random = _rngs.get(pid, np.random.RandomState(int(int(pid)
-        + time.time())))
+    _random = _rngs.get(
+        pid, np.random.RandomState(int(int(pid) + time.time()))
+    )
     _rngs[pid] = _random
 
     ndim = int(np.ceil(2 ** (7 * _random.rand())))
     nwalkers = 2 * ndim + 2
     # nwalkers += nwalkers % 2
-    print ndim, nwalkers
+    print(ndim, nwalkers)
 
     cov = random_cov(ndim)
     icov = np.linalg.inv(cov)
 
-    ens_samp = emcee.EnsembleSampler(nwalkers, ndim, lnprobfn,
-            args=[icov])
+    ens_samp = emcee.EnsembleSampler(nwalkers, ndim, lnprobfn, args=[icov])
     ens_samp.random_state = _random.get_state()
-    pos, lnprob, state = ens_samp.run_mcmc(np.random.randn(nwalkers * ndim)
-            .reshape([nwalkers, ndim]), nsteps)
+    pos, lnprob, state = ens_samp.run_mcmc(
+        np.random.randn(nwalkers * ndim).reshape([nwalkers, ndim]), nsteps
+    )
 
     proposal = np.diag(cov.diagonal())
-    mh_samp = emcee.MHSampler(proposal, ndim, lnprobfn,
-            args=[icov])
+    mh_samp = emcee.MHSampler(proposal, ndim, lnprobfn, args=[icov])
     mh_samp.random_state = state
     mh_samp.run_mcmc(np.random.randn(ndim), nsteps)
 
     f = h5py.File(outfn)
-    f["data"][i, :] = np.array([ndim, np.mean(ens_samp.acor),
-                                np.mean(mh_samp.acor)])
+    f["data"][i, :] = np.array(
+        [ndim, np.mean(ens_samp.acor), np.mean(mh_samp.acor)]
+    )
     f.close()
 
 
@@ -67,7 +69,7 @@ def oned():
     nthreads = 2
 
     outfn = os.path.join(os.path.split(__file__)[0], "gauss_scaling.h5")
-    print outfn
+    print(outfn)
     f = h5py.File(outfn, "w")
     f.create_dataset("data", (niter, 3), "f")
     f.close()

pyproject.toml

@@ -0,0 +1,20 @@
+[build-system]
+requires = ["setuptools>=40.6.0", "wheel", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+[tool.black]
+line-length = 79
+exclude = '''
+/(
+    \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | _build
+  | buck-out
+  | build
+  | dist
+)/
+'''

setup.py

@@ -1,48 +1,72 @@
-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
+#!/usr/bin/env python
 
+# Inspired by:
+# https://hynek.me/articles/sharing-your-labor-of-love-pypi-quick-and-dirty/
+
+import codecs
 import os
-import sys
-from setuptools import setup
-
-if sys.argv[-1] == "publish":
-    os.system("python setup.py sdist; twine upload dist/*")
-    sys.exit()
-
-# Hackishly inject a constant into builtins to enable importing of the
-# package before all the dependencies are built.
-if sys.version_info[0] < 3:
-    import __builtin__ as builtins
-else:
-    import builtins
-builtins.__EMCEE_SETUP__ = True
-import emcee  # NOQA
-
-setup(
-    name="emcee",
-    version=emcee.__version__,
-    author="Daniel Foreman-Mackey",
-    author_email="[email protected]",
-    packages=[
-        "emcee",
-        "emcee.moves", "emcee.backends",
-        "emcee.tests", "emcee.tests.unit", "emcee.tests.integration",
-    ],
-    url="http://emcee.readthedocs.io",
-    license="MIT",
-    description=("The Python ensemble sampling toolkit for affine-invariant "
-                 "MCMC"),
-    long_description=open("README.rst").read(),
-    package_data={"": ["LICENSE", "AUTHORS.rst"]},
-    include_package_data=True,
-    install_requires=["numpy"],
-    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",
-    ],
-    zip_safe=True,
-)
+import re
+
+from setuptools import find_packages, setup
+
+# PROJECT SPECIFIC
+
+NAME = "emcee"
+PACKAGES = find_packages(where="src")
+META_PATH = os.path.join("src", "emcee", "__init__.py")
+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",
+]
+INSTALL_REQUIRES = ["numpy"]
+
+# END PROJECT SPECIFIC
+
+
+HERE = os.path.dirname(os.path.realpath(__file__))
+
+
+def read(*parts):
+    with codecs.open(os.path.join(HERE, *parts), "rb", "utf-8") as f:
+        return f.read()
+
+
+def find_meta(meta, meta_file=read(META_PATH)):
+    meta_match = re.search(
+        r"^__{meta}__ = ['\"]([^'\"]*)['\"]".format(meta=meta), meta_file, re.M
+    )
+    if meta_match:
+        return meta_match.group(1)
+    raise RuntimeError("Unable to find __{meta}__ string.".format(meta=meta))
+
+
+if __name__ == "__main__":
+    setup(
+        name=NAME,
+        use_scm_version={
+            "write_to": os.path.join(
+                "src", NAME, "{0}_version.py".format(NAME)
+            ),
+            "write_to_template": '__version__ = "{version}"\n',
+        },
+        author=find_meta("author"),
+        author_email=find_meta("email"),
+        maintainer=find_meta("author"),
+        maintainer_email=find_meta("email"),
+        url=find_meta("uri"),
+        license=find_meta("license"),
+        description=find_meta("description"),
+        long_description=read("README.rst"),
+        long_description_content_type="text/x-rst",
+        packages=PACKAGES,
+        package_dir={"": "src"},
+        include_package_data=True,
+        install_requires=INSTALL_REQUIRES,
+        classifiers=CLASSIFIERS,
+        zip_safe=False,
+        options={"bdist_wheel": {"universal": "1"}},
+    )