Cookiecutting - build infrastructure

environment.yml

@@ -0,0 +1,9 @@
+name: diffpy.pdffit2
+channels:
+  - conda-forge
+dependencies:
+  - python=3
+  - pip
+  - gsl
+  - gcc
+  - gxx

pyproject.toml

@@ -1,3 +1,53 @@
+[build-system]
+requires = ["setuptools>=62.0", "setuptools-git-versioning<2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "diffpy.pdffit2"
+dynamic=['version']
+authors = [
+  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+]
+maintainers = [
+  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+]
+description = "PDFfit2 - real space structure refinement program."
+keywords = ['PDF structure refinement']
+readme = "README.rst"
+requires-python = ">=3.10"
+classifiers = [
+        'Development Status :: 5 - Production/Stable',
+        'Environment :: Console',
+        'Intended Audience :: Developers',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: BSD License',
+        'Operating System :: MacOS :: MacOS X',
+        'Operating System :: Microsoft :: Windows',
+        'Operating System :: POSIX',
+        'Operating System :: Unix',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
+        'Topic :: Scientific/Engineering :: Physics',
+        'Topic :: Scientific/Engineering :: Chemistry',
+]
+
+[project.urls]
+Homepage = "https://github.com/diffpy/diffpy.pdffit2/"
+Issues = "https://github.com/diffpy/diffpy.pdffit2/issues/"
+
+[tool.setuptools-git-versioning]
+enabled = true
+template = "{tag}"
+dev_template = "{tag}"
+dirty_template = "{tag}"
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["*"]  # package names should match these glob patterns (["*"] by default)
+exclude = ["diffpy.pdffit2.tests*"]  # exclude packages matching these glob patterns (empty by default)
+namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
+
 [tool.black]
 line-length = 115
 include = '\.pyi?$'

requirements/build.txt

@@ -0,0 +1,2 @@
+python
+setuptools

requirements/docs.txt

@@ -0,0 +1,4 @@
+sphinx
+sphinx_rtd_theme
+doctr
+m2r

requirements/run.txt

@@ -0,0 +1 @@
+diffpy.structure

requirements/test.txt

@@ -0,0 +1,5 @@
+flake8
+pytest
+codecov
+coverage
+pytest-env

setup.py

@@ -1,257 +1,71 @@
 #!/usr/bin/env python
 
-# Installation script for diffpy.pdffit2
+# Extensions script for diffpy.pdffit2
 
-"""PDFfit2 - real space structure refinement engine
-
-Packages:   diffpy.pdffit2
-Scripts:    pdffit2
-"""
-
-import os
-import re
+import glob
 import sys
-import warnings
-
-from setuptools import Extension, find_packages, setup
-
-# Use this version when git data are not available, like in git zip archive.
-# Update when tagging a new release.
-FALLBACK_VERSION = "1.4.2"
-
-# determine if we run with Python 3.
-PY3 = sys.version_info[0] == 3
-
-# versioncfgfile holds version data for git commit hash and date.
-# It must reside in the same directory as version.py.
-MYDIR = os.path.dirname(os.path.abspath(__file__))
-versioncfgfile = os.path.join(MYDIR, "diffpy/pdffit2/version.cfg")
-gitarchivecfgfile = os.path.join(MYDIR, ".gitarchive.cfg")
-
-
-def gitinfo():
-    from subprocess import PIPE, Popen
-
-    kw = dict(stdout=PIPE, cwd=MYDIR, universal_newlines=True)
-    proc = Popen(["git", "describe", "--tags", "--match=[v,V,[:digit:]]*"], **kw)
-    desc = proc.stdout.read()
-    proc = Popen(["git", "log", "-1", "--format=%H %ct %ci"], **kw)
-    glog = proc.stdout.read()
-    rv = {}
-    rv["commit"], rv["timestamp"], rv["date"] = glog.strip().split(None, 2)
-    version = ".post".join(desc.strip().split("-")[:2]).lstrip("vV")
-    rv["version"] = version
-    return rv
-
-
-def getversioncfg():
-    if PY3:
-        from configparser import RawConfigParser
-    else:
-        from ConfigParser import RawConfigParser
-    vd0 = dict(version=FALLBACK_VERSION, commit="", date="", timestamp=0)
-    # first fetch data from gitarchivecfgfile, ignore if it is unexpanded
-    g = vd0.copy()
-    cp0 = RawConfigParser(vd0)
-    cp0.read(gitarchivecfgfile)
-    if len(cp0.get("DEFAULT", "commit")) > 20:
-        g = cp0.defaults()
-        mx = re.search(r"\btag: [vV]?(\d[^,]*)", g.pop("refnames"))
-        if mx:
-            g["version"] = mx.group(1)
-    # then try to obtain version data from git.
-    gitdir = os.path.join(MYDIR, ".git")
-    if os.path.exists(gitdir) or "GIT_DIR" in os.environ:
-        try:
-            g = gitinfo()
-        except OSError:
-            pass
-    # finally, check and update the active version file
-
-    cp = RawConfigParser()
-    cp.read(versioncfgfile)
-    d = cp.defaults()
-    rewrite = not d or (g["commit"] and (g["version"] != d.get("version") or g["commit"] != d.get("commit")))
-    if rewrite:
-        cp.set("DEFAULT", "version", g["version"])
-        cp.set("DEFAULT", "commit", g["commit"])
-        cp.set("DEFAULT", "date", g["date"])
-        cp.set("DEFAULT", "timestamp", g["timestamp"])
-        with open(versioncfgfile, "w") as fp:
-            cp.write(fp)
-    return cp
-
-
-versiondata = getversioncfg()
-
-# Helper functions -----------------------------------------------------------
 
+from setuptools import Extension, setup
 
-def get_compiler_type():
-    """find compiler used for building extensions."""
-    cc_arg = [a for a in sys.argv if a.startswith("--compiler=")]
-    if cc_arg:
-        compiler_type = cc_arg[-1].split("=", 1)[1]
-    else:
-        from distutils.ccompiler import new_compiler
+# Define extension arguments here
+ext_kws = {
+    "libraries": [],
+    "extra_compile_args": [],
+    "extra_link_args": [],
+    "include_dirs": [],
+}
 
-        compiler_type = new_compiler().compiler_type
-    return compiler_type
 
+# Figure out the tagged name of boost_python library.
+def get_boost_libraries():
+    """Check for installed boost_python shared library.
 
-def get_gsl_config():
-    """Return dictionary with paths to GSL library."""
-    gslcfgpaths = [os.path.join(p, "gsl-config") for p in ([MYDIR] + os.environ["PATH"].split(os.pathsep))]
-    gslcfgpaths = [p for p in gslcfgpaths if os.path.isfile(p)]
-    rv = {"include_dirs": [], "library_dirs": []}
-    if not gslcfgpaths:
-        wmsg = "Cannot find gsl-config in {!r} nor in system PATH."
-        warnings.warn(wmsg.format(MYDIR))
-        return rv
-    gslcfg = gslcfgpaths[0]
-    with open(gslcfg) as fp:
-        txt = fp.read()
-    mprefix = re.search("(?m)^prefix=(.+)", txt)
-    minclude = re.search(r"(?m)^[^#]*\s-I(\S+)", txt)
-    mlibpath = re.search(r"(?m)^[^#]*\s-L(\S+)", txt)
-    if not mprefix:
-        emsg = "Cannot find 'prefix=' line in {}."
-        raise RuntimeError(emsg.format(gslcfg))
-    p = mprefix.group(1)
-    inc = minclude.group(1) if minclude else (p + "/include")
-    lib = mlibpath.group(1) if mlibpath else (p + "/lib")
-    rv["include_dirs"] += [inc]
-    rv["library_dirs"] += [lib]
-    return rv
-
-
-def get_gsl_config_win():
-    """Return dictionary with paths to GSL library, windwows version.
-    This version is installed with conda.
+    Returns list of required boost_python shared libraries that are installed
+    on the system. If required libraries are not found, an Exception will be
+    thrown.
     """
-    conda_prefix = os.environ["CONDA_PREFIX"]
-    inc = os.path.join(conda_prefix, "Library", "include")
-    lib = os.path.join(conda_prefix, "Library", "lib")
-    rv = {"include_dirs": [], "library_dirs": []}
-    rv["include_dirs"] += [inc]
-    rv["library_dirs"] += [lib]
-    return rv
-
-
-# ----------------------------------------------------------------------------
-
-# compile and link options
-define_macros = []
-os_name = os.name
-if os_name == "nt":
-    gcfg = get_gsl_config_win()
-else:
-    gcfg = get_gsl_config()
-include_dirs = [MYDIR] + gcfg["include_dirs"]
-library_dirs = []
-libraries = []
-extra_objects = []
-extra_compile_args = []
-extra_link_args = []
-
-compiler_type = get_compiler_type()
-if compiler_type in ("unix", "cygwin", "mingw32"):
-    extra_compile_args = ["-std=c++11", "-Wall", "-Wno-write-strings", "-O3", "-funroll-loops", "-ffast-math"]
-    extra_objects += ((p + "/libgsl.a") for p in gcfg["library_dirs"])
-elif compiler_type == "msvc":
-    define_macros += [("_USE_MATH_DEFINES", None)]
-    extra_compile_args = ["/EHs"]
-    libraries += ["gsl"]
-    library_dirs += gcfg["library_dirs"]
-# add optimization flags for other compilers if needed
-
-
-# define extension here
-pdffit2module = Extension(
-    "diffpy.pdffit2.pdffit2",
-    [
-        "pdffit2module/bindings.cc",
-        "pdffit2module/misc.cc",
-        "pdffit2module/pdffit2module.cc",
-        "pdffit2module/pyexceptions.cc",
-        "libpdffit2/Atom.cc",
-        "libpdffit2/LocalPeriodicTable.cc",
-        "libpdffit2/OutputStreams.cc",
-        "libpdffit2/PeriodicTable.cc",
-        "libpdffit2/PointsInSphere.cc",
-        "libpdffit2/StringUtils.cc",
-        "libpdffit2/fit.cc",
-        "libpdffit2/gaussj.cc",
-        "libpdffit2/metric.cc",
-        "libpdffit2/nrutil.cc",
-        "libpdffit2/output.cc",
-        "libpdffit2/parser.cc",
-        "libpdffit2/pdf.cc",
-        "libpdffit2/pdffit.cc",
-        "libpdffit2/pdflsmin.cc",
-        "libpdffit2/scatlen.cc",
-        "libpdffit2/stru.cc",
-    ],
-    include_dirs=include_dirs,
-    libraries=libraries,
-    library_dirs=library_dirs,
-    define_macros=define_macros,
-    extra_compile_args=extra_compile_args,
-    extra_link_args=extra_link_args,
-    extra_objects=extra_objects,
-)
-
-
-with open(os.path.join(MYDIR, "README.rst")) as fp:
-    long_description = fp.read()
-
-# define distribution
+    baselib = "boost_python"
+    major, minor = (str(x) for x in sys.version_info[:2])
+    pytags = [major + minor, major, ""]
+    mttags = ["", "-mt"]
+    boostlibtags = [(pt + mt) for mt in mttags for pt in pytags] + [""]
+    from ctypes.util import find_library
+
+    for tag in boostlibtags:
+        lib = baselib + tag
+        found = find_library(lib)
+        if found:
+            break
+
+    # Show warning when library was not detected.
+    if not found:
+        import platform
+        import warnings
+
+        ldevname = "LIBRARY_PATH"
+        if platform.system() == "Darwin":
+            ldevname = "DYLD_FALLBACK_LIBRARY_PATH"
+        wmsg = ("Cannot detect name suffix for the %r library. " "Consider setting %s.") % (baselib, ldevname)
+        warnings.warn(wmsg)
+
+    libs = [lib]
+    return libs
+
+
+def create_extensions():
+    "Initialize Extension objects for the setup function."
+    blibs = [n for n in get_boost_libraries() if n not in ext_kws["libraries"]]
+    ext_kws["libraries"] += blibs
+    ext = Extension("diffpy.pdffit2.pdffit2_ext", glob.glob("src/extensions/*.cpp"), **ext_kws)
+    return [ext]
+
+
+# Extensions not included in pyproject.toml
 setup_args = dict(
-    name="diffpy.pdffit2",
-    version=versiondata.get("DEFAULT", "version"),
-    packages=find_packages(),
-    test_suite="diffpy.pdffit2.tests",
-    ext_modules=[pdffit2module],
-    include_package_data=True,
-    install_requires=[
-        "six",
-        "diffpy.structure>=3",
-    ],
-    zip_safe=False,
-    author="Simon J.L. Billinge",
-    author_email="sb2896@columbia.edu",
-    maintainer="Pavol Juhas",
-    maintainer_email="pavol.juhas@gmail.com",
-    url="https://github.com/diffpy/diffpy.pdffit2",
-    description="PDFfit2 - real space structure refinement program.",
-    long_description=long_description,
-    long_description_content_type="text/x-rst",
-    license="BSD",
-    keywords="PDF structure refinement",
-    classifiers=[
-        # List of possible values at
-        # http://pypi.python.org/pypi?:action=list_classifiers
-        "Development Status :: 5 - Production/Stable",
-        "Environment :: Console",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: BSD License",
-        "Operating System :: MacOS",
-        "Operating System :: Microsoft :: Windows",
-        "Operating System :: POSIX",
-        "Programming Language :: C++",
-        "Programming Language :: Python :: 2.7",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        "Programming Language :: Python :: 3.12",
-        "Topic :: Scientific/Engineering :: Chemistry",
-        "Topic :: Scientific/Engineering :: Physics",
-    ],
+    ext_modules=[],
 )
 
+
 if __name__ == "__main__":
+    setup_args["ext_modules"] = create_extensions()
     setup(**setup_args)
-
-# End of file